Coronavirus and influenza immunogenic combinations
By using RNAs encoding coronavirus S polypeptide fragments and mutated HA polypeptides, the vaccine composition addresses reduced immune responses and adverse effects, achieving robust immunity against both viruses with minimized RNA dose.
Patent Information
- Authority / Receiving Office
- WO · WO
- Patent Type
- Applications
- Current Assignee / Owner
- BIONTECH SE
- Filing Date
- 2026-01-06
- Publication Date
- 2026-07-09
AI Technical Summary
Existing vaccines for SARS-CoV-2 and influenza often result in reduced immune responses when administered together, particularly against influenza type B HA polypeptides, and high RNA doses can cause adverse side effects.
Compositions comprising RNAs encoding a fragment of a coronavirus S polypeptide lacking the S2 domain and mutated HA polypeptides, along with RNAs encoding influenza HA polypeptides, to induce a robust immune response while minimizing RNA dose and adverse effects.
The solution produces improved immune responses against both coronavirus and influenza antigens with reduced adverse side effects, balancing immune induction and safety.
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Figure US2026010357_09072026_PF_FP_ABST
Abstract
Description
Attorney Docket No. 2013237-1556 (P2037W001)CORONAVI^S^NDJNFLUENZ^LlMMUNQfiEMICXQMBIHMIQHiRelated Applications
[0001] This application claims priority to and the benefit of U. S. Provisional Patent Application No. 63 / 742,396, filed on January 6, 2025, and U. S. Provisional Patent Application No. 63 / 754,538, filed February 5, 2025, the entire contents of which are hereby incorporated by reference in their entirety.Background
[0002] SARS-CoV-2 and influenza virus often cocirculate, with a tendency to have a main peak in winter. Both viruses are associated with increases in deaths relating to respiratory and systemic diseases. Vaccination is an important measure providing protection against infection and complications of COVID-19 and influenza, particularly in populations at higher risk of severe disease. Subject to continuing antigenic drifts or shifts of both viruses, annual vaccination is recommended with tailored vaccines targeting circulating strains. Vaccination programs for SARS-CoV-2 are likely to run concurrently with annual influenza vaccination campaigns.Summary
[0003] The present disclosure, among other things, describes new RNA technologies (e.g., compositions and methods) that can be used to induce an immune response against a coronavirus (including a SARS-CoV-2 virus) and one or more influenza viruses. Compositions comprising one or more RNAs encoding a coronavirus antigen and one or more RNAs encoding an influenza antigen provide certain advantages, for example, as compared to compositions that comprise only one or more RNAs encoding a coronavirus antigen or one or more RNAs encoding an influenza antigen. These advantages include, among others, requiring few injections, which can provide for, e.g., improved convenience and improved vaccination rates against influenza and coronavirus. Given the prevalence of influenza and coronavirus, even small improvements in vaccination rates can result in thousands of deaths being prevented on a yearly basis.
[0004] As demonstrated by data described in the present disclosure, co-administering one or more RNAs encoding a full length coronavirus S polypeptide and one or more RNAs encoding a wild-type influenza hemagglutinin (HA) polypeptide, while inducing a robust immune response against all encoded influenza virus and coronavirus antigens, can result in a reduced immune response against the one or more encoded HA polypeptides as compared to when the one or more RNAs encoding an HA polypeptide are administered without one or more RNAs encoding a coronavirus S polypeptide. Clinical trials have also observed a reduced immune response against an influenza type B HA polypeptide when administered as a trivalent influenza virus and co-administered with an RNA encoding a full length SARS-CoV-2 S polypeptide as compared to the trivalent influenza vaccine administered without the one or more RNAs encoding a full length coronavirus S polypeptide. See Pfizer Inc. Pfizer and BioNTech Provide Update on mRNA-based Combination Vaccine Program Against Influenza and COVID- 19 in Individuals 18-64 Years of Age [press release]. Available from: pfizer.com / news / press-release / press-release-detail / pfizer-and-biontech-provide-update- mma-based-combination. Published: 16 AUG 2024. Among other things, the present disclosure provides certain insights that can be used to mitigate this reduced immune response. In particular, examples of insights provided by the present disclosure include:Page 1 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)• Co-administration of an RNA encoding a fragment of a coronavirus lacking an S2 domain with one or more RNAs encoding an HA polypeptide can produce an Improved immune response against the one or more HA polypeptides as compared to co-administering an RNA encoding a full length coronavirus S polypeptide; and * Co-administration of one or more RNAs encoding an HA polypeptide with a mutated HA cleavage site can produce an improved immune response against the HA polypeptide as compared to co-administering a wild type HA polypeptide in combination with a coronavirus S polypeptide or a fragment of a coronavirus S polypeptide.
[0005] In light of insights described herein, the present disclosure provides compositions that can produce a robust immune response against multiple coronavirus and influenza antigens while minimizing RNA dose and / or administrations. Minimizing RNA dose can be useful, e.g., for mitigating any potential adverse side effects induced by a composition. Clinical trials have shown that administering high doses of RNA (e.g., 100 pg or more of total RNA) can result in certain adverse side effects, including, e.g., fever, muscle pain, headache, etc. When administering a single composition comprising a plurality of RNAs, each encoding a different disease antigen, it can become challenging to administer a sufficient dose of each RNA to induce a robust immune response against an encoded antigen, while keeping the total amount of RNA in the composition low enough to minimize potential adverse side effects. As demonstrated by the present disclosure, RNAs described herein can produce robust immune responses at surprisingly low doses of RNA. Alternatively or additionally, in some embodiments, dose amounts and / or regimens provided herein can balance induction of a robust immune response while minimizing dose, thus inducing a therapeutic response while minimizing any potential adverse side effects.
[0006] Among other things, the present disclosure provides A combination comprising: (a) an RNA encoding a hemagglutinin (HA) polypeptide of a first influenza virus or variant thereof; and (b) an RNA encoding a polypeptide comprising a fragment of a coronavirus S polypeptide or variant thereof.
[0007] in some embodiments, an HA polypeptide of a first influenza virus or variant thereof comprises one or more mutations at an HA cleavage site as compared to a respective wild-type HA polypeptide of the first influenza virus, and wherein the HA cleavage site is within a region of the HA polypeptide corresponding to amino acids 352- 382 of SEQ ID NO: 325.
[0008] In some embodiments, a combination further comprises an RNA encoding a polypeptide comprising a coronavirus S polypeptide or variant thereof.
[0009] In some embodiments, one or more mutations at an HA cleavage site comprise a deletion of three to ten amino acid residues as compared to a respective wild-type HA polypeptide of the first influenza virus.
[0010] In some embodiments, a coronavirus S polypeptide or variant thereof is a prefusion stabilized S polypeptide comprising at least two proline substitutions at positions corresponding to residues 986 and 987 of SEQ ID NO: 1. In some embodiments, a prefusion stabilized S polypeptide further comprises proline substitutions at positions corresponding to residues 817, 892, 899, and 942 of SEQ ID NO: 1.
[0911] In some embodiments, a coronavirus S polypeptide further comprises one or more mutations in a region corresponding to amino acids 682-685 of SEQ ID NO: 1.
[0012] In some embodiments, an RNA encoding the polypeptide comprising the coronavirus S polypeptide or variant thereof comprises (i) a nucleotide sequence according to SEQ ID NO: 286 or a sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 286, (ii) a nucleotide sequence Page 2 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)according to SEQ ID NO: 288 or a sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 288, and / or (iii) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence according to SEQ ID NO: 285 or an amino acid sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 285; (b) an RNA encoding the polypeptide comprising the coronavirus S polypeptide or variant thereof comprises (I) a nucleotide sequence according to SEQ ID NO: 291 or a sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 291, (II) a nucleotide sequence according to SEQ ID NO: 293 or a sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 293, and / or (Hi) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence according to SEQ ID NO: 290 or an amino acid sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 290; or (c) an RNA encoding the polypeptide comprising the coronavirus S polypeptide or variant thereof comprises (i) a nucleotide sequence according to SEQ ID NO: 296 or a sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 296, (ii) a nucleotide sequence according to SEQ ID NO: 298 or a sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 298, and / or (iii) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence according to SEQ ID NO: 295 or an amino acid sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 295.
