SARS-cov-2 vaccine compositions and related methods
SARS-CoV-2 spike proteins with specific amino acid substitutions and stabilization in a prefusion state, encoded by nucleic acid molecules, are used in vaccine compositions to improve immune recognition and stability, addressing the challenges of vaccine efficacy and durability.
Patent Information
- Application Number
- PCT/US2024/033365
- Authority / Receiving Office
- WO · WO
- Patent Type
- Applications
- Current Assignee / Owner
- Priority Date
- 2023-06-12
- Filing Date
- 2024-06-11
- Publication Date
- 2024-12-19
AI Technical Summary
Current SARS-CoV-2 vaccines face challenges in providing long-lasting immunity and stability of the spike protein, which affects their efficacy in preventing and treating COVID-19 infections.
Development of SARS-CoV-2 spike proteins and polypeptides with specific amino acid substitutions, including those in the receptor binding domain, stabilized in a prefusion state, and potentially with additional N-glycosylation sites, encoded by nucleic acid molecules for use in vaccine compositions to induce immune response.
Enhances immune recognition and stability of the spike protein, potentially leading to improved vaccine efficacy and durability of immunity against SARS-CoV-2 infections.
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Figure US2024033365_19122024_PF_FP_ABST
Abstract
Description
SARS-CoV-2 VACCINE COMPOSITIONS AND RELATED METHODSRELATED APPLICATION
[0001] This application claims priority to U.S. Serial No.: 63 / 507,644, filed June 12, 2023, the entire contents of which is incorporated herein by reference.1. FIELD
[0002] This disclosure relates to SARS-CoV-2 spike proteins and polypeptides (e.g., SARS- CoV-2 spike protein and polypeptide immunogens (and immunogenic fragments and / or immunogenic variants thereof)), that comprise at least one set of amino acid substitutions (e.g., described herein) and nucleic acid molecules encoding the same. The disclosure further relates to compositions comprising of the same e.g., vaccine compositions, pharmaceutical compositions) and methods of making and utilizing the same.2. BACKGROUND|0003[ Coronaviruses are a family of enveloped, positive-sense, single stranded RNA viruses that infect a wide variety of mammalian and avian species. The viral genome is packaged into a capsid that is comprised of the viral nucleocapsid protein and surrounded by a lipid envelope. Embedded in the lipid envelope are several proteins, including, the membrane protein, the envelope small membrane protein, hemagglutinin-esterase, and the spike protein. Human coronaviruses typically cause respiratory illnesses, and include, e.g., severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), severe acute respiratory syndrome coronavirus 1 (SARS- CoV-1), and Middle East respiratory syndrome (MERS-CoV).
[0004] SARS-Cov-2 emerged in humans in 2019, spread rapidly, and led to a global pandemic. SARS-CoV-2 is the cause of the coronavirus disease 2019 (COVID-19). COVID-19 caused a continuing public health crisis, with millions of deaths and severe illness attributed to COVID-19 worldwide. Protection against COVID- 19 is mediated in large part by an immune response directed against the SARS-CoV-2 spike protein, a main target of SARS-CoV-2 vaccines. The spike protein mediates binding and entry into host cells, through binding of the receptor binding domain (RBD) to the host cell receptor angiotensin-converting enzyme 2 (ACE2).3. SUMMARY|0005| Provided herein are, inter alia, SARS-CoV-2 spike proteins and polypeptides (e.g., SARS-CoV-2 spike protein and polypeptide immunogens (and immunogenic fragments and / or immunogenic variants thereof)), nucleic acids encoding the same, compositions (e.g., vaccine compositions, pharmaceutical compositions) comprising the SARS-CoV-2 spike proteins and polypeptides (e.g., SARS-CoV-2 spike protein and polypeptide immunogens (and immunogenic fragments and / or immunogenic variants thereof)) or nucleic acids encoding the same, methods of manufacturing, and methods of use including, e.g., methods of preventing, reducing, or treating a SARS-CoV-2 infection, methods of vaccination against a SARS-CoV-2 infection, etc.
[0006] In one aspect, provided herein are nucleic acid molecules comprising at least one coding region encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises at least one (e.g., one) set of amino acid substitutions set forth in Table 2 or Table 4.
[0007] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of the SARS-CoV-2 spike protein receptor binding domain (RED). In some embodiments, the amino acid sequence of the encoded SARS- CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises the SARS-CoV-2 spike protein receptor binding domain (RED). In some embodiments, the amino acid sequence of the encoded SARS- CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) consists of the SARS-CoV-2 spike protein receptor binding domain (RBD).
[0008] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of a full-length SARS-CoV-2 spike protein. In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises a full-length SARS-CoV-2 spike protein. In some embodiments, theamino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) consists of a full-length SARS-CoV-2 spike protein.|0009| In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least one (e.g., one) set of amino acid substitutions set forth in Table 2.|0010| In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, or 1300 amino acids.|00.1.1] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises from about 10-15, 10-20, 10-30, 10-40, 10-50, 10-60, 10-70, 10-80, 10-90, 10-100, 10-200, 10-300, 10-400, 10-500, 10-600, 10-700, 10-800, 10-900, 10-1000, 10-1100, 10-1200, or 10-1300 amino acids.|0012| In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 2, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, or 1300 amino acids set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
[0013] In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 2, the amino acid sequence of the encoded SARS-CoV-2 spike protein ( .g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44)
[0014] In some embodiments, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises a plurality of sets of amino acid substitutions set forth in Table 2.
[0015] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 2, 3, 4, 5, or 6 or more sets of amino acid substitutions set forth in Table 2.
[0016] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%) amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not set forth in Table 2.
[0017] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 2 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44)
[0018] In some embodiments, the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV- 2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is stabilized in a prefusion state.
[0019] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least one amino acid variation relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2), that stabilizes the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) in a prefusion state.
[0020] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises a proline at amino acid position 986 and / or a proline at amino acid position 987, amino acid numbering relative to the amino acid positions set forth in SEQ ID NO: 1
[0021] In some embodiments, the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV- 2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises one or more non-naturally N-glycosylation sites.
[0022] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises the addition of one or more N-glycosylation sites relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).[0023| In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 7-12.
[0024] In some embodiments, the amino acid sequence of encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 13-24.
[0025] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least one (e.g., one) set of amino acid substitutions set forth in Table 4.
[0026] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, or 1300 amino acids.
[0027] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises from about 10-15, 10-20, 10-30, 10-40, 10-50, 10-60, 10-70, 10-80, 10-90, 10-100, 10-200, 10-300, 10-400, 10-500, 10-600, 10-700, 10-800, 10-900, 10-1000, 10-1100, 10-1200, or 10-1300 amino acids.
[0028] In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 4, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, or 1300 amino acids set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44)[0029| In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 4, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43- 44)
[0030] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises a plurality of sets of amino acid substitutions set forth in Table 4.
[0031] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 2, 3, 4, 5, or 6 or more sets of amino acid substitutions set forth in Table 4.
[0032] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more)but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%) amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not set forth in Table 4.|0033| In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 4 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44)
[0034] In some embodiments, the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV- 2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is stabilized in a prefusion state.[0035| In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least one amino acid variation relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2), that stabilizes the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) in a prefusion state.
[0036] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises a proline at amino acid position 986 and / or a proline at amino acid position 987, amino acid numbering relative to the amino acid positions set forth in SEQ ID NO: 1
[0037] In some embodiments, the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV- 2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises one or more non-naturally N-glycosylation sites.
[0038] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises the addition of one or more N-glycosylation sites relativeto the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
[0039] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 25-30.
[0040] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 31-42.
[0041] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least one set of amino acid substitutions set forth in Table 2 and at least one set of amino acid substitutions set forth in Table 4.
[0042] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1 100, 1200, or 1300 amino acids.
[0043] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises from about 10-15, 10-20, 10-30, 10-40, 10-50, 10-60, 10-70, 10-80, 10-90, 10-100, 10-200, 10-300, 10-400, 10-500, 10-600, 10-700, 10-800, 10-900, 10-1000, 10-1100, 10-1200, or 10-1300 amino acids.
[0044] In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 2 and the at least one set of amino acid substitutions set forth in Table 4, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80,90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1 100, 1200, or 1300 amino acids set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44). |0045| In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 2 and the at least one set of amino acid substitutions set forth in Table 4, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 1- 6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
[0046] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises a plurality of sets of amino acid substitutions set forth in Table 2.
[0047] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 2, 3, 4, 5, or 6 or more sets of amino acid substitutions set forth in Table 2.
[0048] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%) amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not set forth in Table 2.
[0049] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 2 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
[0050] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises a plurality of sets of amino acid substitutions set forth in Table 4.
[0051] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 2, 3, 4, 5, or 6 or more sets of amino acid substitutions set forth in Table 4.
[0052] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%) amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not set forth in Table 4.
[0053] In some embodiments, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 4 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
[0054] In some embodiments, the SARS-CoV-2 spike protein e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is stabilized in a prefusion state.
[0055] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least one amino acid variation relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2), that stabilizes the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) in a prefusion state.
[0056] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises a proline at amino acid position 986 and / or a proline at amino acid position 987, amino acid numbering relative to the amino acid positions set forth in SEQ ID NO: 1.
[0057] In some embodiments, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises one or more non-naturally N-glycosylation sites.]0058| In some embodiments, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises the addition of one or more N-glycosylation sites relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).[0059| In some embodiments, the encoded SARS-CoV-2 spike protein is an immunogen (or an immunogenic fragment and / or immunogenic variant thereof).
[0060] In some embodiments, the nucleic acid molecule is RNA or DNA. In some embodiments, the RNA is messenger ribonucleic acid (mRNA). In some embodiments, the nucleic acid molecule comprises at least one modified nucleotide. In some embodiments, the nucleic acid molecule comprises Nl-methyl-pseudouridine, cytosine, adenine, and guanine. In some embodiments, the nucleic acid molecule comprises a heterologous 5 ’-untranslated region (UTR), 3’-UTR, or both a 5’-UTR and 3’-UTR. In some embodiments, the nucleic acid molecule comprises a poly(A) sequence. In some embodiments, the nucleic acid molecule comprises a 5’cap structure. In some embodiments, the nucleotide sequence of the nucleic acid molecule is codon optimized.
[0061] In some embodiments, the nucleic acid molecule further encodes a heterologous polypeptide or protein. In some embodiments, the nucleic acid molecule encodes a signal peptide. In some embodiments, the nucleic acid molecule encodes a homologous or heterologous signal peptide. In some embodiments, the nucleic acid molecule does not encode a signal peptide.
[0062] In one aspect, provided herein are vectors comprising a nucleic acid molecule described herein. In some embodiments, the vector is a non-viral vector (e.g., a plasmid) or a viral vector.
[0063] In one aspect, provided herein are conjugates comprising a nucleic acid molecule described herein operably connected (e.g., directly or indirectly (e.g., via a linker)) to a heterologous moiety (e.g., a heterologous polypeptide or protein).|0064| In one aspect, provided herein are compositions comprising at least one nucleic acid molecules described herein, a vector described herein, or a conjugate described herein.
[0065] In some embodiments, the composition comprises a plurality of nucleic acid molecules described herein, wherein the amino acid sequence of each of the SARS-CoV-2 spike proteins e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) encoded by each nucleic acid molecule of the plurality is different.
[0066] In some embodiments, the plurality comprises at least two nucleic acid molecules described herein, wherein the amino acid sequence of each of the SARS-CoV-2 spike proteins (e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) encoded by each of the at least 2 nucleic acid molecules comprises a different set of amino acid substitutions set forth in Table 2 or Table 4 or a different combination of sets of amino acid substitutions set forth in Table 2 or Table 4.
[0067] In some embodiments, the plurality comprises at least 2, 3, 4, 5, or 6 nucleic acid molecules set forth in any one of claims 1-66, wherein the amino acid sequence of each of the SARS-CoV-2 spike proteins (e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) encoded by each of the at least 2, 3, 4, 5, or 6 nucleic acid molecules comprises a different set of amino acid substitutions set forth in Table 2.
[0068] In some embodiments, the plurality comprises at least 2, 3, 4, 5, or 6 nucleic acid molecules set forth in any one of claims 1-66, wherein the amino acid sequence of each of the SARS-CoV-2 spike proteins (e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) encoded by each of the at least 2, 3, 4, 5, or 6 nucleic acid molecules comprises a different set of amino acid substitutions set forth in Table 4.
[0069] In some embodiments, the plurality comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 nucleic acid molecules set forth in any one of claims 1-66, wherein the amino acid sequence of each of the SARS-CoV-2 spike proteins (e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) encoded by each of the at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 nucleic acid molecules comprises a different set of amino acid substitutions set forth in Table 2 or Table 4.
[0070] In one aspect, provided herein are compositions comprising (a) at least one nucleic acid molecule comprising amino acid substitutions set forth in Table 2; (b) at least one nucleic acid molecule comprising amino acid substitutions set forth in Table 4; and / or (c) at least one nucleic acid molecule comprising amino acid substitutions set forth in Table 2 and amino acid substitutions set forth in Table 4.
[0071] In one aspect, provided herein are compositions comprising at least 2, 3, 4, 5, or 6 nucleic acid molecules, wherein the amino acid sequence of each of the SARS-CoV-2 spike proteins (e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) encoded by of each of the at least 2, 3, 4, 5, or 6 nucleic acid molecules comprises a different set of amino acid substitutions set forth in Table 2.
[0072] In one aspect, provided herein are compositions comprising at least 2, 3, 4, 5, or 6 nucleic acid molecules, wherein the amino acid sequence of each of the SARS-CoV-2 spike proteins (e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) encoded by of each of the at least 2, 3, 4, 5, or 6 nucleic acid molecules comprises a different set of amino acid substitutions set forth in Table 4.
[0073] In one aspect, provided herein are compositions comprising at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 nucleic acid molecules, wherein the amino acid sequence of each of the SARS- CoV-2 spike proteins (e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) encoded by of each of the at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 nucleic acid molecules comprises a different set of amino acid substitutions set forth in Table 2 or Table 4.|0074| In one aspect, provided herein are compositions comprising any one or more (e.g., 1, 2, 3, 4, 5, or 6) of (a) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set A (440E / 456L / 478R / 484V / 505Y) set forth in Table 2; (b) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spikeprotein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set B (405K / 440N / 456V / 478Q / 490P) set forth in Table 2; (c) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set C (403S / 444E / 455W) set forth in Table 2; (d) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set D (346K / 439K / 455S / 505D) set forth in Table 2; (e) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set E (403K / 444T / 453F / 478R) set forth in Table 2; and / or (f) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set F (405D / 417Y / 440R / 478I / 490F) set forth in Table 2.
[0075] In one aspect, provided herein are compositions comprising any one or more (e.g., 1, 2, 3, 4, 5, or 6) of (a) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set G (440E / 456L / 478R / 484V / 505Y / 383N / 396T / 468N) set forth in Table 4; (b) a nucleic acid moleculecomprising at least one coding region encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV- 2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV- 2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set H (405K / 440N / 456V / 478Q / 490P / 383N / 396T / 468N) set forth in Table 4; (c) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set I (403S / 444E / 455W / 383N / 396T / 468N) set forth in Table 4; (d) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set J (346K / 439K / 455S / 505D / 383N / 396T / 468N) set forth in Table 4; (e) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV- 2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS- CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set K (403K / 444T / 453F / 478R / 383N / 396T / 468N) set forth in Table 4; and / or (f) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV- 2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV- 2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution setL (405D / 417Y / 440R / 478I / 490F / 383N / 396T / 468N) set forth in Table 4.(0076] In one aspect, provided herein are compositions comprising any one or more (e.g., any 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12) of (a) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (oran immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set A (440E / 456L / 478R / 484V / 505Y) set forth in Table 2; (b) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV- 2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV- 2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set B (405K / 440N / 456V / 478Q / 490P) set forth in Table 2; (c) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set C (403S / 444E / 455W) set forth in Table 2; (d) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set D (346K / 439K / 455S / 505D) set forth in Table 2; (e) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set E (403K / 444T / 453F / 478R) set forth in Table 2; (f) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set F (405D / 417Y / 440R / 478I / 490F) set forth in Table 2; (g) a nucleic acid molecule comprising at leastone coding region encoding a SARS-CoV-2 spike protein e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set G (440E / 456L / 478R / 484V / 505Y / 383N / 396T / 468N) set forth in Table 4; (h) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set H (405K / 440N / 456V / 478Q / 490P / 383N / 396T / 468N) set forth in Table 4; (i) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV- 2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV- 2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set I (403S / 444E / 455W / 383N / 396T / 468N) set forth in Table 4; (j) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set J (346K / 439K / 455S / 505D / 383N / 396T / 468N) set forth in Table 4; (k) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV- 2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV- 2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set K (403K / 444T / 453F / 478R / 383N / 396T / 468N) set forth in Table 4; and / or (1) a nucleic acid molecule comprising at least one coding region encoding a SARS- CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS- CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenicfragment and / or immunogenic variant thereof)) comprises amino acid substitution set L (405D / 417Y / 440R / 478I / 490F / 383N / 396T / 468N) set forth in Table 4.
[0077] In one aspect, provided herein are compositions comprising a plurality of nucleic acid molecules SARS-CoV-2 spike proteins or polypeptides (e.g., immunogens (or immunogenic fragments and / or immunogenic variants thereof)), wherein the plurality comprises at least 2, 3, 4, 5, 6, or more SARS-CoV-2 spike proteins or polypeptides (e.g., immunogens (or immunogenic fragments and / or immunogenic variants thereof)), wherein (a) the amino acid sequence of each of the encoded 2, 3, 4, 5, or 6 or more SARS-CoV-2 spike proteins or polypeptides (e.g., immunogens (or immunogenic fragments and / or immunogenic variants thereof)) comprises or consists of one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25) of the following amino acid substitutions 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1), wherein the amino acid sequence of each member of the plurality does not contain an identical set of the foregoing amino acid substitutions (i.e., 440E, 456L, 478R, 484V, 5O5Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1)); (b) wherein the amino acid sequence of each of the encoded 2, 3, 4, 5, or 6 or more SARS-CoV-2 spike proteins or polypeptides (e.g., immunogens (or immunogenic fragments and / or immunogenic variants thereof)) comprises or consists of one or more (e. , 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, or 25) of the following amino acid substitutions 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 5O5D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1)), and one or more (e.g., 1, 2, or 3) of the following amino acid substitutions 383N, 396T, 468N (amino acid numbering according to SEQ ID NO: 1), and wherein the amino acid sequence of each member of the plurality does not contain an identical set of the foregoing amino acid substitutions (i.e., 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455 S, 5O5D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1)); or (c) wherein the amino acid sequence of each of the encoded 2, 3, 4, 5, or 6 or more SARS-CoV-2 spike proteins or polypeptides (e.g., immunogens (or immunogenic fragments and / or immunogenic variants thereof)) comprises or consists of one ormore («?.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28) of the following amino acid substitutions 440E, 456L, 478R, 484V, 5O5Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 5O5D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, 490F, 383N, 396T, or 468N (amino acid numbering according to SEQ ID NO: 1)), and one or more (e.g., 1, 2, or 3) of the following amino acid substitutions 383N, 396T, 468N (amino acid numbering according to SEQ ID NO: 1), and wherein the amino acid sequence of each member of the plurality does not contain an identical set of the foregoing amino acid substitutions (i.e., 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, 490F, 383N, 396T, or 468N (amino acid numbering according to SEQ ID NO: 1)).
[0078] In some embodiments, the nucleic acid molecule(s) of a composition described herein are comprised in one or more vectors.[0079 In some embodiments, the nucleic acid molecule(s) or the one or more vectors of a composition described herein are formulated in one or more carrier. In some embodiments, the carrier is a lipid nanoparticle (LNP), liposome, lipoplex, or nanoliposome. In some embodiments, the carrier is an LNP. In some embodiments, the LNP comprises a cationic lipid, a neutral lipid, a cholesterol, and / or a PEG lipid. In some embodiments, the LNP has a mean particle size of between 80 nm and 160 nm.
[0080] In some embodiments, the composition further comprises a nucleic acid molecule encoding a SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) that does not comprise a set of amino acid substitutions set forth in Table 2 or Table 4.[00811 In some embodiments, the composition is a pharmaceutical composition comprising a pharmaceutically acceptable excipient or a vaccine composition. In some embodiments, the composition further comprises an adjuvant.|0082] In one aspect, provided herein are SARS-CoV-2 spike proteins (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), comprises at least one set of amino acid substitutions set forth in Table 2 or Table 4.
[0083] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of the receptor binding domain (RED) of a SARS-CoV-2 spike protein.
[0084] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g, the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of a full-length SARS-CoV-2 spike protein.|0085[ In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least one set of amino acid substitutions set forth in Table 2.
[0086] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g, the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, or 1300 amino acids.
[0087] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises from about 10-15, 10-20, 10-30, 10-40, 10-50, 10-60, 10-70, 10-80, 10-90, 10-100, 10-200, 10-300, 10-400, 10-500, 10-600, 10-700, 10-800, 10-900, 10-1000, 10- 1100, 10-1200, or 10-1300 amino acids.
[0088] In some embodiments, other than the at least one set of amino acid substitutions, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, or 1300 amino acids set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
[0089] In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 2, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV- 2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
[0090] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises a plurality of sets of amino acid substitutions set forth in Table 2.