[0013] In some embodiments, a fragment of a coronavirus S polypeptide or variant thereof comprises a receptor binding domain (RBD). In some embodiments, an RBD comprises: (a) an amino acid sequence corresponding to amino acids 319-528, 327-528, 328-528, 330-528, 319-530, 327-530, 328-530, 330-530, 319-531, 327-531, 328-531, 330-531, 319-537, 327-537, 328-537, 330-537, 330-537, 319-541, 327-541, 328-541, or 330-541 of SEQ ID NO: 1; (b) an amino acid sequence of a region of an S polypeptide of a SARS-CoV-2 variant that corresponds to amino acids 319-528, 327-528, 328-528, 330-528, 319-530, 327-530, 328-530, 330-530, 319-531, 327-531, 328-531, 330-531, 319-537, 327-537, 328-537, 330-537, 330-537, 319-541, 327-541, 328-541, or 330-541 of SEQ ID NO: 1; (c) an amino acid sequence according to SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 325, or SEQ ID NO: 326, or an amino acid sequence of a region of an S polypeptide of a SARS-CoV-2 variant that corresponds to any one of SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 325, or SEQ ID NO: 326; or (d) an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any one of the amino acid sequences recited in (a)-(c).Page 3 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)
[0014] In some embodiments, a fragment of a coronavirus S polypeptide or variant thereof comprises an N-Terminal Domain (NTD). In some embodiments, an NTD comprises: (a) an amino acid sequence corresponding to amino acids 1-209, 14-209, 15-209, 19-209, 20-209, 21-209, 1-305, 14-305, 15-305, 19-305, 20-305, 21-305, 1-311, 14-311, 15-311, 19-311, 20-311, 21-311, 1-318, 14-318, 15-318, 19-318, 20-318, 21-318, 1-302, 14-302, 15-302, 19-302, 20-302, or 21-302 of SEQ ID NO: 1; (b) an amino acid sequence of a region of an S polypeptide of a SARS- CoV-2 variant that corresponds to amino acids 1-209, 14-209, 15-209, 19-209, 20-209, 21-209, 1-305, 14-305, 15- 305, 19-305, 20-305, 21-305, 1-311, 14-311, 15-311, 19-311, 20-311, 21-311, 1-318, 14-318, 15-318, 19-318, 20-318, 21-318, 1-302, 14-302, 15-302, 19-302, 20-302, or 21-302 of SEQ ID NO: 1; or (c) an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any one of the amino acid sequences recited in (a)-(b).
[0015] In some embodiments, a fragment of the coronavirus S polypeptide or variant thereof comprises a fragment of an SI polypeptide comprising: (a) an amino acid sequence corresponding to amino acids 1-528, 14-528, 15-528, 19-528, 20-528, 21-528, 1-530, 14-530, 15-530, 19-530, 20-530, 21-530, 1-531, 14-531, 15-531, 19-531, 20-531, 21-531, 1-537, 14-537, 15-537, 19-537, 20-537, 21-537, 1-541, 14-541, 15-541, 19-541, 20-541, or 21-541 of SEQ ID NO: 1; (b) an amino acid sequence of QCVMPLFNLmTQSYTNSFTRGVYYPDKVFRSSVLHLTQDLFLPFFSNVTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIR GWIFGTTLDSKTQSLUVNNATNVFIKVCEFQFCNDPFILDVYHKNNKSWMESESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNL REFVFKNIDGYFKIYSKHTPnGRDFPQGFSALEPLVDLPIGINITRFQTLLALNRSYLTPGDSSSGWTAGAADYYVGYLQPRTFLLKYN ENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNVTNLCPFHEVFNATTTASVYAWNRTRISNCVADYSVL YNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIKGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKHSGNYDYWYRS LRKSKLKPFERDISTEIYQAGNKPCKGKGPNCYFPLQSYGFRFTYGVGHQPYRWVLSFELLHAPATVCGPK (SEQ ID NO: 20); (c) an amino acid sequence ofQCVNIJTRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDI-FLPFFSNVTWFHAIHVSGTNGrTKRFDNPALPFNDGVYFASTEKSNIIRG WIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYQKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKEGNFKNLRE FVFKNIDGYFKIYSKHTPINLERDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPVDSSSGWTAGAAAYYVGYLQPRTFLLKYNE NGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSN FRVQPTESIVRFPNITN LCPFH EVFNATTFASVYAWN RKRISNCVADYSVIYN FAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKPSGNYNYLYRLFRK SKLKPFERDISTEIYQAGNKPCNGVAGPNCYSPLQSYGFRPTYGVGHQPYRVWLSFELLHAPATVCGPK (SEQ ID NO: 21); (d) an amino acid sequence of a region of an S polypeptide of a SARS-CoV-2 variant that corresponds to any one of the amino acid sequences recited in (a)-(c); or (e)an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any one of the amino acid sequences recited in (a)-(d).
[0016] In some embodiments, a polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises a secretory signal peptide, wherein the secretory signal peptide is at the N-terminus of the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof. In some embodiments, a secretory signal peptide is a secretory signal peptide of a coronavirus S polypeptide or a heterologous secretory signal peptide. In some embodiments, a secretory signal peptide is a SARS-CoV-2 S polypeptide secretory signal peptide comprising: (a) an amino acid sequence corresponding to amino acids 1-13 of SEQ ID NO: 1; (b) an amino Page 4 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)acid sequence corresponding to amino acids 1-16 of SEQ ID NO: 1; (c) an amino acid sequence corresponding to amino acids 1-19 of SEQ ID NO: 1; or (d) an amino acid sequence of a region of an S polypeptide of a SARS-CoV-2 variant corresponding to any one of the amino acid sequences recited in (a)-(c).
[0017] In some embodiments, a secretory signal peptide is an HSV-1 gD protein secretory signal polypeptide comprising an amino acid sequence of MGGAAARLGAVILFVVIVGLHGVRG (SEQ ID NO: 27) or an amino acid sequence having 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more amino acid alterations relative to SEQ ID NO: 27.
[0018] In some embodiments, a polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises a transmembrane region, wherein the transmembrane region is at the C-terminus of the fragment of the coronavirus S polypeptide or variant thereof. In some embodiments, a transmembrane region is a SARS-CoV-2 S polypeptide transmembrane region. In some embodiments, a transmembrane region comprises: (a) an amino acid sequence of EQYIKWPWYIWLGFIAGLIAIVMVnMLCCMTSCCSCLKGCCSCGSCC (SEQ ID NO: 90), or an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 90; (b) an amino acid sequence of EQYIKWPWYIWLGFIAGUAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT (SEQ ID NO: 89), or an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 89; (c) an amino acid sequence corresponding to amino acids 1200-1254 or 1200-1273 of SEQ ID NO: 1, an amino acid sequence of a region of a S polypeptide of a SARS-CoV-2 variant that corresponds to amino acids 1200-1254 or 1200-1273 of SEQ ID NO: 1, or an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to amino acids 1200-1254 or 1200-1273 of SEQ ID NO: 1; (d) an amino acid sequence corresponding to amino acids 1206-1254 or 1206-1273 of SEQ ID NO: 1, an amino acid sequence of a region of a S polypeptide of a SARS-CoV-2 variant that corresponds to amino acids 1206-1254 or 1206-1273 of SEQ ID NO: 1, or an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to amino acids 1206-1254 or 1206-1273 of SEQ ID NO: 1; (e) an amino add sequence corresponding to amino acids 1211-1254 or 1211-1273 of SEQ ID NO: 1, an amino acid sequence of a region of a S polypeptide of a SARS-CoV-2 variant that corresponds to amino acids 1211-1254 or 1211-1273 of SEQ ID NO: 1, or an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to amino acids 1211-1254 or 1211-1273 of SEQ ID NO: 1; or (f) an amino acid sequence corresponding to amino acids 1207-1254 or 1207-1273 of SEQ ID NO: 1, an amino acid sequence of a region of a S polypeptide of a SARS-CoV-2 variant that corresponds to amino acids 1207-1254 or 1207-1273 of SEQ ID NO: 1, or an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to amino acids 1207-1254 or 1207-1273 of SEQ ID NO: 1.
[0019] In some embodiments, a polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises, from N-terminus to C-terminus: a) a secretory signal peptide of a SARS-CoV-2 S Page 5 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)polypeptide comprising an amino acid sequence corresponding to amino acids 1-13, 1-16, or 1-19 of SEQ ID NO: 1, or an amino acid sequence of a region of an S polypeptide of a SARS-CoV-2 variant corresponding to amino acids 1-13, 1-16, or 1-19 of SEQ ID NO: 1; (b) a fragment of an SI polypeptide comprising an amino acid sequence corresponding to amino acids 1-537 of SEQ ID NO: 1, or an amino acid sequence of a region of an S polypeptide of a SARS-CoV-2 variant corresponding to amino acids 1-537 of SEQ ID NO: 1; and (c) a transmembrane region of an S polypeptide of a SARS-CoV-2 virus comprising an amino acid sequence according to SEQ ID NO: 183, SEQ ID NO: 193, SEQ ID NO: 351, SEQ ID NO: 352, or SEQ ID NO: 353, or an amino acid sequence of a region of an S polypeptide of a SARS-CoV-2 variant that corresponds to SEQ ID NO: 183, SEQ ID NO: 193, SEQ ID NO: 351, SEQ ID NO: 352, or SEQ ID NO: 353.
[0020] In some embodiments, a fragment of the SI polypeptide and the transmembrane region are connected to one another by a linker. In some embodiments, a polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises, from N-terminus to C-terminus: (a) a secretory signal peptide of an HSV-1 gD protein; (b) a fragment of an SI polypeptide comprising an amino acid sequence corresponding to amino acids 14-528 of SEQ ID NO: 1, or an amino acid sequence of a region of an S polypeptide of a SARS-CoV-2 variant that corresponds to amino acids 14-528 of SEQ ID NO; 1; and (c) a transmembrane region of an S polypeptide of a SARS-CoV-2 virus comprising an amino acid sequence according to SEQ ID NO: 183, SEQ ID NO: 193, SEQ ID NO: 351, SEQ ID NO: 352, or SEQ ID NO: 353, or an amino acid sequence of a region of an S polypeptide of a SARS-CoV-2 variant that corresponds to SEQ ID NO: 183, SEQ ID NO: 193, SEQ ID NO: 351, SEQ ID NO: 352, or SEQ ID NO: 353.
[0021] In some embodiments, a secretory signal peptide and the fragment of the SI polypeptide; and / or a fragment of the SI poiypeptide and the transmembrane region are connected to one another by a linker.
[0022] In some embodiments, a poiypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises one or more mutations characteristic of a SARS-CoV-2 Omicron variant, a SARS-CoV-2 XBB.1.5 variant, a SARS-CoV-2 JN.l variant, a SARS-CoV-2 KP.2 variant, a SARS-CoV-2 XEC variant, a SARS-CoV-2 XBB1.5 variant, a SARS-CoV-2 MC.l variant, a SARS-CoV-2 KP.3.1.1 variant, or a SARS-CoV-2 LP.8.1 variant.
[0023] In some embodiments, an RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises (i) a nucleotide sequence according to SEQ ID NO: 301 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 301; (ii) a nucleotide sequence according to SEQ ID NO: 303 or a sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 303; and / or (iii) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence according to SEQ ID NO: 300 or an amino acid sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 300.
[0024] In some embodiments, an RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises (i) a nucleotide sequence according to SEQ ID NO: 306 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at ieast 99% identical to SEQ ID NO: 306; (ii)Page 6 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)a nucleotide sequence according to SEQ ID NO: 308 or a sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 308; and / or (iii) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence according to SEQ ID NO: 305 or an amino acid sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 305.
[0025] In some embodiments, an RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises (I) a nucleotide sequence according to SEQ ID NO: 311 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 311; (ii) a nucleotide sequence according to SEQ ID NO: 313 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 313; and / or (iii) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence according to SEQ ID NO: 310 or an amino acid sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 310.
[0026] In some embodiments, an RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises (i) a nucleotide sequence according to SEQ ID NO: 316 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 316; (ii) a nucleotide sequence according to SEQ ID NO: 318 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 318; and / or (iii) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence according to SEQ ID NO: 315 or an amino acid sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 315.
[0027] In some embodiments, (a) an RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises (I) a nucleotide sequence according to SEQ ID NO: 813 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 813, (Ii) a nucleotide sequence according to SEQ ID NO: 815 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 815, and / or (iii) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence according to SEQ ID NO: 812, or an amino acid sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 812; (b) an RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises (i) a nucleotide sequence according to SEQ ID NO: 721 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least Page 7 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 721, (ii) a nucleotide sequence according to SEQ ID NO: 723 or a nucleotide sequence that is at least 70%, at ieast 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 723, and / or (iii) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence according to SEQ ID NO: 817, or an amino acid sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 817; (c) an RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises (I) a nucleotide sequence according to SEQ ID NO: 362 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 362, (ii) a nucleotide sequence according to SEQ ID NO: 364 or a nucleotide sequence that is at least 70%, at least 80%, at ieast 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 364, and / or (iii) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence according to SEQ ID NO: 817, or an amino acid sequence that is at least 70%, at least 80%, at ieast 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 817; (d) an RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises (i) a nucleotide sequence according to SEQ ID NO: 803 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 803, (ii) a nucleotide sequence according to SEQ ID NO: 805 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 805, and / or (iii) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence according to SEQ ID NO: 802, or an amino acid sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 802; (e) an RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises (I) a nucleotide sequence according to SEQ ID NO: 808 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at ieast 99% identical to SEQ ID NO: 808, (ii) a nucleotide sequence according to SEQ ID NO: 810 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 810, and / or (iii) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence according to SEQ ID NO: 807, or an amino acid sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at ieast 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 807; or (f) an RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises (I) a nucleotide sequence according to SEQ ID NO: 819 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at ieast 97%, at least 98%, or at least 99% identical to SEQ ID Page 8 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)NO: 819, (ii) a nucleotide sequence according to SEQ ID NO: 820 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 820, and / or (ill) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence according to SEQ ID NO: 818, or an amino acid sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 818.
[0028] In some embodiments, a first influenza virus or variant thereof is predicted by a health authority and / or based on human serology data from the Northern and / or Southern hemisphere to circulate during a flu season. In some embodiments, a first influenza virus or variant thereof is an H1N1, H1N2, H2N2, H3N1, H3N2, H3N8, H5N1, H5N2, H5N3, H5N8, H5N9, H7N1, H7N2, H7N3, H7N4, H7N7, H7N9, H9N2, H10N7, or H10N8 type A influenza virus. In some embodiments, a first influenza virus or variant thereof is an A / Wisconsin / 588 / 2019 H1N1 virus, and wherein the HA polypeptide comprises an amino acid sequence according to SEQ ID NO: 331, or an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 331.
[0029] In some embodiments, an RNA encoding the HA polypeptide of A / Wisconsin / 588 / 2019 comprises a nucleotide sequence according to SEQ ID NO: 333 or SEQ ID NO: 335, or a nucleotide sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 333 or SEQ ID NO: 335.
[0030] In some embodiments, a first influenza virus is: (a) an A / Cambodia / e0826360 / 2020 H3N2 virus, and wherein the HA polypeptide comprises an amino acid sequence according to SEQ ID NO: 336, or an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 336; or (b) an A / Darwln / 6 / 2021 H3N2 virus, and wherein the HA polypeptide comprises an amino acid sequence according to SEQ ID NO: 320 or an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 320.
[0031] In some embodiments, (a) an RNA encoding the HA polypeptide of A / Cambodia / e0826360 / 2020 H3N2 comprises a nucleotide sequence according to SEQ ID NO: 338 or SEQ ID NO: 337 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 338 or SEQ ID NO: 337; or (b) an RNA encoding the HA polypeptide of A / Darwin / 6 / 2021 comprises a nucleotide sequence according to SEQ ID NO: 322 or SEQ ID NO: 324 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 322 or SEQ ID NO: 324.
[0032] In some embodiments, an first influenza virus or variant thereof is: (a) a B / Washington / 02 / 2019 virus, and wherein the HA polypeptide comprises an amino acid sequence according to SEQ ID NO: 341 or an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 341; (b) a B / Austria / 1359417 / 2021 virus, and wherein the HA polypeptide comprises an amino acid sequence Page 9 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)according to SEQ ID NO: 325, or an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 325; or (c) a B / Phuket / 3073 / 2013 virus, and wherein the HA polypeptide comprises an amino acid sequence according to SEQ ID NO: 346, or an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 346.