[0091] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least 2, 3, 4, 5, or 6 sets of amino acid substitutions set forth in Table 2.
[0092] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%) amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not set forth in Table 2.
[0093] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 2 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
[0094] In some embodiments, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is stabilized in a prefusion state.
[0095] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least one amino acid variation relative to the amino acid sequence set forth in SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2) that stabilizes the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) in a prefusion state.
[0096] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises a proline at amino acid position 986 and / or a proline at amino acid position 987, amino acid numbering relative to the amino acid positions set forth in SEQ ID NO: 1.
[0097] In some embodiments, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises one or more non-naturally N-glycosylation sites.]0098| In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises the addition of one or more N-glycosylation sites relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).[0099| In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 7-12.
[0109] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 13-24.
[0011] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g, the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least one set of amino acid substitutions set forth in Table 4.
[0102] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, or 1300 amino acids.[00103) In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises from about 10-15, 10-20, 10-30, 10-40, 10-50, 10-60, 10-70, 10-80, 10-90, 10-100, 10-200, 10-300, 10-400, 10-500, 10-600, 10-700, 10-800, 10-900, 10-1000, 10- 1100, 10-1200, or 10-1300 amino acids.
[0104] In some embodiments, other than the at least one set of amino acid substitutions the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, or 1300 amino acids set forth in any one of SEQ ID NOS: 1-6 or 43-44 e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44). |00105| In some embodiments, other than the at least one set of amino acid substitutions the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 1- 6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
[0106] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises a plurality of sets of amino acid substitutions set forth in Table 4.100107] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least 2, 3, 4, 5, or 6 sets of amino acid substitutions set forth in Table 4.|00108] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 4.
[0109] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g, substitutions, additions, deletions, etc.) that are not listed in Table 4 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).)00110| In some embodiments, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is stabilized in a prefusion state.[00111) In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g, the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least one amino acid variation relative to the amino acid sequence set forth in in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: l-2)that stabilizes the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) in a prefusion state.[001121 In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises a proline at amino acid position 986 and / or a proline at amino acid position 987, amino acid numbering relative to SEQ ID NO: 1 .
[0113] In some embodiments, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises one or more non-naturally N-glycosylation sites.[0011 J In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g, the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises the addition of one or more N-glycosylation sites relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
[0115] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%,92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 25-30.| 00116 | In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 31-42.|001171 In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least one set of amino acid substitutions set forth in Table 2 and at least one set of amino acid substitutions set forth in Table 4.100.1.181 In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, or 1300 amino acids.
[0119] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises 10-15, 10-20, 10-30, 10-40, 10-50, 10-60, 10-70, 10-80, 10-90, 10- 100, 10-200, 10-300, 10-400, 10-500, 10-600, 10-700, 10-800, 10-900, 10-1000, 10-1100, 10- 1200, or 10-1300 amino acids.
[0120] In some embodiments, other than the at least one set of amino acid substitutions, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, or 1300 amino acids set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g, any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
[0121] In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 2 and the at least one set of amino acid substitutions set forth in Table 4, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%,83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).1'00.1221 In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises a plurality of sets of amino acid substitutions set forth in Table 2.|0O123j In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least 2, 3, 4, 5, or 6 sets of amino acid substitutions set forth in Table 2.(00124] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not set forth in Table 2.
[0125] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 2 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
[0126] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises a plurality of sets of amino acid substitutions set forth in Table 4.
[0127] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 16 sets of amino acid substitutions set forth in Table 4.
[0128] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenicvariant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 4.|00129| In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 4 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
[0130] In some embodiments, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is stabilized in a prefusion state.
[0131] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least one amino acid variation relative to the amino acid sequence set forth in SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2), that stabilizes the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) in a prefusion state.
[0132] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises a proline at amino acid position 986 and / or a proline at amino acid position 987, amino acid numbering relative to the amino acid positions set forth in SEQ ID NO: 1.
[0133] In some embodiments, SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises one or more non-naturally N-glycosylation sites.
[0134] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises the addition of one or more N-glycosylation sites relative to the aminoacid sequence set forth in SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1 -2, 4-5, or 43-44).100135] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises an inactive furin cleavage site.
[0136] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least one amino acid variation in the furin cleavage site that inactivates the furin cleavage site.
[0137] In some embodiments, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) further comprises a heterologous protein. In some embodiments, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises a signal peptide. In some embodiments, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises a homologous or heterologous signal peptide. In some embodiments, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) does not comprise a signal peptide.
[0138] In some embodiments, the SARS-CoV-2 spike protein is an immunogen (or an immunogenic fragment and / or immunogenic variant thereof).|00139| In one aspect, provided herein are fusion proteins comprising a SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) described herein operably connected (e.g., directly or indirectly (e.g., via a linker)) to a heterologous polypeptide or protein.
[0140] In one aspect, provided herein are conjugates comprising a SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) described herein operably connected (e.g, directly or indirectly (e.g., via a linker)) to a heterologous moiety.
[0141] In one aspect, provided herein are compositions comprising at least one SARS-CoV-2 spike protein (e.g., at least one of the SARS-CoV-2 spike protein immunogen (or immunogenicfragment and / or immunogenic variant thereof)) described herein, a fusion protein described herein, a conjugate described herein, or a nucleic acid molecule described herein.|001421 In some embodiments, the composition comprises a plurality of SARS-CoV-2 spike proteins (e.g., a plurality of SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) set forth in any one of claims 92-51, wherein the amino acid sequence of each of the plurality of SARS-CoV-2 spike proteins (e.g., the SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) comprises a different set of amino acid substitutions set forth in Table 2 or Table 4 or a different combination of sets of amino acid substitutions set forth in Table 2 or Table 4.
[0143] In some embodiments, the plurality comprises at least 2, 3, 4, 5, or 6 SARS-CoV-2 spike proteins (e.g., the SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) wherein the amino acid sequence each of the at least 2, 3, 4, 5, or 6 SARS-CoV-2 spike proteins (e.g., the SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) comprises a different set of amino acid substitutions set forth in Table 2.
[0144] In some embodiments, the plurality comprises at least 2, 3, 4, 5, or 6 SARS-CoV-2 spike proteins (e.g., the SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) wherein the amino acid sequence each of the at least 2, 3, 4, 5, or 6 SARS-CoV-2 spike proteins (e.g., the SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) comprises a different set of amino acid substitutions set forth in Table 4.
[0145] In some embodiments, the plurality comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 SARS-CoV-2 spike proteins (e.g., the SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) wherein the amino acid sequence each of the at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 SARS-CoV-2 spike proteins (e.g, the SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) comprises a different set of amino acid substitutions set forth in Table 2 or Table 4.
[0146] In one aspect, provided herein are compositions comprising (a) at least one SARS- CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) that comprises a set of amino acid substitutions set forth in Table 2; (b) at least one SARS-CoV-2 spike proteins (e.g., the SARS-CoV-2 spike proteinimmunogen (or the immunogenic fragment and / or immunogenic variant thereof)) that comprises a set of amino acid substitutions set forth in Table 4; and / or (c) at least one SARS-CoV-2 spike proteins (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) that comprises a set of amino acid substitutions set forth in Table 2 a set of amino acid substitutions set forth in Table 4.
[0147] In one aspect, provided herein are compositions comprising at least 2, 3, 4, 5, or 6 SARS-CoV-2 spike proteins (e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) wherein the amino acid sequence of the at least 2, 3, 4, 5, or 6 SARS-CoV-2 spike proteins (e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) comprises a different set of amino acid substitutions set forth in Table 2.|00148| In one aspect, provided herein are compositions comprising at least 2, 3, 4, 5, or 6 SARS-CoV-2 spike proteins e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) wherein the amino acid sequence of the at least 2, 3, 4, 5, or 6 SARS-CoV-2 spike proteins (e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) comprises a different set of amino acid substitutions set forth in Table 4.
[0149] In one aspect, provided herein are compositions comprising at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 SARS-CoV-2 spike proteins (e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) wherein the amino acid sequence of the at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 SARS-CoV-2 spike proteins (e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) comprises a different set of amino acid substitutions set forth in Table 2 or Table 4.
[0159] In one aspect, provided herein are compositions comprising any one or more (e.g., 1, 2, 3, 4, 5, or 6) of (a) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set A (440E / 456L / 478R / 484V / 505Y) set forth in Table 2; (b) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set B (405K / 440N / 456V / 478Q / 490P) set forth in Table 2; (c) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenicfragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set C (403S / 444E / 455W) set forth in Table 2; (d) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set D (346K / 439K / 455S / 505D) set forth in Table 2; (e) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set E (403K / 444T / 453F / 478R) set forth in Table 2; and / or (f) a SARS-CoV-2 spike protein (e.g., SARS- CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set F (405D / 417Y / 440R / 478I / 490F) set forth in Table 2.|00151] In one aspect, provided herein are compositions comprising any one or more (e.g., 1, 2, 3, 4, 5, or 6) of (a) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set G (440E / 456L / 478R / 484V / 505Y / 383N / 396T / 468N) set forth in Table 4; (b) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set H (405K / 440N / 456V / 478Q / 490P / 383N / 396T / 468N) set forth in Table 4; (c) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set I (403S / 444E / 455W / 383N / 396T / 468N) set forth in Table 4; (d) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set J (346K / 439K / 455S / 505D / 383N / 396T / 468N) set forth in Table 4; (e) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set K (403K / 444T / 453F / 478R / 383N / 396T / 468N) set forth in Table 4; and / or (f) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequencethat comprises amino acid substitution set L (405D / 417Y / 440R / 478I / 490F / 383N / 396T / 468N) set forth in Table 4.|001521 In one aspect, provided herein are compositions comprising any one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12) of (a) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set A (440E / 456L / 478R / 484V / 505Y) set forth in Table 2; (b) a SARS-CoV-2 spike protein (e.g., SARS- CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set B (405K / 440N / 456V / 478Q / 490P) set forth in Table 2; (c) a SARS-CoV-2 spike protein (e.g., SARS- CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set C (403S / 444E / 455W) set forth in Table 2; (d) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set D (346K / 439K / 455S / 505D) set forth in Table 2; (e) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set E (403K / 444T / 453F / 478R) set forth in Table 2; (f) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution setF (405D / 417Y / 440R / 478I / 490F) set forth in Table 2; (g) a SARS-CoV- 2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set G (440E / 456L / 478R / 484V / 505Y / 383N / 396T / 468N) set forth in Table 4; (h) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set H (405K / 440N / 456V / 478Q / 490P / 383N / 396T / 468N) set forth in Table 4; (i) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set I (403S / 444E / 455W / 383N / 396T / 468N) set forth in Table 4; (j) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenicfragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set J (346K / 439K / 455S / 505D / 383N / 396T / 468N) set forth in Table 4; (k) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set K (403K / 444T / 453F / 478R / 383N / 396T / 468N) set forth in Table 4; and / or (1) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set L (405D / 417Y / 440R / 478I / 490F / 383N / 396T / 468N) set forth in Table 4.
[0153] In one aspect, provided herein are compositions comprising a plurality of SARS-CoV- 2 spike proteins or polypeptides (e.g., immunogens (or immunogenic fragments and / or immunogenic variants thereof)), wherein the plurality comprises at least 2, 3, 4, 5, 6, or more SARS-CoV-2 spike proteins or polypeptides (e.g., immunogens (or immunogenic fragments and / or immunogenic variants thereof)), wherein (a) the amino acid sequence of each of the 2, 3, 4, 5, or 6 or more SARS-CoV-2 spike proteins or polypeptides (e.g., immunogens (or immunogenic fragments and / or immunogenic variants thereof)) comprises or consists of one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25) of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1), wherein the amino acid sequence of each member of the plurality does not contain an identical set of the foregoing amino acid substitutions (i.e., 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1)); (b) wherein the amino acid sequence of each of the 2, 3, 4, 5, or 6 or more SARS-CoV-2 spike proteins or polypeptides (e.g., immunogens (or immunogenic fragments and / or immunogenic variants thereof)) comprises or consists of one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25) of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1)), and one or more (e.g., 1, 2, or 3) of the following amino acid substitutions 383N, 396T, 468N (amino acid numbering according to SEQID NO: 1), and wherein the amino acid sequence of each member of the plurality does not contain an identical set of the foregoing amino acid substitutions (i.e., 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1)); or (c) wherein the amino acid sequence of each of the 2, 3, 4, 5, or 6 or more SARS-CoV-2 spike proteins or polypeptides (e.g., immunogens (or immunogenic fragments and / or immunogenic variants thereof)) comprises or consists of one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28) of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, 490F, 383N, 396T, or 468N (amino acid numbering according to SEQ ID NO: 1)), and one or more (e.g., 1, 2, or 3) of the following amino acid substitutions 383N, 396T, 468N (amino acid numbering according to SEQ ID NO: 1), and wherein the amino acid sequence of each member of the plurality does not contain an identical set of the foregoing amino acid substitutions (i.e., 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, 490F, 383N, 396T, or 468N (amino acid numbering according to SEQ ID NO: 1)).
[0154] In some embodiments, the SARS-CoV-2 spike proteins (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) are formulated in one or more carrier. In some embodiments, the carrier is a lipid nanoparticle (LNP), liposome, lipoplex, or nanoliposome. In some embodiments, the carrier is an LNP. In some embodiments, the LNP comprises a cationic lipid, a neutral lipid, a cholesterol, and / or a PEG lipid. In some embodiments, the LNP has a mean particle size of between 80 nm and 160 nm.
[0155] In some embodiments, the composition further comprises a SARS-CoV-2 spike proteins (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) that does not comprise a set of amino acid substitutions set forth in Table 2 or Table 4.
[0156] In some embodiments, the composition is a pharmaceutical composition comprising a pharmaceutically acceptable excipient. In some embodiments, the composition further comprises an adjuvant.[00157} In some embodiments, the carrier is a lipid nanoparticle (LNP), liposome, lipoplex, or nanoliposome. In some embodiments, the carrier is an LNP. In some embodiments, the LNP comprises a cationic lipid, a neutral lipid, a cholesterol, and / or a PEG lipid. In some embodiments, the LNP has a mean particle size of between 80 nm and 160 nm.[0 158) In one aspect, provided herein are nucleic acid molecules encoding a SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) described herein.
[0159] In one aspect, provided herein is a SARS-CoV-2 spike protein (e.g, a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) encoded by a nucleic acid molecule described herein.[00160) In one aspect, provided herein are carriers comprising a nucleic acid molecule described herein, a protein (e.g., a SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) described herein, a vector described herein, a conjugate described herein, a fusion protein described herein, a host cell described herein, a composition described herein, a vaccine composition described herein, or a pharmaceutical composition described herein.)00161 | In some embodiments, the carrier is a lipid nanoparticle (LNP), liposome, lipoplex, or nanoliposome. In some embodiments, the carrier is an LNP. In some embodiments, the LNP comprises a cationic lipid, a neutral lipid, a cholesterol, and / or a PEG lipid. In some embodiments, the LNP has a mean particle size of between 80 nm and 160 nm.
[0162] In one aspect, provided herein are vaccine compositions comprising a nucleic acid molecule described herein, a protein (e.g, a SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) described herein, a vector described herein, a conjugate described herein, a fusion protein described herein, a host cell described herein, a composition described herein, a carrier described herein, or a pharmaceutical composition described herein.
[0163] In some embodiments, the vaccine composition is a prime vaccine composition. In some embodiments, the vaccine composition is a boost vaccine composition. In some embodiments, the vaccine composition is a prime vaccine composition and a boost vaccine composition. In some embodiments, the vaccine composition can be utilized as a prime vaccinecomposition and / or a booster vaccine composition in a homologous or heterologous prime boost vaccine regimen. In some embodiments, the vaccine composition further comprises an adjuvant.
[0164] In one aspect, provided herein are vaccine compositions comprising a messenger ribonucleic acid (mRNA) encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) that comprises at least one amino acid substitution set forth in Table 2 or Table 4, formulated in a lipid nanoparticle, the vaccine composition having the following characteristics: (a) the LNPs comprise a cationic lipid, a neutral lipid, a cholesterol, and a PEG lipid, (b) the LNPs have a mean particle size of between 80 nm and 160 nm, and (c) the mRNA comprises: (i) a 5'-cap structure; (ii) a 5'- UTR; (iii)Nl-methyl-pseudouridine, cytosine, adenine, and guanine; (iv) a 3'-UTR; and (v) a poly- A region.|001.65] In some embodiments, the vaccine composition is a prime vaccine composition. In some embodiments, the vaccine composition is a boost vaccine composition. In some embodiments, the vaccine composition is a prime vaccine composition and a boost vaccine composition. In some embodiments, the vaccine composition can be utilized as a prime vaccine composition and / or a booster vaccine composition in a homologous or heterologous prime boost vaccine regimen. In some embodiments, the vaccine composition further comprises an adjuvant.
[0166] In one aspect, provided herein are pharmaceutical compositions comprising a nucleic acid molecule described herein, a protein (e.g., a SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) described herein, a vector described herein, a conjugate described herein, a fusion protein described herein, a host cell described herein, a composition described herein, a carrier described herein, or a vaccine composition described herein, and a pharmaceutically acceptable excipient. In some embodiments, the pharmaceutical composition further comprises an adjuvant.
[0167] In one aspect, provided herein are pharmaceutical compositions comprising a messenger ribonucleic acid (mRNA) encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV- 2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) that comprises at least one amino acid substitution set forth in Table 2 or Table 4, formulated in a lipid nanoparticle, the pharmaceutical composition having the following characteristics: (a) the LNPs comprise a cationic lipid, a neutral lipid, a cholesterol, and a PEG lipid, (b) the LNPs have a mean particle size of between 80 nm and 160 nm, and (c) the mRNA comprises: (i) a 5'-capstructure; (ii) a 5'-UTR; (iii) Nl-methyl-pseudouridine, cytosine, adenine, and guanine; (iv) a 3'- UTR; and (v) a poly-A region; and a pharmaceutically acceptable excipient. In some embodiments, the pharmaceutical composition further comprises an adjuvant.
[0168] In one aspect, provided herein are host cells comprising a nucleic acid molecule described herein, a protein (e.g., a SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) described herein, a vector described herein, a conjugate described herein, a fusion protein described herein, a composition described herein, a carrier described herein, a vaccine composition described herein, or a pharmaceutical composition described herein.
[0169] In one aspect, provided herein are kits comprising a nucleic acid molecule described herein, a protein (e.g., a SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) described herein, a vector described herein, a conjugate described herein, a fusion protein described herein, a host cell described herein, a composition described herein, a carrier described herein, a vaccine composition described herein, or a pharmaceutical composition described herein. In some embodiments, the kit comprises instructions for use of the nucleic acid molecule, vector, protein (or immunogenic fragment or immunogenic variant thereof), conjugate, fusion protein, carrier, composition, vaccine composition, or pharmaceutical composition.
[0179] In one aspect, provided herein are methods of delivering a nucleic acid molecule, vector, protein (or immunogenic fragment or immunogenic variant thereof), conjugate, fusion protein, host cell, carrier, composition, vaccine composition, or pharmaceutical composition to a subject in need thereof, the method comprising administering to the subject a nucleic acid molecule described herein, a protein (e.g., a SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) described herein, a vector described herein, a conjugate described herein, a fusion protein described herein, a host cell described herein, a composition described herein, a carrier described herein, a vaccine composition described herein, or a pharmaceutical composition described herein, to thereby deliver the nucleic acid molecule, the vector, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), the conjugate, the fusion protein, the host cell, the carrier, the composition, the vaccine composition, or the pharmaceutical composition to the subject.[00171) In some embodiments, the nucleic acid molecule, the vector, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), the conjugate, the fusion protein, the carrier, the composition, the vaccine composition, or the pharmaceutical composition is administered to the subject at least twice. In some embodiments, the subject is a human.
[0172] In some embodiments, the nucleic acid molecule, the vector, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), the conjugate, the fusion protein, the carrier, the composition, the vaccine composition, or the pharmaceutical composition is administered as a prime and / or a boost in a homologous or heterologous prime-boost regimen.
[0173] In some embodiments, the nucleic acid molecule, the vector, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), the conjugate, the fusion protein, the carrier, the composition, the vaccine composition, or the pharmaceutical composition is administered as a boost in a heterologous prime-boost regimen.
[0174] In one aspect, provided herein are methods of inducing or enhancing an immune response in a subject in need thereof, the method comprising administering to the a nucleic acid molecule described herein, a protein (e.g., a SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) described herein, a vector described herein, a conjugate described herein, a fusion protein described herein, a host cell described herein, a composition described herein, a carrier described herein, a vaccine composition described herein, or a pharmaceutical composition described herein, to thereby induce or enhance an immune response the subject. In some embodiments, the subject is a human.
[0175] In some embodiments, the nucleic acid molecule, the vector, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), the conjugate, the fusion protein, the carrier, the composition, the vaccine composition, or the pharmaceutical composition is administered to the subject at least twice.