[0033] In some embodiments, (a) an RNA encoding the HA polypeptide of B / Washington / 02 / 2019 comprises a nucleotide sequence according to SEQ ID NO: 343 or SEQ ID NO: 345, or a nucleotide sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 343 or SEQ ID NO: 345; (b) an RNA encoding the HA polypeptide of B / Austria / 1359417 / 2021 comprises a nucleotide sequence according to SEQ ID NO: 327 or SEQ ID NO: 329, or a nucleotide sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 327 or SEQ ID NO: 329; or (c) an RNA encoding the HA polypeptide of B / Phuket / 3073 / 2013 comprises a nucleotide sequence according to SEQ ID NO: 348 or SEQ ID NO: 350, or a nucleotide sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 348 or SEQ ID NO: 350.
[0034] In some embodiments, a first influenza virus or variant thereof is a B / Austria / 1359417 / 2021 virus, and wherein the HA polypeptide comprises an amino acid sequence according to SEQ ID NO: 330 or an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 330, and comprises one or more mutations at an HA cleavage site within the region of the HA polypeptide corresponding to amino acids 352-382 of SEQ ID NO: 325.
[0035] In some embodiments, a combination further comprises an RNA encoding an HA polypeptide of a second influenza virus or variant thereof, wherein: (a) a first influenza virus or variant thereof is a type A influenza virus and the second influenza virus or variant thereof is a type B influenza virus; (b) a first influenza virus or variant thereof is a type A influenza virus and the second influenza virus or variant thereof is a type A influenza virus; (c) a first influenza virus or variant thereof is a type B influenza virus and the second influenza virus influenza virus or variant thereof is a type A influenza virus; or (d) a first influenza virus or variant thereof is a type B influenza virus and the second influenza virus or variant thereof is a type B influenza virus.
[0036] In some embodiments, a ratio of the amount of RNA encoding the HA polypeptide of the first influenza virus or variant thereof to the amount of RNA encoding the HA polypeptide of the second influenza virus or variant thereof is 1:1, 1:2, 1:3, 1:4, or 1:5. In some embodiments, a combination further comprises an RNA encoding an HA polypeptide of a third influenza virus or variant thereof, wherein: (a) a first influenza virus or variant thereof is a type A influenza virus, the second influenza virus or variant thereof is a type A influenza virus, and the third influenza virus or variant thereof is a type A influenza virus; (b) a first influenza virus or variant thereof is a type A influenza virus, the second influenza virus or variant thereof is a type A influenza virus, and the third influenza virus or variant thereof Is a type B influenza virus; (c) a first influenza virus or variant thereof is a type A influenza virus, the second Page 10 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)influenza virus or variant thereof is a type B influenza virus, and the third influenza virus or variant thereof is a type B influenza virus; (d) a first influenza virus or variant thereof is a type B influenza virus, the second influenza virus or variant thereof is a type A influenza virus, and the third influenza virus or variant thereof is a type A influenza virus; (e) a first influenza virus or variant thereof is a type B influenza virus, the second influenza virus or variant thereof is a type A influenza virus, and the third influenza virus or variant thereof is a type A influenza virus; or (f) a first influenza virus or variant thereof is a type B influenza virus, the second influenza virus or variant thereof is a type A influenza virus, and the third influenza virus or variant thereof is a type B influenza virus.
[0037] In some embodiments, a ratio of the amount of RNA encoding the HA polypeptide of the first influenza virus or variant thereof to the amount of RNA encoding the HA polypeptide of the second influenza virus or variant thereof to the amount of RNA encoding the HA polypeptide of the third influenza virus or variant thereof is 1:1:1, 2:1:1, 3:1:1, 4:1:1, or 5:l:l.
[0038] In some embodiments, a combination further comprises an RNA encoding an HA polypeptide of a fourth influenza virus or variant thereof, wherein: (a) a first influenza virus or variant thereof is a type A influenza virus, the second influenza virus or variant thereof is a type A influenza virus, the third influenza virus or variant thereof is a type A influenza virus, and the fourth influenza virus or variant thereof is a type A influenza virus; (b) a first influenza virus or variant thereof is a type A influenza virus, the second influenza virus or variant thereof is a type A influenza virus, the third influenza virus or variant thereof is a type A influenza virus, and the fourth influenza virus or variant thereof is a type B influenza virus; (c) a first influenza virus or variant thereof is a type A influenza virus, the second influenza virus or variant thereof is a type A influenza virus, the third influenza virus or variant thereof is a type A influenza virus, and the fourth influenza virus or variant thereof is a type B influenza virus; (d) a first influenza virus or variant thereof is a type A influenza virus, the second influenza virus or variant thereof is a type B influenza virus, the third influenza virus or variant thereof is a type A influenza virus, and the fourth influenza virus or variant thereof is a type B influenza virus; (e) a first influenza virus or variant thereof is a type B influenza virus, the second influenza virus or variant thereof is a type B influenza virus, the third Influenza virus or variant thereof is a type B influenza virus, and the fourth influenza virus or variant thereof is a type B influenza virus; (f) a first influenza virus or variant thereof is a type B influenza virus, the second influenza virus or variant thereof is a type B influenza virus, the third influenza virus or variant thereof is a type B influenza virus, and the fourth influenza virus or variant thereof is a type B influenza virus; (g) a first influenza virus or variant thereof is a type B influenza virus, the second influenza virus or variant thereof is a type B influenza virus, the third influenza virus or variant thereof is a type A influenza virus, and the fourth influenza virus or variant thereof is a type A influenza virus; or (h) a first influenza virus or variant thereof is a type B influenza virus, the second influenza virus or variant thereof is a type A influenza virus, the third influenza virus or variant thereof is a type A influenza virus, and the fourth influenza virus or variant thereof is a type A influenza virus.
[0039] In some embodiments, a ratio of the amount of RNA encoding the HA polypeptide of the first influenza virus or variant thereof to the amount of RNA encoding the HA polypeptide of the second influenza virus or variant thereof to the amount of RNA encoding the HA polypeptide of the third influenza virus or variant thereof to the amount of RNA encoding the HA polypeptide of the fourth influenza virus or variant thereof is 1: 1: 1: 1, 2: 1: 1: 1, 3:1:1:1, 4:1:1:1, 5:1:1:1, 2:2:1:1, 3:3:1:1, 4:4:1:1, or 5:5:l:l.Page 11 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)
[0040] In some embodiments, (a) a totai amount of RNA encoding an HA polypeptide of an influenza type A virus is equal to the total amount of RNA encoding an HA polypeptide of an influenza type B virus; or (b) a total amount of RNA encoding an HA poiypeptide of an influenza type B virus is 2, 3, 4, or 5 times greater than the total amount of RNA encoding an HA polypeptide of an influenza type A virus.
[0041] In some embodiments, each RNA comprises a 5' cap, a cap proximal sequence, a 5' UTR sequence, a 3' UTR sequence, and a poly(A) sequence. In some embodiments, each RNA in the combination comprises a single modified uridine in place of each uridine, wherein the modified uridine is Nl-methyl-pseudouridine.
[0042] In some embodiments, the present disclosure provides a composition comprising a combination described herein and where each RNA is formulated in a nanoparticle.
[0043] In some embodiments, (a)an RNA encoding the HA polypeptide of the first influenza virus or variant thereof, the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof, and, if present, the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and the RNA encoding the HA poiypeptide of the fourth influenza virus or variant thereof are each formulated in separate nanoparticles; (b) an RNA encoding the HA polypeptide of the first influenza virus or variant thereof, the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof, and, if present, the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and the RNA encoding the HA polypeptide of the fourth influenza virus are co¬ formulated or variant thereof; or (c) an RNA encoding the fragment of the coronavirus S polypeptide or variant thereof is formulated in a first nanoparticle, and the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, and, if present the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, the RNA encoding the HA poiypeptide of the third influenza virus or variant thereof, and the RNA encoding the HA polypeptide of the fourth influenza virus or variant thereof are co-formulated in a second nanoparticle.
[0044] In some embodiments, a nanoparticle is a lipid nanoparticle (LNP), a polyplex (PLX), a lipidated polyplex (LPLX), a liposome, or a polysaccharide nanoparticle. In some embodiments, a nanopartide is an LNP comprising a cation ically ionizabie iipid, a sterol, a neutral lipid, and a polymer-conjugated lipid. In some embodiments, a polymer-conjugated lipid comprises a PEG-conjugated iipid. In some embodiments, each RNA is encapsulated in an LNP, and wherein the LNP comprises molar ratios of 20-60% ionizable cationic lipid, 5-25% neutral lipid, 25-55% sterol, and 0.5-15% PEG-modified lipid. In some embodiments, each nanoparticle has an average diameter of about 50-150 nm.