[0176] In some embodiments, the nucleic acid molecule, the vector, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), the conjugate, the fusion protein, the carrier, the composition, thevaccine composition, or the pharmaceutical composition is administered as a prime and / or a boost in a homologous or heterologous prime-boost regimen.|00177| In some embodiments, the nucleic acid molecule, the vector, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), the conjugate, the fusion protein, the carrier, the composition, the vaccine composition, or the pharmaceutical composition is administered as a boost in a heterologous prime-boost regimen.[001781 In one aspect, provided herein are methods of preventing, ameliorating, or treating a SARS-CoV-2 infection in a subject in need thereof, the method comprising administering to the subject a nucleic acid molecule described herein, a protein (e.g., a SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) described herein, a vector described herein, a conjugate described herein, a fusion protein described herein, a host cell described herein, a composition described herein, a carrier described herein, a vaccine composition described herein, or a pharmaceutical composition described herein, to thereby prevent, ameliorate, or treat the SARS-CoV-2 infection the subject. In some embodiments, the subject is a human.|00179| In some embodiments, the nucleic acid molecule, the vector, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), the conjugate, the fusion protein, the carrier, the composition, the vaccine composition, or the pharmaceutical composition is administered to the subject at least twice.
[0180] In some embodiments, the nucleic acid molecule, the vector, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), the conjugate, the fusion protein, the carrier, the composition, the vaccine composition, or the pharmaceutical composition is administered as a prime and / or a boost in a homologous or heterologous prime-boost regimen.
[0181] In some embodiments, the nucleic acid molecule, the vector, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), the conjugate, the fusion protein, the carrier, the composition, the vaccine composition, or the pharmaceutical composition is administered as a boost in a heterologous prime-boost regimen.[00182) In one aspect, provided herein are methods of vaccinating a subject against SARS- CoV-2, the method comprising administering to the subject a nucleic acid molecule described herein, a protein (e.g., a SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) described herein, a vector described herein, a conjugate described herein, a fusion protein described herein, a host cell described herein, a composition described herein, a carrier described herein, a vaccine composition described herein, or a pharmaceutical composition described herein, to thereby vaccinate the subject against SARS- CoV-2. In some embodiments, the subject is a human.
[0183] In some embodiments, the nucleic acid molecule, the vector, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), the conjugate, the fusion protein, the carrier, the composition, the vaccine composition, or the pharmaceutical composition is administered to the subject at least twice.
[0184] In some embodiments, the nucleic acid molecule, the vector, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), the conjugate, the fusion protein, the carrier, the composition, the vaccine composition, or the pharmaceutical composition is administered as a prime and / or a boost in a homologous or heterologous prime-boost regimen.
[0185] In some embodiments, the nucleic acid molecule, the vector, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), the conjugate, the fusion protein, the carrier, the composition, the vaccine composition, or the pharmaceutical composition is administered as a boost in a heterologous prime-boost regimen.
[0186] In one aspect, provided herein are methods of vaccinating a subject against SARS- CoV-2, the method comprising administering to the subject (a) an mRNA molecule (e.g., an mRNA molecule described herein) encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) described herein (or a conjugate or fusion protein thereof), (b) a vector comprising the mRNA molecule, (c) a carrier comprising the mRNA molecule or the vector, (d) a vaccine composition comprising the mRNA molecule, the vector, or the carrier, or (e) a pharmaceutical composition comprising the mRNA molecule, the vector, the carrier, or the vaccine composition,to thereby vaccinate the subject against SARS-CoV-2, to thereby vaccinate the subject against SARS-CoV-2. In some embodiments, the subject is a human.1001.87] In some embodiments, the nucleic acid molecule, the vector, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), the conjugate, the fusion protein, the carrier, the composition, the vaccine composition, or the pharmaceutical composition is administered to the subject at least twice.
[0188] In some embodiments, the nucleic acid molecule, the vector, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), the conjugate, the fusion protein, the carrier, the composition, the vaccine composition, or the pharmaceutical composition is administered as a prime and / or a boost in a homologous or heterologous prime-boost regimen.|00189| In some embodiments, the nucleic acid molecule, the vector, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), the conjugate, the fusion protein, the carrier, the composition, the vaccine composition, or the pharmaceutical composition is administered as a boost in a heterologous prime-boost regimen.
[0190] In one aspect, provided herein are methods of vaccinating a subject against SARS- CoV-2, the method comprising administering to the subject a vaccine composition described herein or a pharmaceutical composition described herein, to thereby vaccinate the subject against SARS-CoV-2. In some embodiments, the subject is a human.100191] In some embodiments, the nucleic acid molecule, the vector, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), the conjugate, the fusion protein, the carrier, the composition, the vaccine composition, or the pharmaceutical composition is administered to the subject at least twice.
[0192] In some embodiments, the nucleic acid molecule, the vector, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), the conjugate, the fusion protein, the carrier, the composition, the vaccine composition, or the pharmaceutical composition is administered as a prime and / or a boost in a homologous or heterologous prime-boost regimen.[00193) In some embodiments, the nucleic acid molecule, the vector, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), the conjugate, the fusion protein, the carrier, the composition, the vaccine composition, or the pharmaceutical composition is administered as a boost in a heterologous prime-boost regimen.
[0194] In some embodiments, the nucleic acid molecule, the vector, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), the conjugate, the fusion protein, the carrier, the composition, the vaccine composition, or the pharmaceutical composition is administered to the subject at least twice.
[0195] In some embodiments, the nucleic acid molecule, the vector, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), the conjugate, the fusion protein, the carrier, the composition, the vaccine composition, or the pharmaceutical composition is administered as a prime and / or a boost in a homologous or heterologous prime-boost regimen.
[0196] In some embodiments, the nucleic acid molecule, the vector, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), the conjugate, the fusion protein, the carrier, the composition, the vaccine composition, or the pharmaceutical composition is administered as a boost in a heterologous prime-boost regimen.
[0197] In one aspect, provided herein are nucleic acid molecules (e.g., described herein), proteins (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) (e.g., described herein), vectors (e.g., described herein), conjugates (e.g., described herein), fusion proteins (e.g., described herein), host cells (e.g., described herein), compositions (e.g., described herein), vaccine compositions (e.g., described herein), carriers (e.g., described herein), pharmaceutical compositions (e.g., described herein) for use in inducing or enhancing an immune response in a subject in need thereof; preventing, ameliorating, or treating a SARS-CoV-2 infection in a subject in need thereof; or vaccinating a subject against SARS-CoV- 2.
[0198] In one aspect, provided herein are nucleic acid molecules (e.g., described herein), proteins (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / orimmunogenic variant thereof)) (e.g, described herein), vectors (e.g., described herein), conjugates (e.g., described herein), fusion proteins (e.g., described herein), host cells (e.g., described herein), compositions (e.g., described herein), vaccine compositions (e.g., described herein), carriers (e.g, described herein), pharmaceutical compositions (e.g., described herein) for use as a medicament. In some embodiments, the subject is a human.
[0199] In one aspect, provided herein are uses of nucleic acid molecules (e.g., described herein), proteins (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) (e.g., described herein), vectors (e.g., described herein), conjugates (e.g., described herein), fusion proteins (e.g., described herein), host cells (e.g., described herein), compositions (e.g., described herein), vaccine compositions (e.g., described herein), carriers (e.g., described herein), pharmaceutical compositions (e.g., described herein) for the manufacture of a medicament for the induction or enhancement of an immune response in a subject in need thereof; the prevention, amelioration, or treatment a SARS-CoV-2 infection in a subject in need thereof; or the vaccination a subject against SARS-CoV-2. In some embodiments, the subject is a human.4. BRIEF DESCRIPTION OF THE FIGURES|00200| FIGS. 1A-1C depict a sequence alignment of the amino acid sequence of a reference SARS-CoV-2 spike protein Wuhan-Hu-1 Spike protein sequence (SEQ ID NO: 1) and a variant thereof (SEQ ID NO: 4).5. DETAILED DESCRIPTION[00201 | SARS-CoV-2 continues to evolve into new variants comprising a variety of amino acid variations, e.g., substitutions, deletions, and insertions. Many of the variations are found in the receptor binding domain (RBD) of the spike protein, which is vital for SARS-CoV-2 entry into a cell. As most of the SARS-CoV-2 vaccines and current antibody therapies target the RBD of the spike protein, this creates the potential for the evolution of SARS-CoV-2 variants that evade vaccine-induced immunity, infection-induced immunity, and / or current antibody therapies. The inventors have identified sequence variations in the SARS-CoV-2 spike protein (e.g., in the RBD) that e.g., counter SARS-CoV-2 resistance to vaccine induced immunity and / or are potential SARS- CoV-2 variants. Accordingly, novel SARS-CoV-2 spike proteins (e.g., SARS-CoV-2 spike proteinimmunogens (and immunogenic fragments and / or immunogenic variants thereof)) (or nucleic acid molecules, e.g., mRNAs, encoding such SARS-CoV-2 spike proteins) comprising at least one such sequence variation are good candidates for variant-proof or variant-resistant vaccines against COVID- 19. A such, the current disclosure provides, inter alia, novel immunogens for use in pharmaceutical compositions and vaccines to induce a desired immune response against one or more variants of SARS-CoV-2.TABLE OF CONTENTS5.1 Definitions5.2 SARS-CoV-2 Spike Proteins (e.g., Immunogens)5.2.1 Exemplary Additional Features of SARS-CoV-2 Spike Proteins (e.g., Immunogens)5.2.1.1 Full-Length Spike Proteins and Receptor Binding Fragments5.2.1.2 Stabilization5.2.1.3 Multimerization (e.g., Trimerization) Domains5.2.1.4 Engineered Glycosylation Sites5.2.1.5 Hyperglycosylation5.2.1.6 Additional Variations5.2.1.7 Variations from Different Strains of SARS-CoV-25.2.1.8 Heterologous Proteins and Peptides5.2.1.9 Signal Peptides5.2.1.10 Immunogens5.3 Nucleic Acid Molecules5.3.1 DNA Nucleic Acids5.3.2 RNA Nucleic Acids5.4 Fusions & Conjugates5.5 Compositions (e.g., Vaccine Compositions)5.5.1 Peptide and Protein-Based Vaccines5.5.2 Nucleic Acid-Based Vaccines5.6 Vectors5.7 Carriers5.7.1 Lipid Based Carriers / Lipid Nanoformulations5.7.1.1 Cationic Lipids (Positively Charged) and Ionizable Lipids5.7.1.2 Non-Cationic Lipids (e.g., Phospholipids)5.7.1.3 Structural Lipids5.7.1.4 Polymers and Polyethylene Glycol (PEG) - Lipids5.7.1.5 Percentages of Lipid Nanoformulation Components5.8 Adjuvants5.9 Methods of Use5.9.1 Methods of Delivery5.9.2 Manufacture of a Medicament5.9.3 Methods of Inducing or Enhancing an Immune Response5.9.4 Methods of Preventing, Ameliorating, and / or Treating Infection5.9.5 Methods of Vaccination against SARS-CoV-25.9.5.1 Methods of Vaccinating a Subject against SARS-CoV-25.9.5.2 Methods of Vaccinating a Subject Utilizing a SARS-CoV-2 mRNA Vaccine5.10 Kits5.1 Definitions1002021 The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described.
[0203] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of skill in the art to which the claimed subject matter belongs. It is to be understood that the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive of any subject matter claimed.
[0204] In this application, the use of the singular includes the plural unless specifically stated otherwise. For example, as used in the specification and the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise. Furthermore, use of the term “including” as well as other forms, such as “include,” “includes,” and “included,” is not limiting.(00205) It is understood that wherever aspects are described herein with the language “comprising,” otherwise analogous aspects described in terms of “consisting of’ and “consisting essentially of’ are also provided and vice versa.[00206| The term “and / or” where used herein is to be taken as specific disclosure of each of the two specified features or components with or without the other. Thus, the term “and / or” as used in a phrase such as “A and / or B” herein is intended to include “A and B,” “A or B,” “A” (alone), and “B” (alone). Likewise, the term “and / or” as used in a phrase such as “A, B, and / or C” is intended to encompass each of the following aspects: A, B, and C; A, B, or C; A or C; A or B; B or C; A and C; A and B; B and C; A (alone); B (alone); and C (alone).(00207] As described herein, any concentration range, percentage range, ratio range or integer range is to be understood to include the value of any integer within the recited range and, when appropriate, fractions thereof (such as one tenth and one hundredth of an integer), unless otherwise indicated.(00208) The term “about” refers to a value or composition that is within an acceptable error range for the particular value or composition as determined by one of ordinary skill in the art, which will depend in part on how the value or composition is measured or determined, i.e., the limitations of the measurement system. When particular values or compositions are provided in the application and claims, unless otherwise stated, the meaning of “about” should be assumed to be within an acceptable error range for that particular value or composition.(00209) Where proteins and / or polypeptides are described herein, it is understood that polynucleotides (e.g., RNA (e.g., mRNA) or DNA nucleic acid molecules) encoding the protein or polypeptide are also provided herein.
[0210] Where proteins, polypeptides, nucleic acid molecules, vectors, carriers, etc. are described herein, it is understood that isolated forms of the proteins, polypeptides, nucleic acid molecules, vectors, carriers, etc. are also provided herein.100211] Where proteins, polypeptides, nucleic acid molecules, etc. are described herein, it is understood that recombinant forms of the proteins, polypeptides, nucleic acid molecules, etc. are also provided herein.(00212) Where polypeptides or sets of polypeptides are described herein, it is understood that proteins comprising the polypeptides or sets of polypeptides folded into their three-dimensional structure (i.e., tertiary or quaternary structure) are also provided herein and vice versa.[00213 J As used herein, the term “adjuvant” refers to a substance that causes stimulation of the immune system of a subject when administered to the subject.
[0214] As used herein, the term “administering” refers to the physical introduction of an agent, e.g., a vaccine or therapeutic agent (or a precursor of the agent (e.g., a vaccine or therapeutic agent) that is metabolized or altered (e.g., translation of a nucleic acid molecule) within the body of the subject to produce the agent (e.g., a vaccine or therapeutic agent) in vivo) to a subject, using any of the various methods and delivery systems known to those skilled in the art. Administering can also be performed, for example, once, a plurality of times, and / or over one or more extended periods.
[0215] As used herein, the term “agent” is used generically to describe any macro or micro molecule. Exemplary moieties include, but are not limited to polypeptides, proteins, peptides, nucleic acid molecules (e.g., DNA, RNA), small molecules, carbohydrates, lipids, synthetic polymers (e.g., polymers of PEG).
[0216] As used herein, the term “derived from,” with reference to a polynucleotide refers to a polynucleotide that has at least 70% sequence identity to a reference polynucleotide (e.g., a naturally occurring polynucleotide) or a fragment thereof. The term “derived from,” with reference to a polypeptide or protein refers to a polypeptide or protein that comprises an amino acid sequence that has at least 70% sequence identity to the amino acid sequence of a reference polypeptide or protein (e.g., a naturally occurring polypeptide or protein). The term “derived from” as used herein does not denote any specific process or method for obtaining the polynucleotide, polypeptide, or protein. For example, the polynucleotide, polypeptide, or protein can be recombinant produced or chemically synthesized.
[0217] As used herein, the term “disease” refers to any abnormal condition that impairs physiological function. The term is used broadly to encompass any disorder, illness, abnormality, pathology, sickness, condition, or syndrome in which physiological function is impaired, irrespective of the nature of the etiology. The term disease includes infection (e.g., a viral (e.g., a SARS-Cov-2 infection), bacterial, fungal, protozoal infection). The term disease includes an abnormal condition associated with, caused by, or otherwise related to an infection (e.g., a viral (e.g., a SARS-Cov-2 infection), bacterial, fungal, protozoal infection).
[0218] The terms “DNA” and “polydeoxyribonucleotide” are used interchangeably herein and refer to macromolecules that include multiple deoxyribonucleotides that are polymerized via phosphodiester bonds. Deoxyribonucleotides are nucleotides in which the sugar is deoxyribose.[00219| As used herein, the term “full-length” with reference to a SARS-CoV-2 spike protein refers to a SARS-CoV-2 spike protein, wherein the amino acid sequence of the SARS-CoV-2 spike protein comprises substantially the same number of amino acids as a reference SARS-CoV-2 spike protein. The reference can be a naturally occurring SARS-CoV-2 spike protein.[00220| As used herein, the term “fuse” and grammatical equivalents thereof refer to the operable connection of at least a first polypeptide or protein to a second polypeptide or protein, wherein the first and second polypeptides or proteins are not naturally found operably connected together. For example, the first and second polypeptides or proteins are derived from different proteins. The term fuse encompasses both a direct connection of the at least two polypeptides or proteins through a peptide bond, and the indirect connection through a linker (e.g., a peptide linker).[00221 J As used herein, the term “heterologous”, when used to describe a first element in reference to a second element means that the first element and second element do not exist in nature disposed as described. For example, a polypeptide comprising a “heterologous moiety” means a polypeptide that is joined to a moiety (e.g., small molecule, polypeptide, polynucleotide, carbohydrate, lipid, synthetic polymer (e.g., polymers of PEG), etc.) that is not joined to the polypeptide in nature.
[0222] As used herein, the term “fusion protein” and grammatical equivalents thereof refers to a protein that comprises at least one polypeptide operably connected to another polypeptide, wherein the first and second polypeptides are not naturally found operably connected together. For example, the first and second polypeptides of the fusion protein are each derived from different proteins. In some embodiments, the first and second polypeptides are different. The at least two polypeptides of the fusion protein can be directly operably connected through a peptide bond; or can be indirectly operably connected through a linker (e.g., a peptide linker). Therefore, for example, the term fusion polypeptide encompasses embodiments, wherein Polypeptide A is directly operably connected to Polypeptide B through a peptide bond (Polypeptide A - Polypeptide B), and embodiments, wherein Polypeptide A is operably connected to Polypeptide B through a peptide linker (Polypeptide A - peptide linker - Polypeptide B).(00223) As used herein, the term “half-life extension protein or “half-life extension polypeptide” refers to a protein or polypeptide that when operably connected to another moiety (e.g., a subject moiety) (e.g., a protein), increases the half-life of the subject moiety (e.g., the subject protein) in vivo when administered to a subject (e.g., a human subject). The pharmacokinetic properties of the protein can be evaluated utilizing in vivo models known in the art.|00224] As used herein, the term “heterologous”, when used to describe a first element in reference to a second element means that the first element and second element do not exist in nature disposed as described. For example, a polypeptide comprising a “heterologous moiety” means a polypeptide that is joined to a moiety (e.g., small molecule, polypeptide, nucleic acid molecule, carbohydrate, lipid, synthetic polymer (e.g., polymers of PEG), etc.) that is not joined to the polypeptide in nature.(00225] As used, herein the term “heterologous signal peptide” refers to a signal peptide that is not operably connected to a subject polypeptide or protein in nature. For example, in reference to a polypeptide comprising a signal peptide from human IL-2 operably connected to human IL-12, the human IL-2 signal peptide would constitute a heterologous signal peptide.(00226] As used herein, the term “heterologous prime boost” refers to a prime boost vaccine regimen wherein the prime vaccine composition and the boost (or booster) vaccine composition are different (e.g., the immunogen is different, the form of the immunogen is different (e.g., a nucleic acid (e.g., mRNA) molecule-based vaccine versus a protein-based vaccine), the immunogen is expressed from a different vector (e.g., plasmid, viral vector), the method of delivering the immunogen to the subject is different, etc.).
[0227] As used herein, the term “homologous signal peptide” refers to a signal peptide that is operably connected to a subject polypeptide or protein in nature. For example, in reference to a polypeptide comprising a signal peptide from human IL-2 operably connected to human IL-2, the human IL-2 signal peptide would constitute a homologous signal peptide.
[0228] As used herein, the term “homologous prime boost” refers to a prime boost vaccine regimen wherein the prime vaccine composition and the boost (or booster) vaccine composition are the same.
[0229] As used herein, the term “immunogen” refers to a substance that is capable of inducing an immune response (e.g., an adaptive immune response) in a subject (e.g., a human subject).(00230) As used herein, the term “immunogenic fragment” refers to a fragment of a reference polypeptide or protein that retains an immunogen.100231] As used herein, the term “immunogenic variant” refers to a variant of a reference polypeptide or protein that retains an immunogen. In some embodiments, the polypeptide or protein comprises at least one but no more than 25%, (e.g., no more than 20%, no more than 15%, no more than 12%, no more than 10%, no more than 8%) amino acid variation e.g., substitutions, deletions, additions) compared to the amino acid sequence of a reference polypeptide or protein.100232] As used herein, the term “in combination with” means that two (or more) different agents or treatments are administered to a subject as part of a defined treatment regimen for a particular disease. The treatment regimen defines the doses and periodicity of administration of each agent such that the effects of the separate agents on the subject overlap. In some embodiments, the delivery of the two or more agents is simultaneous or concurrent and the agents may be coformulated. In other embodiments, the two or more agents are not co-formulated and are administered in a sequential manner as part of a prescribed regimen e.g., a prime-boost vaccine regimen). In some embodiments, administration of two or more agents or treatments in combination is such that the reduction in a symptom, or other parameter related to the disease is greater than what would be observed with one agent or treatment delivered alone or in the absence of the other. The effect of the two treatments can be partially additive, wholly additive, or greater than additive (e.g., synergistic). Sequential or substantially simultaneous administration of each agent can be effected by any appropriate route including, but not limited to, oral routes, intravenous routes, intramuscular routes, and direct absorption through mucous membrane tissues. The agents can be administered by the same route or by different routes.
[0233] As used herein, the term “isolated” with reference to an agent (e.g., a polypeptide, protein, or nucleic acid molecule) refers to an agent (e.g., the polypeptide, protein, or nucleic acid molecule) that is substantially free of other cellular components with which it is associated in the natural state.