[0045] In some embodiments, a composition comprises a cryoprotectant.
[0046] In some embodiments, a composition comprises one or more of Tris base, Tris HCI, NaCI, KCI, Na2HPC, and KH2PO4. n some embodiments, a composition comprises about 10 mM Tris buffer, about 10% sucrose, about 0.1 mg / mL total RNA, and a pH of about 7,4,
[0047] In some embodiments, a composition is formulated to provide one or more unit doses, wherein each unit dose comprises 100 pg or less or 90 pg or less of total RNA. In some embodiments, a composition is formulated to provide one or more unit doses, wherein: (a) the total amount of RNA encoding the HA polypeptide of the first influenza virus or variant thereof in each unit dose is about 60 pg, about 45 pg, or about 30 pg; and / or the total amount of RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof Page 12 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)in each unit dose is about 30 g, about 25 pg, about 20 pg, about 15 pg, about 10 pg, about 6 pg, about 5 pg, about 3 pg, or about 1 pg; (b) the total amount of RNA encoding the HA polypeptide of the first Influenza virus or variant thereof in each unit dose is about 60 pg and the total amount of RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof in each unit dose is about 20 pg; (c) the total amount of RNA encoding the HA polypeptide of the first influenza virus or variant thereof in each unit dose is about 60 pg and the total amount of RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof in each unit dose is about 10 pg; (d) the total amount of RNA encoding the HA polypeptide of the first influenza virus or variant thereof in each unit dose is about 60 pg and the total amount of RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof in each unit dose is about 5 pg; (e) the total amount of RNA encoding the HA polypeptide of the first influenza virus or variant thereof in each unit dose is about 45 pg and the total amount of RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof in each unit dose is about 10 pg; (f) the total amount of RNA encoding the HA polypeptide of the first influenza virus or variant thereof in each unit dose is about 45 pg and the total amount of RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or a variant thereof in each unit dose is about 30 pg; or (g) the total amount of RNA encoding the HA polypeptide of the first influenza virus or variant thereof in each unit dose is about 30 pg and the total amount of RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof in each unit dose is about 10 pg.
[0048] In some embodiments, a composition is formulated to provide one or more unit doses, wherein each unit dose comprises: (a) about 20 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof and, if present, about 5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, and about 5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof; (b) about 30 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof and, if present, about 7.5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, and about 7.5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof; (c) about 40 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof and, if present, about 10 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, and about 10 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, wherein the first influenza virus or variant thereof is a type B influenza virus and, if present, the second influenza virus or variant thereof is a type A influenza virus, and the third influenza virus is a type A influenza virus.
[0049] In some embodiments, a composition is formulated to provide one or more unit doses, wherein each unit dose comprises: (a) about 7.5 pg of the RNA encoding the HA polypeptide of the first influenza virus and, if present, about 7.5 pg of the RNA encoding the HA polypeptide of the second influenza virus, about 7.5 pg of the RNA encoding the HA polypeptide of the third influenza virus, and about 7.5 pg of the RNA encoding the HA polypeptide of the fourth influenza virus; (b) about 11.25 pg of the RNA encoding the HA polypeptide of the first influenza virus and, if present, about 11.25 pg of the RNA encoding the HA polypeptide of the second influenza virus, about 11.25 pg of the RNA encoding the HA polypeptide of the third influenza virus, and about 11.25 pg of the RNA encoding the HA polypeptide of the fourth influenza virus; (c) about 2.5 pg of the RNA encoding the HA polypeptide of the first influenza virus and, if present, about 2.5 pg of the RNA encoding the HA polypeptide of the second Page 13 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)influenza virus, about 12.5 pg of the RNA encoding the HA polypeptide of the third influenza virus, and about 12.5 pg of the RNA encoding the HA poiypeptlde of the fourth influenza virus; (d) about 25 pg of the RNA encoding the HA polypeptide of the first influenza virus and, if present, about 25 pg of the RNA encoding the HA polypeptide of the second influenza virus, about 5 pg of the RNA encoding the HA polypeptide of the third influenza virus, and about 5 pg of the RNA encoding the HA polypeptide of the fourth influenza virus; (e) about 15 pg of the RNA encoding the HA polypeptide of the first influenza virus and, if present, about 15 pg of the RNA encoding the HA polypeptide of the second influenza virus, about 15 pg of the RNA encoding the HA polypeptide of the third influenza virus, and about 15 pg of the RNA encoding the HA polypeptide of the fourth influenza virus; wherein: (i) the first influenza virus is a type B influenza virus and, if present, the second influenza virus is a type B influenza virus, the third influenza virus is a type A influenza virus, and the fourth influenza virus is a type A influenza virus; or (ii) the first influenza virus is a type B influenza virus and, if present, the second influenza virus is a type A influenza virus, the third influenza virus is a type A influenza virus, and the fourth influenza virus is a type A influenza virus.
[0050] In some embodiments, a composition is formulated to provide one or more unit doses, wherein each unit dose comprises: (a) about 20 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 5 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof; (b) about 30 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 5 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof; (c) about 40 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 5 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof; (d) about 20 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 10 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof; (e) about 30 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 10 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof; (f) about 40 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 10 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof; (g) about 20 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 20 pg of the RNA encoding the Page 14 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof; (h) about 30 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 20 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof; (i) about 40 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 20 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof; (j) about 20 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 10 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof; (k) about 20 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 15 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof; (I) about 20 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 20 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof; (m) about 20 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 30 pg of the RNA encoding the polypeptide comprising the fragment of tiie coronavirus S polypeptide or variant thereof; (n) about 30 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 10 pg of the RNA encoding the polypeptide comprising the coronavirus S polypeptide or variant thereof; (o) about 30 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 15 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof; (p) about 30 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 20 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof; (q) about 30 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 30 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof; (r) about 40 pg of the RNA encoding the HA Page 15 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)polypeptide of the first influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 10 pg of the RNA encoding the polypeptide comprising the coronavirus S polypeptide or variant thereof; (s) about 40 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 15 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof; (t) about 40 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 20 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof; or (u) about 40 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 30 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof; wherein the first influenza virus is a type B influenza virus, the second influenza virus is a type A influenza virus, and the third influenza virus is a type A influenza virus.
[0051] In some embodiments, the present disclosure provides a pharmaceutical composition comprising (I) a combination as described herein, or a composition as described herein, and (ii) a pharmaceutically acceptable excipient. In some embodiments, a pharmaceutical composition is formulated as: (i) a multi-dose formulation in a vial, (ii) a single-dose formulation in a vial, or (iii) a prefilled syringe.
[0052] In some embodiments, the present disclosure provides a method of inducing an immune response against a coronavirus and an influenza virus in a subject comprising administering a combination as described herein a composition as described herein, or a pharmaceutical composition as described herein to the subject. In some embodiments, a subject is 18 to 64 years old. In some embodiments, a subject is 65 years or older. In some embodiments, a combination, composition, or pharmaceutical composition is administered in a volume of about 200 pL to about 300 pL. In some embodiments, a subject has previousiy been administered a composition that delivers a coronavirus antigen. In some embodiments, a method comprises administering a single dose of the combination, composition, or pharmaceutical composition to the subject. In some embodiments, a method comprises administering two or more doses of the combination, composition, or pharmaceutical composition to the subject, wherein the two doses are administered about 21 days apart; or wherein the subject has previousiy been administered (i) a composition that delivers a coronavirus antigen and an influenza antigen or (ii) a composition that delivers a coronavirus antigen and a composition that delivers an influenza antigen, and wherein the combination, composition, or pharmaceutical composition is administered about 21 days after the subject has been administered (i) or (ii).
[0053] In some embodiments, a method comprises administering three or more doses of the combination, composition, or pharmaceutical composition to the subject, wherein the first dose and the second dose are administered about 21 days apart and the third dose is administered at least about 2 months after the second dose; or wherein the subject has previously been administered two doses of (i) a composition that delivers a coronavirus antigen and an influenza antigen or (ii) a composition that delivers a coronavirus antigen and a composition that Page 16 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)delivers an influenza antigen wherein the combination, composition, or pharmaceutical composition is administered at least about 2 months after the subject has been administered (I) or (ii).