[0234] As used herein, the term “modification” in reference to a nucleic acid sequence refers to a nucleic acid molecule that comprises at least one nucleotide comprising a chemical modification, e.g., a modified sugar moiety, a modified nucleobase, and / or a modified internucleotide linkage, or any combination thereof. Exemplary nucleotide modifications are provided herein, see, e.g., § 5.3 (e.g., § 5.3.2). In certain embodiments of the instant disclosure,inclusion of a deoxynucleotide - which is acknowledged as a naturally occurring form of nucleotide - if present within an RNA molecule (e.g., an mRNA molecule) is considered to constitute a modified nucleotide.|00235| The terms “nucleic acid molecule” and “polynucleotide” are used interchangeably herein and refer to a polymer of DNA or RNA. The nucleic acid molecule can be single-stranded or double-stranded; contain natural, non-natural, or altered nucleotides; and contain a natural, nonnatural, or altered internucleotide linkage, such as a phosphoroamidate linkage or a phosphorothioate linkage, instead of the phosphodiester found between the nucleotides of an unmodified nucleic acid molecule. Nucleic acid molecules include, but are not limited to, all nucleic acid molecules which are obtained by any means available in the art, including, without limitation, recombinant means, e.g., the cloning of nucleic acid molecules from a recombinant library or a cell genome, using ordinary cloning technology and polymerase chain reaction, and the like, and by synthetic means. The skilled artisan will appreciate that, except where otherwise noted, nucleic acid sequences set forth in the instant application will recite thymidine (T) in a representative DNA sequence but where the sequence represents RNA (e.g., mRNA), the thymidines (Ts) would be substituted for uracils (Us). Thus, any of the RNA polynucleotides encoded by a DNA identified by a particular sequence identification number may also comprise the corresponding RNA (e.g., mRNA) sequence encoded by the DNA, where each thymidine (T) of the DNA sequence is substituted with uracil (U).(00236] As used herein, the term “operably connected” and the like refers to the linkage of two moieties in a functional relationship. For example, a polypeptide is operably connected to another polypeptide when they are linked (either directly or indirectly via a peptide linker) in frame such that both polypeptides are functional (e.g., a fusion protein described herein). Or for example, a transcription regulatory polynucleotide e.g., a promoter, enhancer, or other expression control element is operably connected to a polynucleotide that encodes a protein if it affects the transcription of the polynucleotide that encodes the protein. The term “operably connected” can also refer to the conjugation of a moiety to e.g., a polynucleotide or polypeptide (e.g., the conjugation of a PEG polymer to a protein).(00237] As used herein, the term “peptide” refers to a polymer of at least two amino acids linked by peptide bonds. The term “peptide” does not limit the length of the polymer chain of amino acids. It is common in the art to refer to shorter polymers of amino acids (e.g., approximately 2-50 amino acids) as peptides; and to refer to longer polymers of amino acids (e.g., approximately over 50 amino acids) as polypeptides. However, the terms “peptide” and “polypeptide” are used interchangeably herein.1002381 The determination of “percent identity” between two sequences (e.g., peptide or protein (amino acid sequences) or nucleic acid sequences)) can be accomplished using a mathematical algorithm. A specific, non-limiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin S & Altschul SF (1990) PNAS 87: 2264- 2268, modified as in Karlin S & Altschul SF (1993) PNAS 90: 5873-5877, each of which is herein incorporated by reference in its entirety. Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul SF et al., (1990) JMol Biol 215: 403, which is herein incorporated by reference in its entirety. BLAST nucleotide searches can be performed with the NBLAST nucleotide program parameters set, e.g., for score=100, wordlength=12 to obtain nucleotide sequences homologous to a nucleic acid molecule described herein. BLAST protein searches can be performed with the XBLAST program parameters set, e.g., to score 50, wordlength=3 to obtain amino acid sequences homologous to a protein molecule described herein. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul SF et al., (1997) Nuc Acids Res 25: 3389-3402, which is herein incorporated by reference in its entirety. Alternatively, PSI BLAST can be used to perform an iterated search which detects distant relationships between molecules (Id.). When utilizing BLAST, Gapped BLAST, and PSI Blast programs, the default parameters of the respective programs (e.g., of XBLAST and NBLAST) can be used (see, e.g., National Center for Biotechnology Information (NCBI) on the worldwide web, ncbi.nlm.nih.gov). Another specific, non-limiting example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller, 1988, CABIOS 4: 11-17, which is herein incorporated by reference in its entirety. Such an algorithm is incorporated in the ALIGN program (version 2.0) which is part of the GCG sequence alignment software package. When utilizing the ALIGN program for comparing amino acid sequences, a PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used. The percent identity between two sequences can be determined using techniques similar to those described above, with or without allowing gaps. In calculating percent identity, typically only exact matches are counted.
[0239] As used herein the term “pharmaceutical composition” means a composition that is suitable for administration to an animal, e.g., a human subject, and comprises a therapeutic agentand a pharmaceutically acceptable carrier or diluent. A “pharmaceutically acceptable carrier or diluent” means a substance for use in contact with the tissues of human beings and / or non-human animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable therapeutic benefit / risk ratio.
[0240] As used herein, the term “plurality” means 2 or more (e.g., 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 9 or more, or 10 or more).|0024l] As used herein, the term “poly(A) sequence,” refers to a sequence of adenosine nucleotides, typically located at the 3 ’-end of a linear RNA (or in a circular RNA), of up to about 1000 adenosine nucleotides. In some embodiments, the poly(A) sequence is essentially homopolymeric, e.g., a poly(A) sequence of e.g., 100 adenosine nucleotides has essentially the length of 100 nucleotides. In other embodiments, the poly (A) sequence may be interrupted by at least one nucleotide different from an adenosine nucleotide, e.g., a poly(A) sequence of e.g., 100 adenosine nucleotides may have a length of more than 100 nucleotides (comprising 100 adenosine nucleotides and in addition said at least one nucleotide - or a stretch of nucleotides - different from an adenosine nucleotide). It has to be understood that “poly(A) sequence” as defined herein typically relates to RNA - however in the context of the invention, the term likewise relates to corresponding sequences in a DNA molecule (e.g. a “poly(T) sequence”).
[0242] As used herein, the term “prime boost” refers to a vaccine regimen comprising at least an initial vaccine dose and one or more subsequent vaccine doses. The initial vaccine dose comprises the prime vaccine composition and the one or more subsequent vaccine doses are referred to as boost (or booster) vaccine compositions. Prime boost vaccine regimens can comprise more than one booster (e.g., 2, 3, 4, 5, 6, or more, etc.).
[0243] A “prophylactic” treatment is a treatment administered to a subject who does not exhibit signs of a disease or exhibits only early signs for the purpose of decreasing the risk of developing pathology.
[0244] As used herein, the term “protein” refers to a one or more peptides folded into its three- dimensional structure.
[0245] As used herein, the term “receptor binding domain” or “RBD” in reference to the SARS-CoV-2 spike protein refers to the minimal amino acid sequence required for the SARS- CoV-2 spike protein to bind ACE2. The amino acid sequence of an exemplary reference SARS- CoV-2 spike protein RBD is set forth in SEQ ID NO: 3.(00246) The terms “RNA” and “polyribonucleotide” are used interchangeably herein and refer to macromolecules that include multiple ribonucleotides that are polymerized via phosphodiester bonds. Ribonucleotides are nucleotides in which the sugar is ribose. RNA may contain modified nucleotides; and contain natural, non-natural, or altered internucleotide linkages, such as a phosphoroamidate linkage or a phosphorothioate linkage, instead of the phosphodiester found between the nucleotides of an unmodified nucleic acid molecule.|00247j As used herein, the term “SARS-CoV-2 spike protein” refers to the SARS-CoV-2 protein that mediates binding to the host cell receptor angiotensin-converting enzyme 2 (ACE2). An exemplary amino acid sequence of a reference full length SARS-CoV-2 spike protein is set forth in SEQ ID NO: 1. The term SARS-CoV-2 spike protein includes naturally occurring and engineered variants.|00248| As used herein, the term “signal peptide” or “signal sequence” refers to a sequence (e.g., an amino acid sequence) that can direct the transport or localization of a protein to a certain organelle, cell compartment, or extracellular export. The term encompasses both the signal peptide (the amino acid sequence of the signal peptide) and the nucleic acid sequence encoding the signal peptide. Thus, references to a signal peptide in the context of a nucleic acid molecule refers to the nucleic acid sequence encoding the signal peptide.(00249) As used herein, the term “subject” includes any animal, such as a human or other animal. In embodiments, the subject is a vertebrate animal (e.g., mammal, bird, fish, reptile, or amphibian). In embodiments, the subject is a human. In embodiments, the method subject is a nonhuman mammal. In embodiments, the subject is a non-human mammal is such as a non-human primate (e.g., monkeys, apes), ungulate (e.g., cattle, buffalo, sheep, goat, pig, camel, llama, alpaca, deer, horses, donkeys), carnivore (e.g., dog, cat), rodent (e.g., rat, mouse), or lagomorph (e.g., rabbit). In embodiments, the subject is a bird, such as a member of the avian taxa Galliformes (e.g, chickens, turkeys, pheasants, quail), Anseriformes (e.g., ducks, geese), Paleaognathae (e.g, ostriches, emus), Columbiformes (e.g., pigeons, doves), or Psittaciformes (e.g., parrots).(00250) A “therapeutically effective amount” of an agent (e.g., a therapeutic agent, a vaccine) refers to any amount of the agent (e.g., the therapeutic agent, the vaccine) that, when used alone or in combination with another agent (e.g., a therapeutic agent, a vaccine), protects a subject against the onset of a disease (e.g., an infection), ameliorates the severity of a disease (e.g., an infection), and / or promotes disease (e.g., infection) regression evidenced by a decrease in severityof disease (e.g., infection) symptoms, an increase in frequency and duration of disease (e.g., infection) symptom-free periods, or a prevention of impairment or disability due to the disease (e.g., infection) affliction. The ability of an agent (e.g., a therapeutic agent, a vaccine) to do any of the foregoing (or any combination thereof) can be evaluated using a variety of methods known to the skilled practitioner, such as in human subjects during clinical trials, in animal model systems predictive of efficacy in humans, or by assaying the activity of the agent in in vitro assays.|0025l] As used herein, the term “translatable RNA” refers to any RNA that encodes at least one polypeptide or protein and can be translated to produce the encoded polypeptide or protein in vitro, in vivo, in situ or ex vivo. A translatable RNA may be an mRNA or a circular RNA encoding a polypeptide or protein.(00252] As used herein, the terms “treat,” treating,” “treatment,” and the like refer to reducing or ameliorating a disease or infection and / or symptom(s) associated therewith or obtaining a desired pharmacologic and / or physiologic effect. It will be appreciated that, although not precluded, treating a disease or infection does not require that the disease or infection, or symptom(s) associated therewith be completely eliminated. In some embodiments, the effect is therapeutic, i.e., without limitation, the effect partially or completely reduces, diminishes, abrogates, abates, alleviates, decreases the intensity of, or cures a disease and / or adverse symptom attributable to the disease or infection. In some embodiments, the effect is preventative, i.e., the effect protects or prevents an occurrence or reoccurrence of a disease or infection. To this end, the presently disclosed methods comprise administering a therapeutically effective amount of a compositions as described herein.|00253| As used herein, the term “variant” or “variation” with reference to a nucleic acid molecule, refers to a nucleic acid molecule that comprises at least one substitution, alteration, inversion, addition, or deletion of nucleotide compared to a reference nucleic acid molecule. As used herein, the term “variant” or “variation” with reference to a peptide or protein refers to a peptide or protein that comprises at least one substitution, alteration, inversion, addition, or deletion of an amino acid residue compared to a reference peptide or protein.
[0254] As used herein, the term “5 ’-untranslated region” or “5’-UTR” refers to a part of a nucleic acid molecule located 5’ (i.e., “upstream”) of a coding sequence and which is not translated into protein. Typically, a 5’-UTR starts with the transcriptional start site and ends before the start codon of the coding sequence. A 5’-UTR may comprise elements for controlling gene expression,also called regulatory elements. Such regulatory elements may be, e.g., ribosomal binding sites, miRNA binding sites etc. The 5’-UTR may be post-transcriptionally modified, e.g., by enzymatic or post-transcriptional addition of a 5’-cap structure.|00255| As used herein the term “3 ’-untranslated region” or “3’-UTR” refers to a part of a nucleic acid molecule located 3’ (i.e., downstream) of a coding sequence and which is not translated into protein. A 3’-UTR may located between a coding sequence and an (optional) terminal poly(A) sequence of a nucleic acid sequence. A 3'-UTR may comprise elements for controlling gene expression, also called regulatory elements. Such regulatory elements may be, e.g., ribosomal binding sites, miRNA binding sites etc.5.2 SARS-CoV-2 Spike Proteins (e.g., Immunogens)(00256) The SARS-CoV-2 spike protein mediates viral entry into host cells. The spike protein comprises two functional subunits responsible for binding to the host cell receptor (SI subunit) and fusion of the viral and cellular membranes (S2 subunit). The SARS-CoV-2 spike protein is cleaved at the boundary between the SI and S2 subunits, which remain non-covalently associated in the prefusion conformation. The distal SI subunit comprises the RED and contributes to stabilization of the prefusion state of the membrane anchored S2 subunit that contains the fusion machinery. The RBD mediates binding to the host cell receptor ACE2. The spike protein is cleaved by host proteases at the so-called S2’ site located immediately upstream of the fusion peptide. This cleavage has been proposed to activate the protein for membrane fusion via extensive irreversible conformational changes. (See, e.g., Walls, Alexandra C et al. “Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein.” Cell vol. 181,2 (2020): 281-292. e6. doi : 10.1016 / j . cell.2020.02.058, the entire contents of which is incorporated herein by reference for all purposes).(00257) The amino acid sequence of several reference SARS-CoV-2 spike proteins is provided in Table 1 and detailed below.100258] The amino acid sequence of a first reference immature full length SARS-CoV-2 spike protein is provided in SEQ ID NO: 1. The signal peptide is underlined (amino acids 1-13 of SEQ ID NO: 1); the amino acid sequence of the corresponding mature first reference SARS-CoV-2 spike protein lacking the native signal peptide is provided in SEQ ID NO: 2. The amino acidsequence of the RBD of the first reference SARS-CoV-2 spike protein is set forth in SEQ ID NO: 3.
[0259] The amino acid sequence of a second reference immature full length SARS-CoV-2 spike protein is provided in SEQ ID NO: 4. The signal peptide is underlined (amino acids 1-13 of SEQ ID NO: 4); the amino acid sequence of the corresponding mature second reference SARS- CoV-2 spike protein lacking the native signal peptide is provided in SEQ ID NO: 5. The amino acid sequence of the second reference SARS-CoV-2 spike protein comprises a proline at amino acid positions 986 and 987, amino acid numbering relative to SEQ ID NO: 1 (the Wuhan-Hu- 1 Spike Numbering System described herein). This diproline amino acid substitution stabilizes said SARS-CoV-2 spike protein in a prefusion state. The amino acid sequence of the RBD of the second reference SARS-CoV-2 spike protein is set forth in SEQ ID NO: 6.
[0260] The amino acid sequence of a third reference immature full length SARS-CoV-2 spike protein is provided in SEQ ID NO: 43. The signal peptide is underlined (amino acids 1-13 of SEQ ID NO: 43); the amino acid sequence of the corresponding mature first reference SARS-CoV-2 spike protein lacking the native signal peptide is provided in SEQ ID NO: 44. The amino acid sequence of the RBD of the first reference SARS-CoV-2 spike protein is set forth in SEQ ID NO: 6.Table 1. Reference SARS-CoV-2 Spike Proteins and RBDs Thereof.[002611 It is standard in the art to number the amino acid positions within a given SARS-CoV- 2 spike protein according to the corresponding amino acid position in the Wuhan-Hu- 1 Spike reference sequence (SEQ ID NO: 1). As such, unless otherwise indicated, the designation of amino acid positions in the amino acid sequence of a SARS-Cov-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) herein is relative to the amino acid sequence of SEQ ID NO: 1.[00262) A person of ordinary skill in the art can determine the corresponding amino acid for a given amino acid position by (i) aligning the amino acid sequence of the Wuhan-Hu-1 Spike reference sequence (SEQ ID NO: 1) to the amino acid sequence of the query spike protein, (ii) locating the relevant amino acid position in the Wuhan-Hu- 1 Spike reference sequence, and (iii) determining the amino acid located at the corresponding amino acid position in the query spike protein. As query spike proteins may have for example, insertions or deletions of amino acids relative to the Wuhan-Hu- 1 Spike reference sequence, the amino acid corresponding to a particular position in the Wuhan-Hu- 1 Spike reference sequence may not have the same amino acid number if one were to simply count the number of amino acids within the query spike protein.(00263) For example, FIGS. 1A-1C shows an alignment of the Wuhan-Hu-1 Spike reference sequence (SEQ ID NO: 1) to the amino acid sequence of a query spike protein (SEQ ID NO: 4). The query spike protein comprises, inter alia, a deletion of at least three amino acids relative to the Wuhan-Hu- 1 Spike reference sequence (amino acids L24, P25, P26). However, the alignment keeps the corresponding amino acids in the query spike protein (SEQ ID NO: 4) correctly aligned to the Wuhan-Hu-1 Spike reference sequence. For example, if one wanted to locate amino acid position termed 440 in a query spike protein (e.g., SEQ ID NO: 4), one would generate the alignment in FIGS. 1A-1C, locate amino acid position 440 in the Wuhan-Hu- 1 Spike reference sequence (SEQ ID NO: 1) and subsequently locate the corresponding amino acid in the query spike protein (SEQ ID NO: 4), in this example position 440 (according to Wuhan-Hu-1 Spike reference sequence (SEQ ID NO: 1) numbering) in the query spike protein (SEQ ID NO: 4) is lysine (K). Amino acid residue 440 (according to Wuhan-Hu- 1 Spike reference sequence (SEQ ID NO: 1) numbering) in the Wuhan-Hu-1 Spike reference sequence (SEQ ID NO: 1) is asparagine (N). This numbering system is indicated throughout the present disclosure by noting, “amino acid numbering relative to SEQ ID NO: 1” or the like.
[0264] Although amino acid positions of the SARS-CoV-2 spike protein are defined herein relative to the full-length immature SARS-Cov-2 spike protein that contains the native signal sequence; it should be understood that this does not require the SARS-Cov-2 spike proteins (e.g., the SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) described herein to include a native signal sequence.
[0265] As outlined above, provided herein are, inter alia, SARS-CoV-2 spike proteins and polypeptides (e.g., SARS-CoV-2 spike protein and polypeptide immunogens (and immunogenic fragments and / or immunogenic variants thereof)) and nucleic acids encoding the same, that comprise at least one amino acid substitution (e.g., one set of amino acid substitutions described herein, see, e.g., Table 2 and Table 4). Further provided herein are SARS-CoV-2 spike proteins and polypeptides (e.g., SARS-CoV-2 spike protein and polypeptide immunogens (and immunogenic fragments and / or immunogenic variants thereof)) and nucleic acids encoding the same, that comprise any combination of amino acid substitutions described herein (see, e.g., Table 2 and Table 4), e.g., at least one set of amino acid substitutions described in Table 2 and at least one set of amino acid substitutions described in Table 4; at least two sets of amino acidsubstitutions described in Table 2; at least two sets of amino acid substitutions described in Table 4, etc.
[0266] While, exemplary amino acid substitutions are provided herein, for example in Table 2 and Table 4, that specify the parental amino acid and the substituted amino acid; it should be understood that the disclosure covers the substitution of any parental amino acid with the substituted amino acid. As such, the substitutions set forth herein (e.g., in Table 2 and Table 4) include the substitution of any parental amino acid with the substituted amino acid. For example, amino acid substitution Set A set forth in Table 2 incudes the substitution of any amino acid with glutamic acid (E) at amino acid position 440 (amino acid numbering is relative to SEQ ID NO: 1).
[0267] While exemplary amino acid substitutions are provided herein, for example in Table 2 and Table 4, that specify the parental amino acid and the substituted amino acid; it is to be understood that the disclosure includes the substitution of any parental amino acid with the substituted amino acid or a physiochemically similar amino acid to the substituted amino acid set forth in Table 2 and Table 4. A person of ordinary skill in the art can determine which amino acids would be considered physiochemically similar to any given substituted amino acid set forth in Table 2 and Table 4 utilizing standard methods (e.g., based on the physiochemical properties (e.g., charge, polarity, etc.) of each amino acid).
[0268] Sets of amino acid substitutions included in one or more of the SARS-CoV-2 spike protein immunogens described herein are provided in the are provided in Table 2. The amino acid numbering set forth in Table 2 is relative to SEQ ID NO: 1 (the Wuhan-Hu-1 Spike Numbering System described herein).Table 2. Sets of Amino Acid Substitutions of SARS-CoV-2 Immunogens.(00269) In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25) of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1). In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1).(00270) In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455 S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1 ) and comprises or consists of one or more amino acid variations that are not set forth in Table 2. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1) and comprises or consists of 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid variations that are not set forth in Table 2. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455 S, 5O5D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1) and comprises or consists of 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid variations that are not set forth in Table 2. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1) and comprises or consists of from 1-10, 1-9, 1-8, 1-7, 1-6, 1-5, 1-4, 1-3, or 1-2 amino acid variations that are not set forth in Table 2. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455 S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1) and comprises or consists of at least one but no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid variations that are not set forth in Table 2.
[0271] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25) of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1) and comprises or consists of any one or more (e.g., 1, 2, or 3) of the following amino acid substitutions of 383N, 396T, 468N (amino acid numbering according to SEQ ID NO: 1). In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises orconsists of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1) comprises or consists of any one or more (e.g., 1, 2, or 3) of the following amino acid substitutions of 383N, 396T, 468N (amino acid numbering according to SEQ ID NO: 1).|00272] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2 and comprises or consists of any one or more of the following amino acid substitutions of 383N, 396T, 468N (amino acid numbering according to SEQ ID NO: 1). In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2 and comprises or consists of any one or more of the following amino acid substitutions of 383N, 396T, 468N (amino acid numbering according to SEQ ID NO: 1).
[0273] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of substitution set A (440E / 456L / 478JL484V / 505Y), substitution set B (405Kz440N / 456V / 478Q / 490P), substitution set C (403S / 444E / 455W), substitution set D (346K 439K / 455S / 505D), substitution set E (403K / 444T / 453F 478R), and / or substitution set F (405D / 417Y / 440R / 478I / 490F) as set forth in Table 2. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of substitution set A (440E / 456L / 478R / 484V / 505Y), substitution set B (405K 440N / 456V / 478Q / 490P), substitution set C (403S / 444E / 455W), substitution set D (346K / 439KZ455S / 505D), substitution set E (403K / 444T / 453F / 478R), or substitution set F (405D / / 417Y / 440 478L / 490F) as set forth in Table 2.(00274) In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2.(00275) In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1 of the sets of amino acid substitutions set forth in Table 2 (i.e., set A, B, C, D, E, or F). In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1 of the sets of amino acid substitutions set forth in Table 2 (i.e., set A, B, C, D, E, or F).(00276] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of one or more amino acid variations that are not set forth in Table 2. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid variations that are not set forth in Table 2. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid variations that are not set forth in Table 2. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of from 1-10, 1-9, 1-8, 1-7, 1-6, 1-5, 1-4, 1-3, or 1-2 amino acid variations that are not set forth in Table 2. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of at least one but no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid variations that are not set forth in Table 2. In some embodiments, the amino acid variants not listed in Table 2 are found in one or more circulating variants of SARS-CoV-2.
[0277] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of one or more variations that are not set forth in Table 2, relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 2 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44.|00278| In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 1-6 or 43-44.
[0279] In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 2, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44.
[0280] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenicfragment and / or immunogenic variant thereof)) comprises or consists of one or more variations that are not set forth in Table 2, relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-3. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 2 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-3.
[0281] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 1-3.
[0282] In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 2, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 1-3.
[0283] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of one or more variations that are not set forth in Table 2, relative to the amino acid sequence set forth in any one of SEQ ID NOS: 4-6. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.)that are not listed in Table 2 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 4-6.
[0284] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 4-6.
[0285] In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 2, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 4-6.
[0286] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of one or more variations that are not set forth in Table 2, relative to the amino acid sequence set forth in SEQ ID NO: 1 or 3. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 2 relative to the amino acid sequence set forth in SEQ ID NO: 1 or 3.
[0287] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in SEQ ID NO: 1 or 3.(00288) In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 2, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in SEQ ID NO: 1 or 3.|00289) In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of one or more variations that are not set forth in Table 2, relative to the amino acid sequence set forth in SEQ ID NO: 2 or4. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1 or more (e.g., 1, 2, 3, 4,5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 2 relative to the amino acid sequence set forth in SEQ ID NO: 2 or 4.|00290| In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in SEQ ID NO: 2 or 4.[00291 ) In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 2, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g, the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in SEQ ID NO: 2 or 4.[00292) In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of one or more variationsthat are not set forth in Table 2, relative to the amino acid sequence set forth in SEQ ID NO: 3 or 6. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 2 relative to the amino acid sequence set forth in SEQ ID NO: 3 or 6.|0029 1 In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in SEQ ID NO: 3 or 6.(00294) In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 2, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in SEQ ID NO: 3 or 6.(00295) In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25) of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455 S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1). In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S,444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1).
[0296] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1) and comprises one or more amino acid variations that are not set forth in Table 2. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1) and comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid variations that are not set forth in Table 2. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, or 25 of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455 S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1) and comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid variations that are not set forth in Table 2. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1) and comprises from 1-10, 1-9, 1-8, 1-7, 1-6, 1-5, 1-4, 1-3, or 1-2 amino acid variations that are not set forth in Table 2. In some embodiments,the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV- 2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1) and comprises at least one but no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid variations that are not set forth in Table 2.[002971 In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25) of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455 S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1) and comprises any one or more (e.g., 1, 2, or 3) of the following amino acid substitutions of 383N, 396T, 468N (amino acid numbering according to SEQ ID NO: 1). In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1) comprises any one or more (e.g., 1, 2, or 3) of the following amino acid substitutions of 383N, 396T, 468N (amino acid numbering according to SEQ ID NO: 1).
[0298] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2 and comprises any one or more of the following amino acid substitutions of 383N, 396T, 468N (amino acid numbering according to SEQ ID NO: 1). In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenicfragment and / or immunogenic variant thereof)) comprises 1 , 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2 and comprises any one or more of the following amino acid substitutions of 383N, 396T, 468N (amino acid numbering according to SEQ ID NO: 1).|00299| In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises substitution set A (440E / 456L / 478R484V / 505Y), substitution set B (405K / 440N / 456V / 478Q / 490P), substitution set C (403S / 444E / 455W), substitution set D (346K 439K / 455S / 505D), substitution set E (403K / 444T / 453F / 478R), and / or substitution set F (405D 417Y / 440R / 478I / 490F) as set forth in Table 2. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises substitution set A (440E 456L 478R 484V 5O5Y), substitution set B (405K / 440N / 456V / 478Q / 490P), substitution set C (403S / 444E / 455W), substitution set D (346K / 439K / 455S / 505D), substitution set E (403K / 444T / 453F / 478R), or substitution set F (405D / 417Y / 440RA78I 90F) as set forth in Table 2.|00300| In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2.
[0301] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 of the sets of amino acid substitutions set forth in Table 2 (i.e., set A, B, C, D, E, or F). In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 of the sets of amino acid substitutions set forth in Table 2 (i.e., set A, B, C, D, E, or F).(00302) In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises one or more amino acid variations that are not set forth in Table 2. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid variations that are not set forth in Table 2. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid variations that are not set forth in Table 2. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises from 1-10, 1-9, 1-8, 1-7, 1-6, 1-5, 1-4, 1-3, or 1-2 amino acid variations that are not set forth in Table 2. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least one but no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid variations that are not set forth in Table 2. In some embodiments, the amino acid variants not listed in Table 2 are found in one or more circulating variants of SARS-CoV-2.(00303) In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises one or more variations that are not set forth in Table 2, relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 2 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44. (00304) In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenicfragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 1-6 or 43-44.
[0305] In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 2, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44.
[0306] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises one or more variations that are not set forth in Table 2, relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-3. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 2 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-3.
[0307] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 1-3.
[0308] In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 2, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 1-3.100309] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises one or more variations that are not set forth in Table 2, relative to the amino acid sequence set forth in any one of SEQ ID NOS: 4-6. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 2 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 4-6.|00310| In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g, the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 4-6.
[0311] In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 2, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 4-6.
[0312] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g, the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises one or more variations that are not set forth in Table 2, relative to the amino acid sequence set forth in SEQ ID NO: 1 or 3. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more)but less than 20% (e.g, less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 2 relative to the amino acid sequence set forth in SEQ ID NO: 1 or 3.|003131 In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in SEQ ID NO: 1 or 3.
[0314] In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 2, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in SEQ ID NO: 1 or 3.
[0315] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises one or more variations that are not set forth in Table 2, relative to the amino acid sequence set forth in SEQ ID NO: 2 or 4. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 2 relative to the amino acid sequence set forth in SEQ ID NO: 2 or 4.
[0316] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in SEQ ID NO: 2 or 4.
[0317] In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 2, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in SEQ ID NO: 2 or 4.
[0318] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises one or more variations that are not set forth in Table 2, relative to the amino acid sequence set forth in SEQ ID NO: 3 or 6. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 2 relative to the amino acid sequence set forth in SEQ ID NO: 3 or 6.|003l9| In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in SEQ ID NO: 3 or 6.[00320J In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 2, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g, the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in SEQ ID NO: 3 or 6.
[0321] The amino acid sequence of exemplary SARS-CoV-2 spike proteins (e.g., immunogens) comprising at least one of the sets of amino acid substitutions set forth above in Table 2 is provided in Table 3. Table 3 provides the amino acid sequence of the RBD (SEQ IDNOS: 7-12) and the full-length spike protein (immature SEQ ID NOS: 19-24 and mature SEQ ID NOS: 13-18) of six exemplary SARS-CoV-2 immunogens (A-F) that comprise the corresponding set of amino acid substitutions set forth above in Table 2 (i.e., set A, B, C, D, E, or F).Table 3. Amino Acid Sequence of Exemplary SARS-CoV-2 Proteins (e.g.. VaccineImmunogens).
[0322] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g, the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids of any SARS-CoV-2 protein set forth in Table 3.
[0323] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenicfragment and / or immunogenic variant thereof)) comprises or consists of at least 1 , 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2, and the other than the at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of any SARS-Cov-2 protein set forth in Table 3.
[0324] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of one or more (e.g., 1, 2, 3, 4, 5, or more) of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1), and the other than the one or more (e.g., 1, 2, 3, 4, 5, or more) of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455 S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1), the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of any SARS-Cov-2 protein set forth in Table 3.
[0325] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of substitution set A (440E / 456L / 478R484V / 505Y), substitution set B (405K / 440N / 456V / 478Q / 490P), substitution set C (403S / 444E / 455W), substitution set D (346K 439K / 455S / 505D), substitution set E (403K / 444T / 453F / 478R), and / or substitution set F (405D 417Y / 440B / 478E490F) as set forth in Table 2; and other than said substitution set (i.e., A, B, C, D, E, and / or F) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,99%, or 100% identical to the amino acid sequence of any SARS-Cov-2 protein set forth in Table 3.|00326| In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of substitution set A (440E / 456L / 478R / 484V / 505Y), substitution set B (405K / 440N / 456V 478Q / 490P), substitution set C (403S / 444E / 455W), substitution set D (346K / 439K / 455S 505D), substitution set E (403K / 444T / 453F / 478R), or substitution setF (405D / 417Y / 440R / 478E490F) as set forth in Table 2; and other than said substitution set (i.e., A, B, C, D, E, or F) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of any SARS-Cov-2 protein set forth in Table 3.|00327| In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 7-24. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2, and the other than the at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 7- 24.[00328) In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to acontiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 7-12. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2, and the other than the at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 7- 12.|00329| In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 13-24. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2, and the other than the at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 13- 24.(00330) In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%,87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 13-18. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2, and the other than the at least 1, 2, 3, 4, 5, or 6 e.g., 1) of the sets of amino acid substitutions set forth in Table 2, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 13- 18.[00331 J In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 19-24. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2, and the other than the at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 19- 24.
[0332] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenicfragment and / or immunogenic variant thereof)) comprises at least 1 , 2, 3, 4, 5, or 6 (e.g, 1) of the sets of amino acid substitutions set forth in Table 2, and the other than the at least 1, 2, 3, 4, 5, or 6 (e.g, 1) of the sets of amino acid substitutions set forth in Table 2, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of any SARS-Cov-2 protein set forth in Table 3.
[0333] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises one or more (e.g., 1, 2, 3, 4, 5, or more) of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 5O5D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1), and the other than the one or more (e.g., 1, 2, 3, 4, 5, or more) of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1), the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of any SARS-Cov-2 protein set forth in Table 3.
[0334] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises substitution set A (440E / 456L / 478R484V / 505Y), substitution set B (405K / 440N / 456V / 478Q / 490P), substitution set C (403S / 444E / 455W), substitution set D (346K 439K / 455S / 505D), substitution set E (403K / 444T / 453F / 478R), and / or substitution set F (405D 417Y / 440B / 478E490F) as set forth in Table 2; and other than said substitution set (i.e., A, B, C, D, E, and / or F) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,99%, or 100% identical to the amino acid sequence of any SARS-Cov-2 protein set forth in Table 3.)00335| In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises substitution set A (440E / 456L / 478R / 484V / 505Y), substitution set B (405K / 440N / 456V 478Q / 490P), substitution set C (403S / 444E / 455W), substitution set D (346K / 439K / 455S 505D), substitution set E (403K / 444T / 453F / 478R), or substitution setF (405D / 417Y / 440R / 478E490F) as set forth in Table 2; and other than said substitution set (i.e., A, B, C, D, E, or F) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of any SARS-Cov-2 protein set forth in Table 3.|00336| In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 7-24. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2, and the other than the at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2, the amino acid sequence of the SARS- CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 7- 24.[00337) In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to acontiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 7-12. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2, and the other than the at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2, the amino acid sequence of the SARS- CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 7- 12.|00338| In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 13-24. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2, and the other than the at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2, the amino acid sequence of the SARS- CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 13- 24.(00339) In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%,87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 13-18. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2, and the other than the at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2, the amino acid sequence of the SARS- CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 13- 18.
[0340] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 19-24. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2, and the other than the at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 2, the amino acid sequence of the SARS- CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 19- 24.
[0341] Sets of amino acid substitutions included in one or more of the SARS-CoV-2 spike protein immunogens described herein are provided in the are provided in Table 4. The amino acidnumbering set forth in Table 4 is relative to SEQ ID NO: 1 (the Wuhan-Hu-1 Spike Numbering System described herein).Table 4. Amino Acid Substitutions in SARS-CoV-2 Immunogens.
[0342] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28) of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, 490F, 383N, 396T, or 468N (amino acid numbering according to SEQ ID NO: 1). In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28 of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455S, 5O5D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, 490F, 383N, 396T, or 468N (amino acid numbering according to SEQ ID NO: 1).
[0343] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28 of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455S, 5O5D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, 490F, 383N, 396T, or 468N (amino acid numbering according to SEQ ID NO: 1) and comprises or consists of one or more amino acid variations that are not set forth in Table 4. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28 of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, 490F, 383N, 396T, or 468N (amino acid numbering according to SEQ ID NO: 1) and comprises or consists of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28 amino acid variations that are not set forth in Table 4. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28 of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455S, 5O5D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, 490F, 383N, 396T, or 468N (amino acid numbering according to SEQ ID NO: 1) and comprises or consists of 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid variations that are not set forth in Table 4. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV- 2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28 of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, 490F, 383N, 396T, or 468N (amino acid numbering according to SEQ ID NO: 1) and comprises or consists of from 1-10, 1-9, 1-8, 1-7, 1-6, 1-5, 1-4, 1-3, or 1-2 amino acid variations that are not set forth in Table 4. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variantthereof)) comprises or consists of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28 of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 505D,403K, 444T, 453F, 405D, 417Y, 440R, 4781, 490F, 383N, 396T, or 468N (amino acid numbering according to SEQ ID NO: 1) and comprises or consists of at least one but no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid variations that are not set forth in Table 4.|00344] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of substitution set G (440E / 456L / 478R / 484V / 505Y / 383N / 396T / 468N), substitution set H (405K / 440N / 456V / 478Q / 490PZ383N / 396T / 468N), substitution set I (403 S / 444E / 455W / 383N / 396T 468N), substitution set J (346IG439K7455 S / 505D / 383N / 396TZ468N), substitution set(403K / 444T / 453F / 478R / 383N / 396T / 468N), and / or substitution set L(405D / 417Y 440R / 478V490F / 383N / 396T / 468N) as set forth in Table 4. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV- 2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of substitution set(440E / 456L / 478R / 484V / 505Y / 383N / 396T / 468N), substitution set(405K / 440N / 456V / 478Q / 490P 383N / 396T / 468N), substitution set(403 S 444E 455 W 383N / 396T / 468N), substitution set J (346K / 439K / 455 S 505D / 383N / 396T / 468N), substitution set K (403K / 444T / 453F 478R / 383N / 396T / 468N), or substitution set L(405D / 417Y / 440R / 478I / 490E / 383N / 396T / 468N) as set forth in Table 4.
[0345] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 4. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variantthereof)) comprises or consists of 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 4.|00346| In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of one or more amino acid variations that are not set forth in Table 4. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid variations that are not set forth in Table 4. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid variations that are not set forth in Table 4. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of from 1-10, 1-9, 1-8, 1-7, 1-6, 1-5, 1-4, 1-3, or 1-2 amino acid variations that are not set forth in Table 4. In some embodiments, the amino acid sequence of the SARS- CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of at least one but no more than 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid variations that are not set forth in Table 4. . In some embodiments, the amino acid variants not listed in Table 4 are found in one or more circulating variants of SARS-CoV-2.
[0347] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of one or more variations that are not set forth in Table 4, relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g, less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions,deletions, etc.) that are not listed in Table 4 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44.|00348| In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 1-6 or 43-44.
[0349] In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 4, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44.
[0350] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of one or more variations that are not set forth in Table 4, relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-3. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 4 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-3.
[0351] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to acontiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 1-3.|003521 In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 4, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 1-3.
[0353] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of one or more variations that are not set forth in Table 4, relative to the amino acid sequence set forth in any one of SEQ ID NOS: 4-6. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 4 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 4-6.
[0354] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 4-6.
[0355] In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 4, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 4-6.(00356) In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of one or more variations that are not set forth in Table 4, relative to the amino acid sequence set forth in SEQ ID NO: 1 or3. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 4 relative to the amino acid sequence set forth in SEQ ID NO: 1 or 3.
[0357] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in SEQ ID NO: 1 or 3.|00358| In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 4, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in SEQ ID NO: 1 or 3.
[0359] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of one or more variations that are not set forth in Table 4, relative to the amino acid sequence set forth in SEQ ID NO: 2 or4. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1 or more (e.g., 1, 2, 3, 4,5. 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%,less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 4 relative to the amino acid sequence set forth in SEQ ID NO: 2 or 4.
[0360] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in SEQ ID NO: 2 or 4.
[0361] In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 4, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in SEQ ID NO: 2 or 4.
[0362] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of one or more variations that are not set forth in Table 4, relative to the amino acid sequence set forth in SEQ ID NO: 3 or 6. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 4 relative to the amino acid sequence set forth in SEQ ID NO: 3 or 6.
[0363] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in SEQ ID NO: 3 or 6.(00364) In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 4, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in SEQ ID NO: 3 or 6.|00365] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28) of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, 490F, 383N, 396T, or 468N (amino acid numbering according to SEQ ID NO: 1). In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28 of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, 490F, 383N, 396T, or 468N (amino acid numbering according to SEQ ID NO: 1)
[0366] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28 of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455S, 5O5D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, 490F, 383N, 396T, or 468N (amino acid numbering according to SEQ ID NO: 1) and comprises or consists of one or more amino acid variations that are not set forth in Table 4. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, 26, 27, or 28 of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, 490F, 383N, 396T, or 468N (amino acid numbering according to SEQ ID NO: 1) and comprises or consists of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28 amino acid variations that are not set forth in Table 4. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28 of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455S, 5O5D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, 490F, 383N, 396T, or 468N (amino acid numbering according to SEQ ID NO: 1) and comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid variations that are not set forth in Table 4. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28 of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, 490F, 383N, 396T, or 468N (amino acid numbering according to SEQ ID NO: 1) and comprises from 1-10, 1-9, 1 -8, 1-7, 1-6, 1 -5, 1-4, 1-3, or 1-2 amino acid variations that are not set forth in Table 4. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28 of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 5O5D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, 490F, 383N, 396T, or 468N (amino acid numbering according to SEQ ID NO: 1) and comprises at least one but no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid variations that are not set forth in Table 4.
[0367] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenicI l lfragment and / or immunogenic variant thereof)) comprises substitution set G(440E / 456L / 478JC484V / 505Y / 383N / 396T / 468N), substitution set H(405K / 440N / 456V / 478Q / 490P / 383N / 396T / 468N), substitution set I(403S / 444E / 455W / 383N / 396T 468N), substitution set J(346K / 439K / 455S / 505D / 383N / 396T 468N), substitution set K(403KZ444T / 453F / 478R / 383N / 396T / 468N), and / or substitution set L(405D / 417Y 440R / 478E490F / 383N / 396T / 468N) as set forth in Table 4. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV- 2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of substitution set G (440E / 456L / 478R / 484V / 505Y / 383N / 396T / 468N), substitution set H(405K / 440N 456V / 478Q / 490P 383N / 396T / 468N), substitution set I(403S / 444E / 455W / 383N / 396T / 468N), substitution set J(346K / 439K / 455S 505D / 383N / 396T / 468N), substitution set K(403K / 444T / 453F / 478R / 383N / 396T / 468N), or substitution set L (405D / 417Y / 440R 478I 490F / 383N / 396T / 468N) as set forth in Table 4.|00368| In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 4. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 4.[00369) In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises one or more amino acid variations that are not set forth in Table 4. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid variations that are not set forth in Table 4. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spikeprotein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid variations that are not set forth in Table 4. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises from 1-10, 1-9, 1-8, 1-7, 1-6, 1-5, 1-4, 1-3, or 1-2 amino acid variations that are not set forth in Table 4. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least one but no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid variations that are not set forth in Table 4. . In some embodiments, the amino acid variants not listed in Table 4 are found in one or more circulating variants of SARS-CoV-2.