[0054] In some embodiments, a method further comprising administering one or more vaccines against a non¬ coronavirus and non-influenza disease, wherein the one or more vaccines comprise a vaccine against a respiratory virus. In some embodiments, a method results in induction of an immune response against a coronavirus and an influenza virus in the subject, wherein the immune response comprises production of antibodies and / or a T cell response directed against one or more coronaviruses and one or more influenza viruses.
[0055] In some embodiments, a method prevents or reduces the chance of a coronavirus and / or an influenza infection in the subject, prevents or mitigates deleterious symptoms associated with a coronavirus and / or an influenza infection in the subject, increases the likelihood of experiencing an asymptomatic coronavirus and / or influenza infection in the subject, and / or treats a coronavirus and / or influenza infection.Brief Description of the Drawing
[0056] Figs. 1A-1B show exemplary in vitro expression of influenza HA from RNA encoding wild-type or alternate B / Victoria HA ("altB," comprising a mutated HA cleavage site). LNP-formulated monovalent RNA (mIRV) encoding wild-type (wt) or altB HA from B / Austria / 1359417 / 2021 (B / Victoria) was transfected into (A) HEK293T cells and (B) primary human skeletal muscle cells. Fig. 1A shows exemplary protein expression in HEK293T cells was measured using a broadly reactive, prefusion conformation-specific anti-HA monoclonal antibody. Cells were labeled and the percentage of live cells expressing HA protein was enumerated using an image reader (Cytation 5 Cell Imaging Multimode Reader, BioTek). Expression was measured by quantifying the number of cells that had a positive signal for bound anti-HA antibody. Data shown is mean with standard deviation of duplicate measurements from one experiment. Fig. IB shows exemplary primary human skeletal muscle cells were lysed with a detergent solution and liquid chromatography-mass spectrometry proteomics analysis was performed, HA protein abundance relative to ~8,000 non-specific cellular proteins was measured. Data shown is mean with standard deviation of triplicate measurements from one experiment. " DP" refers to drug product.
[0057] Fig. 2 shows exemplary in vitro expression of influenza HA from RNA encoding wild-type or altB HA in a panel of B / Victoria lineage viruses. LNP-formulated monovalent RNA (mIRV) encoding wild-type (wt) or altB HA (comprising a mutated HA cleavage site) from B / Victoria lineage strains B / Brisbane / 60 / 2008, B / Colorado / 06 / 2017, B / Austria / 1359417 / 2021, B / Catalonia / 3514402NS / 2023, and B / Netherlands / 10335 / 2023 was transfected into HEK293T cells. Protein expression was measured using a broadly reactive, prefusion conformation-specific anti-HA monoclonal antibody. Cells were labeled and the percentage of live cells expressing HA protein was enumerated using an image reader (Cytation 5 Cell Imaging Multimode Reader, BioTek). Expression was measured by quantifying the mean fluorescence intensity (MFI) of cells that had a positive signal for bound anti-HA antibody. Data shown is the average MFI of duplicate measurements over a range of doses (0.19-200 ng) from one experiment.
[0058] Figs. 3A-3B show exemplary in vitro expression of SARS-CoV-2 S antigen encoded by RNA encoding a fragment of a SARS-CoV-2 S polypeptide (BNT162b8 or BNT162b9). HEK293T / 17 ceiis were transfected with LNP- formulated RNA encoding Omicron KP.2-adapted BNT162b8 (Fig. 3A) or BNT162b9 (Fig. 3B) encoding an NTD-RBD SI design or BNT162b2 encoding full length KP.2 S glycoprotein. S cell-surface expression was evaluated via flow cytometry analysis of ACE2 binding. Data shown is geometric mean fluorescence intensity (GMFI) with standard deviation of triplicate wells from one experiment out of three performed.Page 17 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)
[0059] Figs. 4A-4B show exemplary functional antibody and virus neutralization titers elicited by immunization of mice with monovaient influenza RNA vaccines encoding wild-type or alternate B / Victoria HA. Female BALB / c mice were immunized IM ~4 weeks apart (Days 0 and 27) with 0.2 pg of LNP-formulated monovalent RNA vaccine encoding wild-type (wt) or altB HA from B / Austria / 1359417 / 2021 (B, / Victoria). Functional antibody and virus neutralization titers against B / Austria / 1359417 / 2021 (B, / Victoria) were measured by HAI (Fig. 4A) and MNT (Fig.4B) assays, respectively, on Day 41 (2 weeks post-dose 2). All titers are reported as geometric mean titer (GMT) with 95% confidence interval. Each data point represents one animal. Statistical comparisons were performed using a two-sample t-test, * indicates pcO. Ol. LOD refers to limit of detection.
[0060] Figs. 5A-5B show exemplary functional antibody and virus neutralization titers elicited by immunization of mice with trivalent influenza RNA vaccines encoding wild-type or alternate B / Victoria HA. Female BALB / c mice were immunized IM 4 weeks apart (Days 0 and 28) with 1.2 pg of LNP-formulated trivalent RNA vaccine (comprising 0.2 pg H1N1, 0.2 pg H3N2, and 0.8 pg B / Victoria) encoding wild-type HA from A / Wisconsin / 67 / 2022 (H1N1) and A / Darwin / 6 / 2021 (H3N2), and either wild-type (wt) or altB HA from B / Austria / 1359417 / 2021 (B / Victoria). Functional antibody and virus neutralization titers against the vaccine strains were measured by HAI (Fig. 5A) and MNT (Fig.5B) assays, respectively, on Day 42 (2 weeks post-dose two). Ail titers are reported as geometric mean titer (GMT) with 95% confidence interval. Each data point represents one animal. Statistical comparisons were performed using two-way analysis of variance (ANOVA), * indicates pcO. Ol; ns refers to "not significant;" LOD refers to "limit of detection."
[0061] Fig. 6 shows exemplary SARS-CoV-2 (KP.2) pseudovirus neutralization titers elicited by immunization of COVID 19 vaccine-experienced mice with combination vaccines containing a trivalent influenza RNA vaccine encoding wild-type B / Victoria HA and BNT162b8 or BNT162b9 COVID- 19 RNA vaccine. Female BALB / c mice were immunized IM on Days 0 and 21 with BNT162b2 WT (0.5 pg), on Day 49 with BNT162b2 WT+BA.4 / 5 (0.5 pg) and on Day 95 with combination vaccines that contained 1.2 pg of LNP-formulated trivalent RNA vaccine (0.2 pg H1N1, 0.2 pg H3N2, and 0.8 pg B / Victoria) encoding wild-type HA from A / Wisconsln / 67 / 2022 (H1N1), A / Darwin / 6 / 2021 (H3N2), and B / Austria / 1359417 / 2021 (B / Victoria), and either BNT162b2 KP.2 (0.5 pg), BNT162b8 KP.2 (0.1 pg, 0.25 pg, or 0.5 pg) or BNT162b9 KP.2 (0.1 pg, 0.5 pg). Virus neutralization titers against the SARS-CoV-2 KP.2 lineage pseudovirus were measured by pVNT assay on Day 118 (~3 weeks post-boost). The number above each bar indicates the 50% neutralizing geometric mean titer (GMT) with 95% confidence interval of 10 mice per vaccine group. LOD refers to limit of detection.
[0062] Fig. 7 shows exemplary SARS-CoV-2 (KP.2) pseudovirus neutralization titers elicited by immunization of COVID 19 vaccine-experienced mice with combination vaccines containing a trivalent influenza RNA vaccine encoding alternate B / Victoria HA and BNT162b8 or BNT162b9 COVID- 19 RNA vaccine. Female BALB / c mice were immunized IM on Days 0 and 21 with BNT162b2 WT (0.5 pg), on Day 49 with BNT162b2 WT+BA.4 / 5 (0.5 pg) and on Day 95 with combination vaccines that contained 1.2 pg of LNP-formulated trivalent RNA vaccine (0.2 pg H1N1, 0.2 pg H3N2, 0.8 pg B / Victoria) encoding wild-type HA from A / Wisconsin / 67 / 2022 (H1N1) and A / Darwin / 6 / 2021 (H3N2), and alternate B (altB) HA from B / Austria / 1359417 / 2021 (B / Victoria), and either BNT162b2 KP.2 (0.5 pg), BNT162b8 KP.2 (0.1 pg, 0.25 pg, or 0.5 pg), or BNT162b9 KP.2 (0.1 pg, 0.5 pg). Virus neutralization titers against the SARS-CoV-2 KP.2 lineage pseudovirus were measured by pVNT assay on Day 118 (~3 weeks post-dose 4). The numberPage 18 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)above each bar indicates the 50% neutralizing geometric mean titer (GMT) with 95% confidence interval of 10 mice per vaccine group. LOD, limit of detection.