[0370] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises one or more variations that are not set forth in Table 4, relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 4 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44. |00371 | In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g, the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 1-6 or 43-44.
[0372] In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 4, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g, the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / orimmunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44.[003731 In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises one or more variations that are not set forth in Table 4, relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-3. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 4 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-3.
[0374] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 1-3.
[0375] In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 4, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 1-3.
[0376] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises one or more variations that are not set forth in Table 4, relative to the amino acid sequence set forth in any one of SEQ ID NOS: 4-6. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / orimmunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 4 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 4-6.
[0377] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 4-6.
[0378] In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 4, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 4-6.|00379| In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises one or more variations that are not set forth in Table 4, relative to the amino acid sequence set forth in SEQ ID NO: 1 or 3. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 4 relative to the amino acid sequence set forth in SEQ ID NO: 1 or 3.
[0380] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to acontiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in SEQ ID NO: 1 or 3.|003811 In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 4, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in SEQ ID NO: 1 or 3.
[0382] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises one or more variations that are not set forth in Table 4, relative to the amino acid sequence set forth in SEQ ID NO: 2 or 4. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 4 relative to the amino acid sequence set forth in SEQ ID NO: 2 or 4.
[0383] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in SEQ ID NO: 2 or 4.
[0384] In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 4, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in SEQ ID NO: 2 or 4.(00385) In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises one or more variations that are not set forth in Table 4, relative to the amino acid sequence set forth in SEQ ID NO: 3 or 6. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g, the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 4 relative to the amino acid sequence set forth in SEQ ID NO: 3 or 6.
[0386] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in SEQ ID NO: 3 or 6.|00387| In some embodiments, other than the at least one set of amino acid substitutions set forth in Table 4, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in SEQ ID NO: 3 or 6.(00388) The amino acid sequence of exemplary SARS-CoV-2 spike proteins (e.g., immunogens) comprising at least one of the sets of amino acid substitutions set forth above in Table 4 is provided in Table 5. Table 5 provides the amino acid sequence of the receptor binding domain (SEQ ID NOS: 25-30) and the full-length spike protein (immature SEQ ID NOS: 37-42 and mature SEQ ID NOS: 31-36) of six exemplary SARS-CoV-2 immunogens (G-L) that comprise the corresponding set of amino acid substitutions set forth above in Table 4 (i.e., set G, H, I, J, K, or L).Table 5. Amino Acid Sequence of SARS-CoV-2 Vaccine Proteins (e.g.. Immunogens).[00389J In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500,600, 700, 800, 900, 1000, 1100, or 1200 amino acids of any SARS-CoV-2 protein set forth in Table 3.|00390| In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of at least 1, 2, 3, 4, 5, or 6 e.g., 1) of the sets of amino acid substitutions set forth in Table 4, and the other than the at least 1, 2, 3, 4, 5, or 6 e.g., 1) of the sets of amino acid substitutions set forth in Table 4, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of any SARS-Cov-2 protein set forth in Table 3.|003911 In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, or more) of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, 490F, 383N, 396T, or 468N (amino acid numbering according to SEQ ID NO: 1), and the other than the one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, or more) of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 5O5D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, 490F, 383N, 396T, or 468N (amino acid numbering according to SEQ ID NO: 1), the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS- CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of any SARS-Cov-2 protein set forth in Table 5.[00392) In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of substitution set G (440E / 456L / 478R 484V / 505Y / 383N / 396T / 468N), substitution set H(405K / 440N / 456V / 478Q / 490P 383N / 396T / 468N), substitution set I(403S / 444E / 455W / 383N / 396T / 468N), substitution set J(346K / 439K / 455 S 505D / 383N / 396T / 468N), substitution set K(403K / 444T / 453F 478R / 383N / 396T / 468N), and / or substitution set L(405D / 417Y / 440R 478I 490F / 383N / 396T / 468N) as set forth in Table 4; and other than said substitution set (i.e., G, H, I, J, K, and / or L) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%,87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of any SARS-Cov-2 protein set forth in Table 5.
[0393] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein r polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) )mprises or consists of substitution set G (440E / 456L / 478R 484V / 505Y / 383N / 396T / 468N), substitution set H (405K 440N 456V 478Q 490P 383N 396T 468N), substitution set I (403S / 444E / 455W / 383N / 396T / 468N), substitution set J (346K / 439K455S / 505D / 383N / 396T / 468N), substitution set K (403K / 444T / 453F / 478R 83N / 396T / 468N), or substitution set Las set forth in Table 4; and other than said substitution set (i.e., G, H, I, I, K, or L) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of any SARS-Cov-2 protein set forth in Table 5.
[0394] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 25-42. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 4, and the other than the at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 4, the amino acid sequence ofthe SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 25- 42.
[0395] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 25-30. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 4, and the other than the at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 4, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 25- 30.|00396| In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 31-42. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 4, and the other than the at least 1, 2, 3, 4, 5, or6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 4, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 31- 42.|00397] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 31-36. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 4, and the other than the at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 4, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 31- 36.
[0398] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 37-42. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of thesets of amino acid substitutions set forth in Table 4, and the other than the at least 1 , 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 4, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 37- 42.
[0399] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 4, and the other than the at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 4, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of any SARS-Cov-2 protein set forth in Table 3.
[0400] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, or more) of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 5O5D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, 490F, 383N, 396T, or 468N (amino acid numbering according to SEQ ID NO: 1), and the other than the one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, or more) of any of the following amino acid substitutions 440E, 456L, 478R, 484V, 5O5Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, 490F, 383N, 396T, or 468N (amino acid numbering according to SEQ ID NO: 1), the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%,96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of any SARS-Cov-2 protein set forth in Table 5.|004011 In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises substitution set(440E / 456L / 478R / 484V / 505Y / 383N / 396T / 468N), substitution set(405KA40N / 456VA78Q / 490P / 383NZ396T / 468N), substitution set I (403S 444E / 455W / 383N / 396T / 468N), substitution set (346R / 439K / 455S 05D / 383N 396T / 468N), substitution set K (403KA44T / 453F / 478R / 383N / 396T / 468N), and / or substitution set L(405D / 417Y / 440R / 478I 490F / 383N / 396T 468N) as set forth in Table 4; and other than said substitution set (i.e., G, H, I, J, K, and / or L) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of any SARS-Cov-2 protein set forth in Table 5.
[0402] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises substitution set(440E / 456L / 478R484V / 505 383N / 396T / 468N), substitution set(405K / 440N / 456V / 478Q / 490PZ383N / 396T / 468N), substitution set I (403S / 444E / 455W / 383N / 396T 468N), substitution set (346K / 439K / 455 S / 505 D 383N / 396T 468 N ), substitution set(403K / 444T / 453FZ478R / 383N / 396T / 468N), or substitution set L(405D / 417Y 440R / 478I / 490F / 383N / 396T / 468N) as set forth in Table 4; and other than said substitution set (i.e., G, H, I, J, K, or L) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence of any SARS-Cov-2 protein set forth in Table 5.
[0403] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500,600, 700, 800, 900, 1000, 1 100, or 1200 amino acids set forth in any one of SEQ ID NOS: 25-42. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 4, and the other than the at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 4, the amino acid sequence of the SARS- CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 25- 42.
[0404] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 25-30. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 4, and the other than the at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 4, the amino acid sequence of the SARS- CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 25- 30.
[0405] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to acontiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 31-42. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 4, and the other than the at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 4, the amino acid sequence of the SARS- CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 31- 42.|00406| In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 31-36. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 4, and the other than the at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 4, the amino acid sequence of the SARS- CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 31- 36.(00407) In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%,87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, or 1200 amino acids set forth in any one of SEQ ID NOS: 37-42. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 4, and the other than the at least 1, 2, 3, 4, 5, or 6 (e.g., 1) of the sets of amino acid substitutions set forth in Table 4, the amino acid sequence of the SARS- CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 37- 42.[00408J In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least one set of amino acid substitutions set forth in Table 2 and at least one set of amino acid substitutions set forth in Table 4. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 2, 3, 4, 5, or 6 (e.g., 1) sets of amino acid substitutions set forth in Table 2. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 2, 3, 4, 5, or 6 (e.g., 1) sets of amino acid substitutions set forth in Table 4. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV- 2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) that are not listed in Table 2 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more)but less than 20% (e.g, less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 2 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprisesl or more (e.g, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) that are not listed in Table 4 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g, the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprisesl or more (e.g, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g, less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g, substitutions, additions, deletions, etc.) that are not listed in Table 4 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44. In some embodiments, the amino acid variants not listed in Table 2 or Table 4 are found in one or more circulating variants of SARS-CoV-2. In some embodiments, the SARS- CoV-2 spike protein or polypeptide e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises an amino acid sequence comprising at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid variations that are not listed in Table 2 or Table 4. In some embodiments, the SARS-CoV-2 spike protein or polypeptide (e.g, the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises an amino acid sequence comprising or consisting of 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid variations that are not listed in Table 2 or Table 4. In some embodiments, the amino acid variants not listed in Table 2 or Table 4 are found in one or more circulating variants of SARS-CoV-2.
[0409] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least about 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, or 1300 amino acids. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises no more than about 10, 15, 20, 30, 40,50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, or 1300 amino acids. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises from about 10-1300, 10-1200, 10-1100, 10-1000, 10-900, 10-800, 10-700, 10-600, 10-500, 10-400, 10-500, 10-400, 10-300, 10-250, 10- 200, 10-100, 10-90, 10-80, 10-70, 10-60, 10-50, 10-40, 10-30, 10-20, 10-1300, 20-1300, 30-1300, 40-1300, 50-1300, 60-1300, 70-1300, 80-1300, 90-1300, 100-1300,10-250, 20-250, 30-250, 40- 250, 50-250, 60-250, 70-250, 80-250, 90-250, or 100-250 amino acids.5.2.1 Exemplary Additional Features of SARS-CoV-2 Spike Proteins (e.g., Immunogens)
[0410] The SARS-CoV-2 spike proteins or polypeptides (e.g., the SARS-CoV-2 spike protein or polypeptide immunogens (or immunogenic fragments and / or immunogenic variants thereof)) can exhibit additional structural and functional features. Exemplary additional structural and functional features are provided below.5.2.1.1 Full-Length Spike Proteins and Receptor Binding Fragments[004111 In some embodiments, the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS- CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises a full-length SARS-CoV-2 spike protein. In some embodiments, the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) consists of a full- length SARS-CoV-2 spike protein.[00412J In some embodiments, the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS- CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises a fragment of a full-length SARS-CoV-2 spike protein that is capable of binding the ACE2 receptor. In some embodiments, the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) consists of a fragment of a full-length SARS-CoV- 2 spike protein that is capable of binding the ACE2 receptor.
[0413] In some embodiments, the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS- CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least a portion of a RBD of the SARS-CoV-2 spike protein. In someembodiments, the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises a RBD of the SARS-CoV-2 spike protein. In some embodiments, the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) consists of at least a portion of a RBD of the SARS-CoV-2 spike protein. In some embodiments, the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) consists of a RBD of the SARS-CoV-2 spike protein.
[0414] In some embodiments, the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS- CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least a portion of the RBD of the SARS-CoV-2 spike protein. In some embodiments, the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises the RBD of the SARS-CoV-2 spike protein. In some embodiments, the SARS- CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) consists of at least a portion of the RBD of the SARS-CoV-2 spike protein. In some embodiments, the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) consists of the RBD of the SARS- CoV-2 spike protein.|00415| In some embodiments, the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS- CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises the ectodomain of the SARS-CoV-2 spike protein. In some embodiments, the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises the ectodomain of the SARS-CoV-2 spike protein.
[0416] In some embodiments, the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS- CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) does not include the transmembrane domain of the SARS-CoV-2 spike protein. In some embodiments, the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) does not include the cytoplasmic domain of the SARS-CoV-2 spike protein. In some embodiments, the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) does not include the transmembrane domain or the cytoplasmic domain of the SARS-CoV-2 spike protein.5.2.1.2 Stabilization[00417) In some embodiments, the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS- CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is modified to improve stability of the protein produced. In some embodiments, the ectodomain of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is modified to improve stability of the protein produced.
[0418] In some embodiments, the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS- CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is stabilized in a prefusion state. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least one amino acid variation that stabilizes said SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) in a prefusion state. In some embodiments, the amino acid sequence of the SARS- CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least one amino acid variation relative to the amino acid sequence set forth in any one of SEQ ID NO: 1 that stabilizes the SARS-CoV-2 spike protein or polypeptide (e.g, the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) in a prefusion state.
[0419] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g, the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises a proline at one or more of position 817, 892, 899, 986, and / or 987, amino acid numbering relative to the amino acid positions set forth inSEQ ID NO: 1 . In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises a proline at positions 817, 892, 899,986, and 987, amino acid numbering relative to the amino acid positions set forth in SEQ ID NO: 1.
[0420] In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least one amino acid variation relative to the amino acid sequence set forth in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 6, or SEQ ID NO: 43, or SEQ ID NO:44 that stabilizes the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) in a prefusion state. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof))comprises a proline at amino acid position 986 and / or a proline at amino acid position987, amino acid numbering amino acid numbering relative to SEQ ID NO: 1. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof))comprises a proline at amino acid position 986 and / or a proline at amino acid position 987, amino acid numbering relative to SEQ ID NO: 1 .
[0421] In some embodiments, the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS- CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises an inactive furin cleavage site. In order to be able to trigger fusion, the spike protein of SARS-Cov-2 has to be cleaved into the SI and S2 subunit. The cleavage site in SARS-Cov-2 is a polybasic motif (RRAR (SEQ ID NO: 45)) (for example, amino acids 682-685 of SEQ ID NO: 1) that can be activated by furin-like proteases. Modifications to the furin cleavage site that inactivate it are known in the art. See, e.g., Amanat F, Strohm ei er S, Rathnasinghe R, et al. Introduction of two prolines and removal of the polybasic cleavage site leads to optimal efficacy of a recombinant spike-based SARS-CoV-2 vaccine in the mouse model. Preprint. bioRxiv. 2020;2020.09.16.300970. Published 2020 Sep 17. doi: 10.1101 / 2020.09.16.300970 (describes the replacement of the RRAR (SEQ ID NO: 45) cleavage site with a single alanine); andWO2022203963 (which describes the replacement of the RRAR (SEQ ID NO: 45) cleavage site with the amino acid sequence QQAQ (SEQ ID NO: 46)), the entire contents of each of which are incorporated by reference herein. In some embodiments, the amino acid sequence of the SARS- CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least one amino acid variation in the furin cleavage site that inactivates the furin cleavage site. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein or polypeptide (e.g., the SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises a replacement of the RRAR (SEQ ID NO: 45) cleavage site with a single alanine. In some embodiments, the amino acid sequence of the SARS-CoV-2 spike protein ...
Claims
CLAIMSWhat is claimed is:
1. A nucleic acid molecule comprising at least one coding region encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises at least one (e.g., one) set of amino acid substitutions set forth in Table 2 or Table 4.
2. The nucleic acid molecule of claim 1, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of the SARS-CoV-2 spike protein receptor binding domain (RBD).
3. The nucleic acid molecule of claim 1 or 2, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of a full- length SARS-CoV-2 spike protein.
4. The nucleic acid molecule of any one of the preceding claims, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least one (e.g., one) set of amino acid substitutions set forth in Table 2.
5. The nucleic acid molecule of any one of the preceding claims, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, or 1300 amino acids.
6. The nucleic acid molecule of any one of the preceding claims, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises from about 10-15, 10-20, 10-30, 10-40, 10-50, 10-60, 10-70, 10-80, 10-90, 10-100, 10-200, 10-300,10-400, 10-500, 10-600, 10-700, 10-800, 10-900, 10-1000, 10-1 100, 10-1200, or 10-1300 amino acids.
7. The nucleic acid molecule of any one of the preceding claims, wherein other than the at least one set of amino acid substitutions set forth in Table 2, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, or 1300 amino acids set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
8. The nucleic acid molecule of any one of the preceding claims, wherein other than the at least one set of amino acid substitutions set forth in Table 2, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44)9. The nucleic acid molecule of any one of the preceding claims, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises a plurality of sets of amino acid substitutions set forth in Table 2.
10. The nucleic acid molecule of any one of the preceding claims, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 2, 3, 4, 5, or 6 or more (e.g., 2, 3, 4, 5 or 6) sets of amino acid substitutions set forth in Table 2.
11. The nucleic acid molecule of any one of the preceding claims, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%) amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not set forth in Table 2.
12. The nucleic acid molecule of any one of the preceding claims, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 2 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43- 44)13. The nucleic acid molecule of any one of the preceding claims, wherein the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is stabilized in a prefusion state.
14. The nucleic acid molecule of any one of the preceding claims, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least one amino acid variation relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g, any one of SEQ ID NOS: 1-2), that stabilizes the SARS-CoV-2 spike protein (e.g, the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) in a prefusion state.
15. The nucleic acid molecule of any one of the preceding claims, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g, the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises a proline at amino acid position 986 and / or a proline at amino acid position 987, amino acid numbering relative to the amino acid positions set forth in SEQ ID NO: 1.
16. The nucleic acid molecule of any one of the preceding claims, wherein the encoded SARS-CoV-2 spike protein (e.g, the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises one or more non-naturally N- glycosylation sites.
17. The nucleic acid molecule of any one of the preceding claims, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g, the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises theaddition of one or more N-glycosylation sites relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
18. The nucleic acid molecule of any one of the preceding claims, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 7-12.
19. The nucleic acid molecule of any one of the preceding claims, wherein the amino acid sequence of encoded SARS-CoV-2 spike protein (e.g, the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 13-24.
20. The nucleic acid molecule of any one of claims 1-3, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g, the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least one (e.g., one) set of amino acid substitutions set forth in Table 4.
21. The nucleic acid molecule of claim 20, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, or 1300 amino acids.
22. The nucleic acid molecule of any one of claims 20-21, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises from about 10-15, 10- 20, 10-30, 10-40, 10-50, 10-60, 10-70, 10-80, 10-90, 10-100, 10-200, 10-300, 10-400, 10-500, 10-600, 10-700, 10-800, 10-900, 10-1000, 10-1100, 10-1200, or 10-1300 amino acids.
23. The nucleic acid molecule of any one of claims 20-22, wherein other than the at least one set of amino acid substitutions set forth in Table 4, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%,86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, or 1300 amino acids set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44)24. The nucleic acid molecule of any one of claims 20-23, wherein other than the at least one set of amino acid substitutions set forth in Table 4, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of any one of SEQ ID NOS: 1-6 or 43- 44 e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44)25. The nucleic acid molecule of any one of claims 20-24, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises a plurality of sets of amino acid substitutions set forth in Table 4.
26. The nucleic acid molecule of any one of claims 20-25, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 2, 3, 4, 5, or 6 or more (e.g., 2, 3, 4, 5, or 6) sets of amino acid substitutions set forth in Table 4.
27. The nucleic acid molecule of any one of claims 20-26, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g, less than 15%, less than 12%, less than 10%, less than 8%, less than 5%) amino acid variations (e.g, substitutions, additions, deletions, etc.) that are not set forth in Table 4.
28. The nucleic acid molecule of any one of claims 20-27, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g, substitutions, additions, deletions,etc.) that are not listed in Table 4 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44)29. The nucleic acid molecule of any one of claims 20-28, wherein the encoded SARS-CoV- 2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is stabilized in a prefusion state.
30. The nucleic acid molecule of any one of claims 20-29, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least one amino acid variation relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2), that stabilizes the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) in a prefusion state.
31. The nucleic acid molecule of any one of claims 20-30, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises a proline at amino acid position 986 and / or a proline at amino acid position 987, amino acid numbering relative to the amino acid positions set forth in SEQ ID NO: 1.
32. The nucleic acid molecule of any one of claims 20-31, wherein the encoded SARS-CoV- 2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises one or more non-naturally N-glycosylation sites.
33. The nucleic acid molecule of any one of claims 20-32, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises the addition of one or more N-glycosylation sites relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
34. The nucleic acid molecule of any one of claims 20-33, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 25-30.
35. The nucleic acid molecule of any one of claims 20-34, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 31-42.
36. The nucleic acid molecule of any one of claims 1-3, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least one set of amino acid substitutions set forth in Table 2 and at least one set of amino acid substitutions set forth in Table 4.
37. The nucleic acid molecule of claim 36, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, or 1300 amino acids.
38. The nucleic acid molecule of any one of claims 36-37, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises from about 10-15, 10- 20, 10-30, 10-40, 10-50, 10-60, 10-70, 10-80, 10-90, 10-100, 10-200, 10-300, 10-400, 10-500, 10-600, 10-700, 10-800, 10-900, 10-1000, 10-1100, 10-1200, or 10-1300 amino acids.
39. The nucleic acid molecule of any one of claims 36-38, wherein other than the at least one set of amino acid substitutions set forth in Table 2 and the at least one set of amino acid substitutions set forth in Table 4, the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, or 1300 amino acids set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g, any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
40. The nucleic acid molecule of any one of claims 36-39, wherein other than the at least one set of amino acid substitutions set forth in Table 2 and the at least one set of amino acid substitutions set forth in Table 4, the amino acid sequence of the encoded SARS-CoV-2 spikeprotein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
41. The nucleic acid molecule of any one of claims 36-40, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises a plurality of sets of amino acid substitutions set forth in Table 2.