[0063] Figs. 8A-8C show exemplary Influenza virus neutralization titers elicited by immunization of COVID-19 vaccine-experienced mice with combination vaccines containing a trivalent influenza RNA vaccine encoding wild-type or alternate B / Victoria HA and BNT162b8 or BNT162b9 COVID-19 RNA vaccine. Female BALB / c mice were immunized IM on Days 0 and 21 with BNT162b2 WT (0.5 pg), on Day 49 with BNT162b2 WT+BA.4 / 5 (0.5 pg) and on Day 95 with combination vaccines that contained 1.2 pg of LNP-formulated trivalent influenza RNA vaccine (0.2 pg H1N1, 0.2 pg H3N2, 0.8 pg B / Victoria) encoding wild-type (wt) HA from A / Wisconsin / 67 / 2022 (H1N1) and A / Darwin / 6 / 2021 (H3N2), and wt or alternate B (altB) HA from B / Austria / 1359417 / 2021 (B / Victoria), and either BNT162b2 KP.2 (0.5 pg), BNT162b8 KP.2 (0.1 pg, 0.25 pg, or 0.5 pg), or BNT162b9 KP.2 (0.1 pg, 0.5 pg). Virus neutralization titers against B / Austria / 1359417 / 2021 (B / Victoria) (Fig. 8A), A / Wisconsin / 67 / 2022 (H1N1) (Fig. 88), and A / Darwin / 6 / 2021 (H3N2) (Fig.8C) were measured by MNT assay on Day 118 (~3 weeks post-dose 4). The number above each bar indicates the 50% neutralizing geometric mean titer (GMT) with 95% confidence interval of 10 mice per vaccine group. LOD, limit of detection.
[0064] Fig. 9 shows an exemplary schematic summarizing exemplary clinical trial protocol for testing the safety and efficacy of combinations described here.
[0065] Fig. 10 is an exemplary schematic of the various domains (RBD) of a coronavirus spike protein expressed in sequence with a trimerization domain, according to some aspects disclosed herein.
[0066] Fig. 11 is a schematic of the various domains (RBD, NTD) of a coronavirus spike protein expressed in sequence with a trimerization domain, as well as a transmembrane domain and C-terminal domain, according to some aspects disclosed herein.
[0067] Fig. 12 is a schematic of the various domains (RBD, NTD) of a coronavirus spike protein expressed in sequence with and without a trimerization domain, linked to a self-assembling protein domain, according to some aspects disclosed herein.
[0068] Fig. 13 shows the oligomeric state characterization using size-exclusion-chromatography for the secreted antigen constructs.
[0069] Fig. 14 is a schematic showing a method for altering a polynucleotide sequence to remove slippery sequences and / or out-of-frame start codons, according to an illustrative embodiment.
[0070] Fig. 15 is a block flow diagram showing a method for generating sequence-optimized polynucleotide sequences subject to one or more fidelity constraints, according to an illustrative embodiment.
[0071] Fig. 16 depicts a block flow diagram showing a method for generating sequence-optimized polynucleotide sequences subject to one or more fidelity constraints, according to an illustrative embodiment.
[0072] Figs. 17A-17C depict schematics of exemplary nucleotide sequences. Fig. 17A is a schematic showing a polynucleotide sequence (SEQ ID NO: 316) with slippery sequences and out-of-frame start codons identified (via colored highlight), according to an illustrative embodiment. Fig. 178 is a schematic showing a modified version of sequence SEQ ID NO: 722, in which an exemplary sequence has been altered to remove slippery sequences and out-of-frame start codons, according to an illustrative embodiment. Fig. 17C is a schematic showing a polynucleotide sequence (SEQ ID NO: 362), having been codon optimized using fidelity constraints to avoid slippery sequences and out-of-frame start codons, according to an illustrative embodiment.Page 19 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)
[0073] Figs. 18A-18D are graphs showing in-vitro-measured (via flow cytometry) SARS-CoV-2 antigen expression as a function of transfected RNA quantity, according to an illustrative embodiment.
[0074] Fig. 19 is a table summarizing proof of concept (POC) results for Cohort 1 vaccine groups.
[0075] Fig. 20 is a table summarizing signs of clinical activity (SOCA) results for Cohort 1 and Cohort 1A vaccine groups.
[0076] Figs. 21A-21B are tables summarizing demographic characteristics of Cohort 1 vaccine groups.
[0077] Fig. 22 is a graph of Cohort 1 vaccine group reports of local reactions ranked by maximum severity within 7 davs after study vaccine.
[0078] Fig. 23 is a graph of Cohort 1 vaccine group reports of systemic events ranked by maximum severity within 7 davs after study vaccine.
[0079] Fig. 24 is a table summarizing number of Cohort 1 vaccine group participants reporting adverse events through 1 month after vaccination.
[0080] Fig. 25 is a table summarizing geometic mean titers (GMTs) and geometric mean fold rises (GMFRs) of SARS-CoV-2 Omicron KP.2 neutralizing titers for Cohort 1 vaccine groups.
[0081] Fig. 26 is a table summarizing GMTs and GMFRs of strain-specific Hemagglutination Inhibition (HAI) celi-based titers for Cohort 1 vaccine groups before vaccination and 1 month after vaccination.
[0082] Figs. 27A-27B are tables summarizing proof of concept (POC) results for Cohort 1A vaccine groups.Fig. 27A shows POC results with influenza cell-based HAI. Fig. 27B shows POC results with influenza egg-based HAI.
[0083] Fig. 28 is a graph of Cohort 1A vaccine group reports of local reactions ranked by severity within 7 davs after vaccine.
[0084] Fig. 29 is a graph of Cohort 1A vaccine group reports of systemic events ranked by severity within 7 davs after vaccine.
[0085] Fig. 30 is a table summarizing number of Cohort 1A vaccine group participants reporting adverse events through 1 month after vaccination.
[0086] Fig. 31 is a table summarizing geometic mean titers (GMTs) and geometric mean fold rises (G Rs) of SARS-CoV-2 Omicron KP.2 neutralizing titers for Cohort 1A vaccine groups.
[0087] Figs. 32A-32B are table summarizing GMTs and GMFRs of strain-specific Hemagglutination Inhibition(HAI) titers for Cohort 1A vaccine groups, Fig. 32A is a table summarizing GMTs and G FRs of strain¬ specific Hemagglutination Inhibition (HAI) cell-based titers for Cohort 1A vaccine groups measured before vaccination and 1 month after vaccination. Fig. 32B is a table summarizing GMTs and GMFRs of strain-specific Hemagglutination Inhibition(HAI) egg-based titers for Cohort 1A vaccine groups measured before vaccination and 1 month after vaccination.
[0088] Figs. 33A-33D are tables summarizing proof of concept (POC) results for Cohort 2 vaccine groups.Fig. 33A summarizes POC results for cell-based HAI titers compared to an enhanced influenza vaccine (EIV;Fluzone® High-Dose). Fig. 33B summarizes POC results for egg-based HAI titers compared to an enhanced influenza vaccine (EIV; Fluzone® High-Dose). Fig. 33C summarizes proof of concept (POC) results for Cohort 2 vaccine groups. Fig 33D summarizes POC results for egg-based HAI titers compared to a standard-dose influenza vaccine (TIV2; Fluarix®),Page 20 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)
[0089] Fig. 34 is a graph of Cohort 2 vaccine group reports of locai reactions ranked by maximum severity within 7 davs after study vaccine.
[0090] Fig. 35 is a graph of Cohort 2 vaccine group reports of systemic events ranked by maximum severity within 7 davs after study vaccine.
[0091] Fig. 36 is a table summarizing number of Cohort 2 vaccine group participants reporting adverse events through 1 month after vaccination.
[0092] Fig. 37 is a table summarizing GMTs and GMFRs of SARS-CoV-2 Omicron KP.2 neutralizing titers for Cohort 2 vaccine groups.
[0093] Figs. 38A-38F are tables summarizing GMTs and GMFRs of strain-specific Hemagglutination Inhibition(HAI) cell-based titers for Cohort 2 vaccine groups before vaccination and 1 month after vaccination.