42. The nucleic acid molecule of any one of claims 36-41, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 2, 3, 4, 5, or 6 or more sets of amino acid substitutions set forth in Table 2.
43. The nucleic acid molecule of any one of claims 36-42, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g, less than 15%, less than 12%, less than 10%, less than 8%, less than 5%) amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not set forth in Table 2.
44. The nucleic acid molecule of any one of claims 36-43, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g, the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g, less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 2 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
45. The nucleic acid molecule of any one of claims 36-44, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises a plurality of sets of amino acid substitutions set forth in Table 4.
46. The nucleic acid molecule of any one of claims 36-45, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises at least 2, 3, 4, 5, or 6 or more sets of amino acid substitutions set forth in Table 4.
47. The nucleic acid molecule of any one of claims 36-46, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%) amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not set forth in Table 4.
48. The nucleic acid molecule of any one of claims 36-47, wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 4 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
49. The nucleic acid molecule of any one of claims 36-48, wherein the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is stabilized in a prefusion state.
50. The nucleic acid molecule of any one of claims 36-49, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least one amino acid variation relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2), that stabilizes the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) in a prefusion state.
51. The nucleic acid molecule of any one of claims 36-50, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises a proline at amino acidposition 986 and / or a proline at amino acid position 987, amino acid numbering relative to the amino acid positions set forth in SEQ ID NO: 1.
52. The nucleic acid molecule of any one of claims 36-51, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises one or more non-naturally N-glycosylation sites.
53. The nucleic acid molecule of any one of any one of claims 36-52, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises the addition of one or more N-glycosylation sites relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
54. The nucleic acid molecule of any one of the preceding claims, wherein the encoded SARS-CoV-2 spike protein is an immunogen (or an immunogenic fragment and / or immunogenic variant thereof).
55. The nucleic acid molecule of any one of the preceding claims, wherein the nucleic acid molecule is RNA or DNA.
56. The nucleic acid molecule of any one of the preceding claims, wherein the RNA is messenger ribonucleic acid (mRNA).
57. The nucleic acid molecule of any one of the preceding claims, wherein the nucleic acid molecule comprises at least one modified nucleotide.
58. The nucleic acid molecule of any one of the preceding claims, wherein the nucleic acid molecule comprises Nl-methyl-pseudouridine, cytosine, adenine, and guanine.
59. The nucleic acid molecule of any one of the preceding claims, wherein the nucleic acid molecule comprises a heterologous 5 ’-untranslated region (UTR), 3’-UTR, or both a 5’-UTR and 3’-UTR.
60. The nucleic acid molecule of any one of the preceding claims, wherein the nucleic acid molecule comprises a poly(A) sequence.
61. The nucleic acid molecule of any one of the preceding claims, wherein the nucleic acid molecule comprises a 5 ’cap structure.
62. The nucleic acid molecule of any one of the preceding claims, wherein the nucleotide sequence of the nucleic acid molecule is codon optimized.
63. The nucleic acid molecule of any one of the preceding claims, wherein the nucleic acid molecule further encodes a heterologous polypeptide or protein.
64. The nucleic acid molecule of any one of the preceding claims, wherein the nucleic acid molecule encodes a signal peptide.
65. The nucleic acid molecule of any one of the preceding claims, wherein the nucleic acid molecule encodes a homologous or heterologous signal peptide.
66. The nucleic acid molecule of any one of the preceding claims, wherein the nucleic acid molecule does not encode a signal peptide.
67. A vector comprising the nucleic acid molecule of any one of the preceding claims.
68. The vector of claim 67, wherein the vector is a non-viral vector (e.g, a plasmid) or a viral vector.
69. A conjugate comprising the nucleic acid molecule of any one of claims 1-66 operably connected (e.g., directly or indirectly (e.g., via a linker)) to a heterologous moiety (e.g., a heterologous polypeptide or protein).
70. A composition comprising at least one of the nucleic acid molecules set forth in any one of claims 1-66, the vector of any one of claims 67-68, or the conjugate of claim 69.
71. The composition of claim 70, comprising a plurality of nucleic acid molecules set forth in any one of claims 1-66, wherein the amino acid sequence of each of the SARS-CoV-2 spike proteins (e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) encoded by each nucleic acid molecule of the plurality is different.
72. The composition of claim 71, wherein the plurality comprises at least two nucleic acid molecules set forth in any one of claims 1-66, wherein the amino acid sequence of each of the SARS-CoV-2 spike proteins (e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) encoded by each of the at least 2 nucleic acid molecules comprises a different set of amino acid substitutions set forth in Table 2 or Table 4 or a different combination of sets of amino acid substitutions set forth in Table 2 or Table 4.
73. The composition of claim 71, wherein the plurality comprises at least 2, 3, 4, 5, or 6 nucleic acid molecules set forth in any one of claims 1-66, wherein the amino acid sequence of each of the SARS-CoV-2 spike proteins (e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) encoded by each of the at least 2,3, 4, 5, or 6 nucleic acid molecules comprises a different set of amino acid substitutions set forth in Table 2.
74. The composition of claim 71, wherein the plurality comprises at least 2, 3, 4, 5, or 6 nucleic acid molecules set forth in any one of claims 1-66, wherein the amino acid sequence of each of the SARS-CoV-2 spike proteins (e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) encoded by each of the at least 2, 3, 4, 5, or 6 nucleic acid molecules comprises a different set of amino acid substitutions set forth in Table 4.
75. The composition of claim 71, wherein the plurality comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 nucleic acid molecules set forth in any one of claims 1-66, wherein the amino acid sequence of each of the SARS-CoV-2 spike proteins e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) encoded by each of the at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 nucleic acid molecules comprises a different set of amino acid substitutions set forth in Table 2 or Table 4.
76. A composition comprising(a) at least one nucleic acid molecule set forth in any one of claims 4-19;(b) at least one nucleic acid molecule set forth in any one of claims 20-35; and / or(c) at least one nucleic acid molecule set forth in any one of claims 36-53.
77. A composition comprising at least 2, 3, 4, 5, or 6 nucleic acid molecules, wherein the amino acid sequence of each of the SARS-CoV-2 spike proteins (e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) encoded by of each of the at least 2, 3, 4, 5, or 6 nucleic acid molecules comprises a different set of amino acid substitutions set forth in Table 2.
78. A composition comprising at least 2, 3, 4, 5, or 6 nucleic acid molecules, wherein the amino acid sequence of each of the SARS-CoV-2 spike proteins (e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) encoded by of each of the at least 2, 3, 4, 5, or 6 nucleic acid molecules comprises a different set of amino acid substitutions set forth in Table 4.
79. A composition comprising at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 nucleic acid molecules, wherein the amino acid sequence of each of the SARS-CoV-2 spike proteins (e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenicvariants thereof)) encoded by of each of the at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1, or 12 nucleic acid molecules comprises a different set of amino acid substitutions set forth in Table 2 or Table 4.
80. A composition comprising any one or more (e.g., 1, 2, 3, 4, 5, or 6) of(a) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV- 2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS- CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set A (440E / 456L / 478R / 484V / 505Y) set forth in Table 2;(b) a nucleic acid molecule comprising at least one coding region encoding a SARS- CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set B (405K / 440N / 456V / 478Q / 490P) set forth in Table 2;(c) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV- 2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS- CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set C (403S / 444E / 455W) set forth in Table 2;(d) a nucleic acid molecule comprising at least one coding region encoding a SARS- CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set D (346K / 439K / 455S / 505D) set forth in Table 2;(e) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV- 2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS- CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenicfragment and / or immunogenic variant thereof)) comprises amino acid substitution set E (403K / 444T / 453F / 478R) set forth in Table 2; and / or(f) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV- 2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS- CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set F (405D / 417Y / 440R / 478I / 490F) set forth in Table 2.
81. A composition comprising any one or more e.g., 1, 2, 3, 4, 5, or 6) of(a) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV- 2 spike protein e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS- CoV-2 spike protein e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set G (440E / 456L / 478R / 484V / 505Y / 383N / 396T / 468N) set forth in Table 4;(b) a nucleic acid molecule comprising at least one coding region encoding a SARS- CoV-2 spike protein e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set H (405K / 440N / 456V / 478Q / 490P / 383N / 396T / 468N) set forth in Table 4;(c) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV- 2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS- CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set I (403S / 444E / 455W / 383N / 396T / 468N) set forth in Table 4;(d) a nucleic acid molecule comprising at least one coding region encoding a SARS- CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or animmunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set J (346K / 439K / 455S / 505D / 383N / 396T / 468N) set forth in Table 4;(e) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV- 2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS- CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set K (403K / 444T / 453F / 478R / 383N / 396T / 468N) set forth in Table 4; and / or(f) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV- 2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS- CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set L (405D / 417Y / 440R / 478I / 490F / 383N / 396T / 468N) set forth in Table 4.
82. A composition comprising any one or more (e.g., any 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12) of(a) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV- 2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS- CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set A (440E / 456L / 478R / 484V / 505Y) set forth in Table 2;(b) a nucleic acid molecule comprising at least one coding region encoding a SARS- CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set B (405K / 440N / 456V / 478Q / 490P) set forth in Table 2;(c) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV- 2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set C (403S / 444E / 455W) set forth in Table 2;(d) a nucleic acid molecule comprising at least one coding region encoding a SARS- CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set D (346K / 439K / 455S / 505D) set forth in Table 2;(e) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV- 2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS- CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set E (403K / 444T / 453F / 478R) set forth in Table 2;(f) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV- 2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS- CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set F (405D / 417Y / 440R / 478I / 490F) set forth in Table 2;(g) a nucleic acid molecule comprising at least one coding region encoding a SARS- CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set G (440E / 456L / 478R / 484V / 505Y / 383N / 396T / 468N) set forth in Table 4;(h) a nucleic acid molecule comprising at least one coding region encoding a SARS- CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or animmunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set H (405K / 440N / 456V / 478Q / 490P / 383N / 396T / 468N) set forth in Table 4;(i) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV- 2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS- CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set I (403S / 444E / 455W / 383N / 396T / 468N) set forth in Table 4;(j) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV- 2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS- CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set J (346K / 439K / 455S / 505D / 383N / 396T / 468N) set forth in Table 4;(k) a nucleic acid molecule comprising at least one coding region encoding a SARS- CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set K (403K / 444T / 453F / 478R / 383N / 396T / 468N) set forth in Table 4; and / or(l) a nucleic acid molecule comprising at least one coding region encoding a SARS-CoV- 2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the encoded SARS- CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) comprises amino acid substitution set L (405D / 417Y / 440R / 478I / 490F / 383N / 396T / 468N) set forth in Table 4.
83. A composition comprising a plurality of nucleic acid molecules SARS-CoV-2 spike proteins or polypeptides (e.g., immunogens (or immunogenic fragments and / or immunogenic variants thereof)), wherein the plurality comprises at least 2, 3, 4, 5, 6, or more SARS-CoV-2 spike proteins or polypeptides (e.g., immunogens (or immunogenic fragments and / or immunogenic variants thereof)), wherein(a) the amino acid sequence of each of the encoded 2, 3, 4, 5, or 6 or more SARS-CoV-2 spike proteins or polypeptides (e.g., immunogens (or immunogenic fragments and / or immunogenic variants thereof)) comprises or consists of one or more e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25) of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1), wherein the amino acid sequence of each member of the plurality does not contain an identical set of the foregoing amino acid substitutions (i.e., 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1));(b) wherein the amino acid sequence of each of the encoded 2, 3, 4, 5, or 6 or more SARS-CoV-2 spike proteins or polypeptides (e.g., immunogens (or immunogenic fragments and / or immunogenic variants thereof)) comprises or consists of one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25) of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1)), and one or more (e.g., 1, 2, or 3) of the following amino acid substitutions 383N, 396T, 468N (amino acid numbering according to SEQ ID NO: 1), and wherein the amino acid sequence of each member of the plurality does not contain an identical set of the foregoing amino acid substitutions (i.e., 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1)); or(c) wherein the amino acid sequence of each of the encoded 2, 3, 4, 5, or 6 or more SARS-CoV-2 spike proteins or polypeptides (e.g., immunogens (or immunogenic fragments and / or immunogenic variants thereof)) comprises or consists of one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28) of the following amino acid substitutions 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, 490F, 383N, 396T, or 468N (amino acid numbering according to SEQ ID NO: 1)), and oneor more (e.g, 1, 2, or 3) of the following amino acid substitutions 383N, 396T, 468N (amino acid numbering according to SEQ ID NO: 1), and wherein the amino acid sequence of each member of the plurality does not contain an identical set of the foregoing amino acid substitutions (i.e., 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, 490F, 383N, 396T, or 468N (amino acid numbering according to SEQ ID NO: 1)).
84. The composition of any one of claims 70-83, wherein the nucleic acid molecule(s) are comprised in one or more vectors.
85. The composition of any one of claims 70-84, wherein the nucleic acid molecule(s) or the one or more vectors are formulated in one or more carrier.
86. The composition of claim 85, wherein the carrier is a lipid nanoparticle (LNP), liposome, lipoplex, or nanoliposome.
87. The composition of any one of claims 85-86, wherein the carrier is an LNP.
88. The composition of claim 87, wherein the LNP comprises a cationic lipid, a neutral lipid, a cholesterol, and / or a PEG lipid.
89. The composition of claim 87 or 88, wherein the LNP has a mean particle size of between 80 nm and 160 nm90. The composition of any one of claims 70-89, further comprising a nucleic acid molecule encoding a SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) that does not comprise a set of amino acid substitutions set forth in Table 2 or Table 4.
91. The composition of any one of claims 70-90, wherein the composition is a pharmaceutical composition comprising a pharmaceutically acceptable excipient or a vaccine composition.
92. The composition of any one of claims 70-91, further comprising an adjuvant.
93. A SARS-CoV-2 spike protein (e.g, a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)), wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g, the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), comprises at least one set of amino acid substitutions set forth in Table 2 or Table 4.
94. The SARS-CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) of claim 93, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of the receptor binding domain (RBD) of a SARS-CoV-2 spike protein.
95. The SARS-CoV-2 spike protein e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) of claim 93 or 94, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises or consists of a full-length SARS-CoV-2 spike protein.
96. The SARS-CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 93-95, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least one set of amino acid substitutions set forth in Table 2.
97. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of claim 96, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, or 1300 amino acids .
98. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of claim 96 or 97, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises from about 10-15, 10-20, 10-30, 10-40, 10-50, 10-60, 10-70, 10-80, 10-90, 10-100, 10-200, 10- 300, 10-400, 10-500, 10-600, 10-700, 10-800, 10-900, 10-1000, 10-1100, 10-1200, or 10-1300 amino acids.
99. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 96-98, wherein other than the at least one set of amino acid substitutions, the amino acid sequence of theSARS-CoV-2 spike protein e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, or 1300 amino acids set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
100. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 96-99, wherein other than the at least one set of amino acid substitutions set forth in Table 2, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
101. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 96-100, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises a plurality of sets of amino acid substitutions set forth in Table 2.
102. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 96-101, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least 2, 3, 4, 5, or 6 sets of amino acid substitutions set forth in Table 2.
103. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 96-102, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%) amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not set forth in Table 2.
104. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 96-103, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 2 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
105. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 96-104, wherein the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is stabilized in a prefusion state.
106. The SARS-CoV-2 spike protein (e.g, the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 96-105, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least one amino acid variation relative to the amino acid sequence set forth in SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2) that stabilizes the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) in a prefusion state.
107. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 96-106, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises a proline at amino acid position 986 and / or a proline at amino acid position 987, amino acid numbering relative to the amino acid positions set forth in SEQ ID NO: 1.
108. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 96-107, wherein the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or theimmunogenic fragment and / or immunogenic variant thereof)) comprises one or more non- naturally N-glycosylation sites.
109. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 96-108, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises the addition of one or more N-glycosylation sites relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
110. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 96-109, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 7-12.
111. The SARS-CoV-2 spike protein (e.g, the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 96-110, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 13-24.
112. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 93-95, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least one set of amino acid substitutions set forth in Table 4.
113. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of claim 112, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g, the SARS-CoV-2 spike proteinimmunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, or 1300 amino acids.
114. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of claim 112 or 113, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises from about 10-15, 10-20, 10-30, 10-40, 10-50, 10-60, 10-70, 10-80, 10-90, 10-100, 10-200, 10- 300, 10-400, 10-500, 10-600, 10-700, 10-800, 10-900, 10-1000, 10-1100, 10-1200, or 10-1300 amino acids.
115. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 112-114, wherein other than the at least one set of amino acid substitutions the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, or 1300 amino acids set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
116. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 112-115, wherein other than the at least one set of amino acid substitutions the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g, any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
117. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 112-116, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spikeprotein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises a plurality of sets of amino acid substitutions set forth in Table 4.
118. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 112-117, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least 2, 3, 4, 5, or 6 sets of amino acid substitutions set forth in Table 4.
119. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 112-118, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 4.
120. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 112-119, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 4 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
121. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 112-120, wherein the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is stabilized in a prefusion state.
122. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 112-121, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof))comprises at least one amino acid variation relative to the amino acid sequence set forth in in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: l-2)that stabilizes the SARS- CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) in a prefusion state.
123. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 112-122, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g, the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises a proline at amino acid position 986 and / or a proline at amino acid position 987, amino acid numbering relative to SEQ ID NO: 1.
124. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 112-123, wherein the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises one or more non- naturally N-glycosylation sites.
125. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 112-124, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises the addition of one or more N-glycosylation sites relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
126. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 112-125, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 25-30.
127. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 112-126,wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 31-42.
128. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 93-95, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least one set of amino acid substitutions set forth in Table 2 and at least one set of amino acid substitutions set forth in Table 4.
129. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of claim 128, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, or 1300 amino acids.
130. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of claim 128 or 129, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises 10- 15, 10-20, 10-30, 10-40, 10-50, 10-60, 10-70, 10-80, 10-90, 10-100, 10-200, 10-300, 10-400, 10- 500, 10-600, 10-700, 10-800, 10-900, 10-1000, 10-1100, 10-1200, or 10-1300 amino acids.
131. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 128-130, wherein other than the at least one set of amino acid substitutions, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a contiguous stretch of at least 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150,200, 300, 400, 500, 600, 700, 800, 900, 1000, 1 100, 1200, or 1300 amino acids set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
132. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 128-131, wherein other than the at least one set of amino acid substitutions set forth in Table 2 and the at least one set of amino acid substitutions set forth in Table 4, the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
133. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 128-132, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises a plurality of sets of amino acid substitutions set forth in Table 2.
134. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 128-133, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least 2, 3, 4, 5, or 6 sets of amino acid substitutions set forth in Table 2.
135. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 128-134, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not set forth in Table 2.
136. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 128-135, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spikeprotein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 2 relative to the amino acid sequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
137. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 128-136, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises a plurality of sets of amino acid substitutions set forth in Table 4.
138. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 128-137, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 16 sets of amino acid substitutions set forth in Table 4.
139. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 128-138, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 4.
140. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 128-139, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises 1 or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or more) but less than 20% (e.g., less than 15%, less than 12%, less than 10%, less than 8%, less than 5%), amino acid variations (e.g., substitutions, additions, deletions, etc.) that are not listed in Table 4 relative to the amino acidsequence set forth in any one of SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
141. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 128-140, wherein the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) is stabilized in a prefusion state.
142. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 128-141, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least one amino acid variation relative to the amino acid sequence set forth in SEQ ID NOS: 1-6 or 43-44 (e.g., any one of SEQ ID NOS: 1-2), that stabilizes the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) in a prefusion state.
143. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 128-142, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises a proline at amino acid position 986 and / or a proline at amino acid position 987, amino acid numbering relative to the amino acid positions set forth in SEQ ID NO: 1 .
144. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 128-143, wherein SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises one or more non- naturally N-glycosylation sites.
145. The SARS-CoV-2 spike protein (e.g, the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 128-144, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises the addition of one or more N-glycosylation sites relative to the amino acid sequence set forth in SEQ ID NOS: 1-6 or 43-44 (e.g, any one of SEQ ID NOS: 1-2, 4-5, or 43-44).
146. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 128-145, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises an inactive furin cleavage site.
147. The SARS-CoV-2 spike protein e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 128-146, wherein the amino acid sequence of the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises at least one amino acid variation in the furin cleavage site that inactivates the furin cleavage site.
148. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 93-147, wherein the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) further comprises a heterologous protein.
149. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 93-148, wherein the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises a signal peptide.
150. The SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 93-149, wherein the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) comprises a homologous or heterologous signal peptide.
151. The SARS-CoV-2 spike protein (e.g, the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 93-150, wherein the SARS-CoV-2 spike protein (e.g, the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) does not comprise a signal peptide.
152. The SARS-CoV-2 spike protein (e.g, the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 93-151,wherein the SARS-CoV-2 spike protein is an immunogen (or an immunogenic fragment and / or immunogenic variant thereof).
153. A fusion protein comprising the SARS-CoV-2 spike protein (e.g, the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 93-152 operably connected (e.g., directly or indirectly (e.g., via a linker)) to a heterologous polypeptide or protein.
154. A conjugate comprising the SARS-CoV-2 spike protein (e.g, the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 93-152 operably connected (e.g, directly or indirectly (e.g, via a linker)) to a heterologous moiety.
155. A composition comprising at least one SARS-CoV-2 spike protein (e.g, at least one of the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) set forth in any one of claims 93-152 or 177, the fusion protein of claim 153, the conjugate of claim 154, or the nucleic acid molecule of claim 175.
156. The composition of claim 155, wherein the composition comprises a plurality of SARS- CoV-2 spike proteins (e.g, a plurality of SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) set forth in any one of claims 93- 52, wherein the amino acid sequence of each of the plurality of SARS-CoV-2 spike proteins (e.g., the SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) comprises a different set of amino acid substitutions set forth in Table 2 or Table 4 or a different combination of sets of amino acid substitutions set forth in Table 2 or Table 4.
157. The composition of claim 156, wherein the plurality comprises at least 2, 3, 4, 5, or 6 SARS-CoV-2 spike proteins (e.g., the SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) wherein the amino acid sequence each of the at least 2, 3, 4, 5, or 6 SARS-CoV-2 spike proteins (e.g, the SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) comprises a different set of amino acid substitutions set forth in Table 2.
158. The composition of claim 156, wherein the plurality comprises at least 2, 3, 4, 5, or 6 SARS-CoV-2 spike proteins (e.g., the SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) wherein the amino acid sequence each of the atleast 2, 3, 4, 5, or 6 SARS-CoV-2 spike proteins (e.g., the SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) comprises a different set of amino acid substitutions set forth in Table 4.
159. The composition of claim 156, wherein the plurality comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 SARS-CoV-2 spike proteins (e.g., the SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) wherein the amino acid sequence each of the at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 SARS-CoV-2 spike proteins (e.g., the SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) comprises a different set of amino acid substitutions set forth in Table 2 or Table 4.
160. A composition comprising(a) at least one SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) set forth in any one of claims 96- 111;(b) at least one SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) set forth in any one of claims 112-127; and / or(c) at least one SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) set forth in any one of claims 128-147.
161. A composition comprising at least 2, 3, 4, 5, or 6 SARS-CoV-2 spike proteins (e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) wherein the amino acid sequence of the at least 2, 3, 4, 5, or 6 SARS-CoV-2 spike proteins (e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) comprises a different set of amino acid substitutions set forth in Table 2.
162. A composition comprising at least 2, 3, 4, 5, or 6 SARS-CoV-2 spike proteins (e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) wherein the amino acid sequence of the at least 2, 3, 4, 5, or 6 SARS-CoV-2 spike proteins (e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / orimmunogenic variants thereof)) comprises a different set of amino acid substitutions set forth in Table 4.
163. A composition comprising at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 SARS-CoV-2 spike proteins (e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) wherein the amino acid sequence of the at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 SARS-CoV-2 spike proteins (e.g., SARS-CoV-2 spike protein immunogens (or immunogenic fragments and / or immunogenic variants thereof)) comprises a different set of amino acid substitutions set forth in Table 2 or Table 4.
164. A composition comprising any one or more (e.g., 1, 2, 3, 4, 5, or 6) of(a) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set A (440E / 456L / 478R / 484V / 505Y) set forth in Table 2;(b) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set B (405K / 440N / 456V / 478Q / 490P) set forth in Table 2;(c) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set C (403S / 444E / 455W) set forth in Table 2;(d) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set D (346K / 439K / 455S / 505D) set forth in Table 2;(e) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set E (403K / 444T / 453F / 478R) set forth in Table 2; and / or(f) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acidsequence that comprises amino acid substitution set F (405D / 417Y / 440R / 478I / 490F) set forth in Table 2.
165. A composition comprising any one or more (e.g., 1, 2, 3, 4, 5, or 6) of(a) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set G (440E / 456L / 478R / 484V / 505Y / 383N / 396T / 468N) set forth in Table 4;(b) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set H (405K / 440N / 456V / 478Q / 490P / 383N / 396T / 468N) set forth in Table 4;(c) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set I (403S / 444E / 455W / 383N / 396T / 468N) set forth in Table 4;(d) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set J (346K / 439K / 455S / 505D / 383N / 396T / 468N) set forth in Table 4;(e) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set K (403K / 444T / 453F / 478R / 383N / 396T / 468N) set forth in Table 4; and / or(f) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set L (405D / 417Y / 440R / 478I / 490F / 383N / 396T / 468N) set forth in Table 4.
166. A composition comprising any one or more (e.g, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12) of(a) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acidsequence that comprises amino acid substitution set A (440E / 456L / 478R / 484V / 505Y) set forth in Table 2;(b) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set B (405K / 440N / 456V / 478Q / 490P) set forth in Table 2;(c) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set C (403S / 444E / 455W) set forth in Table 2;(d) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set D (346K / 439K / 455S / 505D) set forth in Table 2;(e) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set E (403K / 444T / 453F / 478R) set forth in Table 2;(f) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set F (405D / 417Y / 440R / 478I / 490F) set forth in Table 2;(g) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set G (440E / 456L / 478R / 484V / 505Y / 383N / 396T / 468N) set forth in Table 4;(h) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set H (405K / 440N / 456V / 478Q / 490P / 383N / 396T / 468N) set forth in Table 4;(i) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acidsequence that comprises amino acid substitution set T (403S / 444E / 455W / 383N / 396T / 468N) set forth in Table 4;(j) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set J (346K / 439K / 455S / 505D / 383N / 396T / 468N) set forth in Table 4;(k) a SARS-CoV-2 spike protein (e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set K (403K / 444T / 453F / 478R / 383N / 396T / 468N) set forth in Table 4; and / or(l) a SARS-CoV-2 spike protein e.g., SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)) comprising an amino acid sequence that comprises amino acid substitution set L (405D / 417Y / 440R / 478I / 490F / 383N / 396T / 468N) set forth in Table 4.
167. A composition comprising a plurality of SARS-CoV-2 spike proteins or polypeptides (e.g., immunogens (or immunogenic fragments and / or immunogenic variants thereof)), wherein the plurality comprises at least 2, 3, 4, 5, 6, or more SARS-CoV-2 spike proteins or polypeptides (e.g., immunogens (or immunogenic fragments and / or immunogenic variants thereof)), wherein(a) the amino acid sequence of each of the 2, 3, 4, 5, or 6 or more SARS-CoV-2 spike proteins or polypeptides (e.g., immunogens (or immunogenic fragments and / or immunogenic variants thereof)) comprises or consists of one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25) of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1), wherein the amino acid sequence of each member of the plurality does not contain an identical set of the foregoing amino acid substitutions (i.e., 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1));(b) wherein the amino acid sequence of each of the 2, 3, 4, 5, or 6 or more SARS-CoV-2 spike proteins or polypeptides (e.g., immunogens (or immunogenic fragments and / orimmunogenic variants thereof)) comprises or consists of one or more (e.g., 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25) of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1)), and one or more (e. ., 1, 2, or 3) of the following amino acid substitutions 383N, 396T, 468N (amino acid numbering according to SEQ ID NO: 1), and wherein the amino acid sequence of each member of the plurality does not contain an identical set of the foregoing amino acid substitutions (z.e., 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, or 490F (amino acid numbering according to SEQ ID NO: 1)); or(c) wherein the amino acid sequence of each of the 2, 3, 4, 5, or 6 or more SARS-CoV-2 spike proteins or polypeptides (e.g., immunogens (or immunogenic fragments and / or immunogenic variants thereof)) comprises or consists of one or more (e.g, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28) of the following amino acid substitutions 440E, 456L, 478R, 484V, 505 Y, 405K, 440N, 456V, 478Q, 490P, 403 S, 444E, 455W, 346K, 439K, 455S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, 490F, 383N, 396T, or 468N (amino acid numbering according to SEQ ID NO: 1)), and one or more (e.g., 1, 2, or 3) of the following amino acid substitutions 383N, 396T, 468N (amino acid numbering according to SEQ ID NO: 1), and wherein the amino acid sequence of each member of the plurality does not contain an identical set of the foregoing amino acid substitutions (z.e., 440E, 456L, 478R, 484V, 505Y, 405K, 440N, 456V, 478Q, 490P, 403S, 444E, 455W, 346K, 439K, 455 S, 505D, 403K, 444T, 453F, 405D, 417Y, 440R, 4781, 490F, 383N, 396T, or 468N (amino acid numbering according to SEQ ID NO: 1)).
168. The composition of any one of claims 155-167, wherein the SARS-CoV-2 spike proteins (e.g, the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) are formulated in one or more carrier.
169. The composition of claim 168, wherein the carrier is a lipid nanoparticle (LNP), liposome, lipoplex, or nanoliposome.
170. The composition of any one of claims 168-169, wherein the carrier is an LNP.171 . The composition of claim 170, wherein the LNP comprises a cationic lipid, a neutral lipid, a cholesterol, and / or a PEG lipid.
172. The composition of claim 170 or 171, wherein the LNP has a mean particle size of between 80 nm and 160 nm.
173. The composition of any one of claims 155-172, further comprising a SARS-CoV-2 spike proteins (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) that does not comprise a set of amino acid substitutions set forth in Table 2 or Table 4.
174. The composition of any one of claims 155-173, wherein the composition is a pharmaceutical composition comprising a pharmaceutically acceptable excipient.
175. The composition of any one of claims 155-174, further comprising an adjuvant.
176. A nucleic acid molecule encoding the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 93-152.
177. A SARS-CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) encoded by the nucleic acid molecule of any one of claims 1-66.
178. A carrier comprising the nucleic acid molecule of any one of claims 1-66 or 176, the protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 93-152 or 177, the vector of any one of claims 67-68, the conjugate of claim 69 or 154, the fusion protein of claim 153, the host cell of claim 193, the composition of any one of claims 70-92 or 155-175, the vaccine composition of any one of claims 183-189, or the pharmaceutical composition of any one of claims 190-192.
179. The carrier of claim 178, wherein the carrier is a lipid nanoparticle (LNP), liposome, lipoplex, or nanoliposome.
180. The carrier of claim 179, wherein the carrier is an LNP.
181. The carrier of claim 179 or 180, wherein the LNP comprises a cationic lipid, a neutral lipid, a cholesterol, and / or a PEG lipid.
182. The carrier of any one of claims 179-181, wherein the LNP has a mean particle size of between 80 nm and 160 nm.
183. A vaccine composition comprising the nucleic acid molecule of any one of claims 1 -66 or 176, the protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 93-152 or 177, the vector of any one of claims 67-68, the conjugate of claim 69 or 154, the fusion protein of claim 153, the host cell of claim 193, the composition of any one of claims 70-92 or 155-175, the carrier of any one of claims 178-182, or the pharmaceutical composition of any one of claims 190-192.
184. The vaccine composition of claim 183, wherein the vaccine composition is a prime vaccine composition.
185. The vaccine composition of claim 183 or 184, wherein the vaccine composition is a boost vaccine composition.
186. The vaccine composition of any one of claims 183-185, wherein the vaccine composition is a prime vaccine composition and a boost vaccine composition.
187. The vaccine composition of any one of claims 183-186, wherein the vaccine composition can be utilized as a prime vaccine composition and / or a booster vaccine composition in a homologous or heterologous prime boost vaccine regimen.
188. A vaccine composition comprising a messenger ribonucleic acid (mRNA) encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) that comprises at least one amino acid substitution set forth in Table 2 or Table 4, formulated in a lipid nanoparticle, the vaccine composition having the following characteristics: (a) the LNPs comprise a cationic lipid, a neutral lipid, a cholesterol, and a PEG lipid, (b) the LNPs have a mean particle size of between 80 nm and 160 nm, and (c) the mRNA comprises: (i) a 5'-cap structure; (ii) a 5'-UTR; (iii) Nl- methyl-pseudouridine, cytosine, adenine, and guanine; (iv) a 3'-UTR; and (v) a poly-A region.
189. The vaccine composition of any one of claims 183-188, wherein the vaccine composition further comprises an adjuvant.
190. A pharmaceutical composition comprising the nucleic acid molecule of any one of claims 1-66 or 176, the protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 93-152 or 177, the vector of any one of claims 67-68, the conjugate of claim 69 or 154, the fusion protein of claim 153, the host cell of claim 193, the composition of any one of claims 70-92 or 155-175, the vaccinecomposition of any one of claims 183-189, or the carrier of any one of claims 178-182, and a pharmaceutically acceptable excipient.
191. A pharmaceutical composition comprising a messenger ribonucleic acid (mRNA) encoding a SARS-CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein immunogen (or an immunogenic fragment and / or immunogenic variant thereof)) that comprises at least one amino acid substitution set forth in Table 2 or Table 4, formulated in a lipid nanoparticle, the pharmaceutical composition having the following characteristics: (a) the LNPs comprise a cationic lipid, a neutral lipid, a cholesterol, and a PEG lipid, (b) the LNPs have a mean particle size of between 80 nm and 160 nm, and (c) the mRNA comprises: (i) a 5'-cap structure; (ii) a 5'- UTR; (iii) Nl-methyl-pseudouridine, cytosine, adenine, and guanine; (iv) a 3'-UTR; and (v) a poly-A region; and a pharmaceutically acceptable excipient..
192. The pharmaceutical composition of any one of claims 190-191, wherein the pharmaceutical composition further comprises an adjuvant.
193. A host cell comprising the nucleic acid molecule of any one of claims 1-66 or 176, the protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 93-152 or 177, the vector of any one of claims 67-68, the conjugate of claim 69 or 154, the fusion protein of claim 153, the carrier of any one of claims 178-182, the composition of any one of claims 70-92 or 155-175, the vaccine composition of any one of claims 183-189, or the pharmaceutical composition of any one of claims 190-192.
194. A kit comprising the nucleic acid molecule of any one of claims 1-66 or 176, the protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 93-152 or 177, the vector of any one of claims 67-68, the conjugate of claim 69 or 154, the fusion protein of claim 153, the host cell of claim 193, the composition of any one of claims 70-92 or 155-175, the vaccine composition of any one of claims 183-189, the carrier of any one of claims 178-182, or the pharmaceutical composition of any one of claims 190-191.
195. The kit of claim 194, comprising instructions for use of the nucleic acid molecule, vector, protein (or immunogenic fragment or immunogenic variant thereof), conjugate, fusion protein, carrier, composition, vaccine composition, or pharmaceutical composition.
196. A method of delivering a nucleic acid molecule, vector, protein (or immunogenic fragment or immunogenic variant thereof), conjugate, fusion protein, host cell, carrier, composition, vaccine composition, or pharmaceutical composition to a subject in need thereof, the method comprising administering to the subject the nucleic acid molecule of any one of claims 1-66 or 176, the protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 93-152 or 177, the vector of any one of claims 67-68, the conjugate of claim 69 or 154, the fusion protein of claim 153, the host cell of claim 193, the composition of any one of claims 70-92 or 155-175, the vaccine composition of any one of claims 183-189, the carrier of any one of claims 178-182, or the pharmaceutical composition of any one of claims 190-191, to thereby deliver the nucleic acid molecule, the vector, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), the conjugate, the fusion protein, the host cell, the carrier, the composition, the vaccine composition, or the pharmaceutical composition to the subject.
197. A method of inducing or enhancing an immune response in a subject in need thereof, the method comprising administering to the subject the nucleic acid molecule of any one of claims 1-66 or 176, the protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 93-152 or 177, the vector of any one of claims 67-68, the conjugate of claim 69 or 154, the fusion protein of claim 153, the host cell of claim 193, the composition of any one of claims 70-92 or 155-175, the vaccine composition of any one of claims 183-189, the carrier of any one of claims 178-182, or the pharmaceutical composition of any one of claims 190-191, to thereby induce or enhance an immune response the subject.
198. A method of preventing, ameliorating, or treating a SARS-CoV-2 infection in a subject in need thereof, the method comprising administering to the subject the nucleic acid molecule of any one of claims 1-66 or 176, the protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 93-152 or 177, the vector of any one of claims 67-68, the conjugate of claim 69 or 154, the fusion protein of claim 153, the host cell of claim 193, the composition of any one of claims 70-92 or 155-175, the vaccine composition of any one of claims 183-189, the carrier of any one of claims 178-182,or the pharmaceutical composition of any one of claims 190-191, to thereby prevent, ameliorate, or treat the SARS-CoV-2 infection the subject.
199. A method of vaccinating a subject against SARS-CoV-2, the method comprising administering to the subject the nucleic acid molecule of any one of claims 1-66 or 176, the protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 93-152 or 177, the vector of any one of claims 67-68, the conjugate of claim 69 or 154, the fusion protein of claim 153, the host cell of claim 193, the composition of any one of claims 70-92 or 155-175, the vaccine composition of any one of claims 183-189, the carrier of any one of claims 178-182, or the pharmaceutical composition of any one of claims 190-191, to thereby vaccinate the subject against SARS-CoV- 2.
200. A method of vaccinating a subject against SARS-CoV-2, the method comprising administering to the subject (a) an mRNA molecule (e.g., an mRNA molecule described herein) encoding the SARS-CoV-2 spike protein (e.g., a SARS-CoV-2 spike protein or polypeptide immunogen (or immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 93-152 or 177 (or a conjugate or fusion protein thereof), (b) a vector comprising the mRNA molecule, (c) a carrier comprising the mRNA molecule or the vector, (d) a vaccine composition comprising the mRNA molecule, the vector, or the carrier, or (e) a pharmaceutical composition comprising the mRNA molecule, the vector, the carrier, or the vaccine composition, to thereby vaccinate the subject against SARS-CoV-2, to thereby vaccinate the subject against SARS-CoV-2.
201. A method of vaccinating a subject against SARS-CoV-2, the method comprising administering to the subject the vaccine composition of any one of claims 183-189 or the pharmaceutical composition of any one of claims 200-192, to thereby vaccinate the subject against SARS-CoV-2.
202. The method of any one of claims 196-201, wherein the nucleic acid molecule, the vector, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), the conjugate, the fusion protein, the carrier, the composition, the vaccine composition, or the pharmaceutical composition is administered to the subject at least twice.
203. The method of any one of claims 196-202, wherein the subject is a human.
204. The method of any one of claims 196-203, wherein the nucleic acid molecule, the vector, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), the conjugate, the fusion protein, the carrier, the composition, the vaccine composition, or the pharmaceutical composition is administered as a prime and / or a boost in a homologous or heterologous prime-boost regimen.
205. The method of any one of claims 196-204, wherein the nucleic acid molecule, the vector, the SARS-CoV-2 spike protein (e.g., the SARS-CoV-2 spike protein immunogen (or immunogenic fragment and / or immunogenic variant thereof)), the conjugate, the fusion protein, the carrier, the composition, the vaccine composition, or the pharmaceutical composition is administered as a boost in a heterologous prime-boost regimen.
206. The nucleic acid molecule of any one of claims 1-66 or 176, the protein (e.g., the SARS- CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 93-152 or 177, the vector of any one of claims 67-68, the conjugate of claim 69 or 154, the fusion protein of claim 153, the host cell of claim 193, the composition of any one of claims 70-92 or 155-175, the vaccine composition of any one of claims 183-189, the carrier of any one of claims 178-182, or the pharmaceutical composition of any one of claims 190-191 for use in inducing or enhancing an immune response in a subject in need thereof; preventing, ameliorating, or treating a SARS-CoV-2 infection in a subject in need thereof; or vaccinating a subject against SARS-CoV-2.
207. Use of the nucleic acid molecule of any one of claims 1-66 or 176, the protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 93-152 or 177, the vector of any one of claims 67-68, the conjugate of claim 69 or 154, the fusion protein of claim 153, the host cell of claim 193, the composition of any one of claims 70-92 or 155-175, the vaccine composition of any one of claims 183-189, the carrier of any one of claims 178-182, or the pharmaceutical composition of any one of claims 190-191 for the manufacture of a medicament.
208. Use of the nucleic acid molecule of any one of claims 1-66 or 176, the protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 93-152 or 177, the vector of any one of claims 67-68, the conjugate of claim 69 or 154, the fusion protein of claim 153, the host cell of claim 193, the composition of any one of claims 70-92 or 155-175, the vaccine composition of any one ofclaims 183-189, the carrier of any one of claims 178-182, or the pharmaceutical composition of any one of claims 190-191 for the manufacture of a medicament for the induction or enhancement of an immune response in a subject in need thereof; the prevention, amelioration, or treatment a SARS-CoV-2 infection in a subject in need thereof; or the vaccination a subject against SARS-CoV-2.
208. A nucleic acid molecule of any one of claims 1-66 or 176, a protein (e.g., a SARS-CoV-2 spike protein immunogen (or a immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 93-152 or 177, a vector of any one of claims 67-68, a conjugate of claim 69 or 154, a fusion protein of claim 153, a host cell of claim 193, a composition of any one of claims 70-92 or 155-175, a vaccine composition of any one of claims 183-189, a carrier of any one of claims 178-182, or a pharmaceutical composition of any one of claims 190-191 for use in a method of the inducing or enhancing an immune response in a subject in need thereof; the prevention, amelioration, or treatment a SARS-CoV-2 infection in a subject in need thereof; or the vaccination a subject against SARS-CoV-2, the method comprising administering to the subject in need thereof the nucleic acid molecule of any one of claims 1-66 or 176, the protein (e.g., the SARS-CoV-2 spike protein immunogen (or the immunogenic fragment and / or immunogenic variant thereof)) of any one of claims 93-152 or 177, the vector of any one of claims 67-68, the conjugate of claim 69 or 154, the fusion protein of claim 153, the host cell of claim 193, the composition of any one of claims 70-92 or 155-175, the vaccine composition of any one of claims 183-189, the carrier of any one of claims 178-182, or the pharmaceutical composition of any one of claims 190-191.
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