[0094] Fig. 39 is a table summarizing proof of concept (POC) results for Cohort 1, CohortlA, and Cohort 2 vaccine groups (cell-based HAI assay / SARS-CoV-2 neutralization assay).
[0095] Fig. 40 is a table summarizing proof of concept (POC) results for Cohort 1, CohortlA, and Cohort 2 vaccine groups (cell-based HAI assay / SARS-CoV-2 neutralization assay).
[0096] Figs. 41A-41B are tables summarizing proof of concept (POC) results for Cohort 3 vaccine groups with Influenza cell-based HAI versus EIV (Fluzone® HD) (Fig. 41A) and Influenza egg-based HAI versus EIV (Fluzone® HD) (Fig. 41B)
[0097] Fig.42 is a graph of Cohort 3 vaccine group reports of local reactions ranked by maximum severity within 7 davs after study vaccine.
[0098] Fig.43 is a graph of Cohort 3 vaccine group reports of systemic events ranked by maximum severity within 7 davs after study vaccine.
[0099] Fig. 44 is a table summarizing number of Cohort 3 vaccine group participants reporting adverse events through 1 month after vaccination.
[0100] Figs. 45A-45F are tables summarizing GMTs and GMFRs of strain-specific Hemagglutination Inhibition(HAI) cell-based titers for Cohort 2 vaccine groups before vaccination and 1 month after vaccination.
[0101] Fig. 46 is a table summarizing geometic mean titers (GMTs) and geometric mean fold rises (GMFRs) of SARS-CoV-2 Omicron KP.2 neutralizing titers for Cohort 3 vaccine groups before vaccination and 1 month after vaccination.Definitions
[0102] In general, terminology used herein is in accordance with its understood meaning in the art, unless clearly indicated otherwise. In order that the present invention may be more readily understood, certain terms are first defined below. Additional definitions for the following terms and other terms are set forth throughout the specification. Meanings of these and other terms in particular instances throughout this specification will be clear to those skilled in the art from context.
[0103] About The term "about", when used herein in reference to a value, refers to a value that is similar, in context to the referenced value. In general, those skilled in the art, familiar with the context, will appreciate the relevant degree of variance encompassed by "about" in that context. For example, in some embodiments, the term "about" may encompass a range of values that within 25%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, or less of the referred value.Page 21 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)
[0104] Agent. As used herein, the term "agent", may refer to a physical entity or phenomenon. In some embodiments, an agent may be characterized by a particular feature and / or effect. In some embodiments, an agent may be a compound, molecule, or entity of any chemical class inciuding, for example, a small molecule, polypeptide, nucleic acid, saccharide, lipid, metal, or a combination or complex thereof. In some embodiments, the term "agent" may refer to a compound, molecuie, or entity that comprises a polymer. In some embodiments, the term may refer to a compound or entity that comprises one or more polymeric moieties. In some embodiments, the term "agent" may refer to a compound, molecule, or entity that is substantially free of a particular polymer or polymeric moiety. In some embodiments, the term may refer to a compound, molecule, or entity that lacks or is substantially free of any polymer or polymeric moiety.
[0105] Amino acid: In its broadest sense, as used herein, the term "amino acid" refers to a compound and / or substance that can be, is, or has been incorporated into a polypeptide chain, e.g., through formation of one or more peptide bonds. In some embodiments, an amino acid has the general structure H2N-C(H)(R)-COOH. In some embodiments, an amino acid is a naturally occurring amino acid. In some embodiments, an amino acid is a non-natural amino acid; in some embodiments, an amino acid is a D-amino acid; in some embodiments, an amino acid is an L-amino acid. " Standard amino acid" refers to any of the twenty standard L-amino acids commonly found in naturally occurring peptides. " Nonstandard amino acid" refers to any amino acid, other than the standard amino acids, regardless of whettier it is prepared synthetically or obtained from a natural source. In some embodiments, an amino acid, including a carboxy- and / or amino-terminal amino acid in a polypeptide, can contain a structural modification as compared with the general structure above. For example, in some embodiments, an amino acid may be modified by methylation, amidation, acetylation, pegylation, glycosylation, phosphorylation, and / or substitution (e.g., of the amino group, the carboxylic acid group, one or more protons, and / or the hydroxyl group) as compared with the general structure. In some embodiments, such modification may, for example, alter the circulating half-life of a polypeptide containing the modified amino acid as compared with one containing an otherwise identical unmodified amino acid. In some embodiments, such modification does not significantly alter a relevant activity of a polypeptide containing the modified amino acid, as compared with one containing an otherwise identical unmodified amino acid. As will be clear from context, in some embodiments, the term "amino acid" may be used to refer to a free amino acid; in some embodiments it may be used to refer to an amino acid residue of a polypeptide.
[0106] Antibody agent. As used herein, the term "antibody agent" refers to an agent that specifically binds to a particular antigen. In some embodiments, the term encompasses a polypeptide or polypeptide complex that includes immunoglobulin structural elements sufficient to confer specific binding. For example, in some embodiments, an antibody agent is or comprises a polypeptide whose amino acid sequence includes one or more structural elements recognized by those skilled in the art as a complementarity determining region (CDR); in some embodiments an antibody agent is or comprises a polypeptide whose amino acid sequence includes at least one CDR (e.g., at least one heavy chain CDR and / or at least one light chain CDR) that is substantially identical to one found in a reference antibody. In some embodiments an included CDR is substantially identical to a reference CDR in that it is either identical in sequence or contains between 1-5 amino acid substitutions as compared with the reference CDR. In some embodiments an included CDR is substantially identical to a reference CDR in that it shows at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with the reference CDR. In some embodiments an included CDR is substantially identical to a reference CDR in that it Page 22 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)shows at least 96%, 96%, 97%, 98%, 99%, or 100% sequence identity with the reference CDR. In some embodiments an included CDR is substantially identical to a reference CDR in that at least one amino acid within the included CDR is deleted, added, or substituted as compared with the reference CDR but the included CDR has an amino acid sequence that is otherwise identical with that of the reference CDR. In some embodiments an included CDR is substantially identical to a reference CDR in that 1-5 amino acids within the included CDR are deleted, added, or substituted as compared with the reference CDR but the included CDR has an amino acid sequence that is otherwise identical to the reference CDR. In some embodiments an included CDR is substantially identical to a reference CDR in that at least one amino acid within the included CDR is substituted as compared with the reference CDR but the included CDR has an amino acid sequence that is otherwise identical with that of the reference CDR. In some embodiments an included CDR is substantially identical to a reference CDR in that 1-5 amino acids within the included CDR are deleted, added, or substituted as compared with the reference CDR but the included CDR has an amino acid sequence that is otherwise identical to the reference CDR. In some embodiments, an antibody agent is or comprises a polypeptide whose amino acid sequence includes structural elements recognized by those skilled in the art as an immunoglobulin variable domain. In some embodiments, an antibody agent in or comprises a polypeptide whose amino acid sequence includes structural elements recognized by those skilled in the art to correspond to CDRsl, 2, and 3 of an antibody variable domain; in some such embodiments, an antibody agent in or comprises a polypeptide or set of polypeptides whose amino acid sequence(s) together include structural elements recognized by those skilled in the art to correspond to both heavy chain and light chain variable region CDRs, e.g., heavy chain CDRs 1, 2, and / or 3 and light chain CDRs 1, 2, and / or 3. In some embodiments, an antibody agent is a polypeptide protein having a binding domain which is homologous or largely homologous to an immunoglobulin-binding domain. In some embodiments, an antibody agent may be or comprise a polyclonal antibody preparation. In some embodiments, an antibody agent may be or comprise a monoclonal antibody preparation. In some embodiments, an antibody agent may include one or more constant region sequences that are characteristic of a particular organism, such as a camel, human, mouse, primate, rabbit, rat; in many embodiments, an antibody agent may include one or more constant region sequences that are characteristic of a human. In some embodiments, an antibody agent may include one or more sequence elements that would be recognized by one skilled in the art as a humanized sequence, a primatized sequence, a chimeric sequence, etc. In some embodiments, an antibody agent may be a canonical antibody (e.g., may comprise two heavy chains and two light chains). In some embodiments, an antibody agent may be in a format selected from, but not limited to, intact IgA, IgG, IgE or IgM antibodies; bi- or multi- specific antibodies (e.g., Zybodies®, etc); antibody fragments such as Fab fragments, Fab' fragments, F(ab')2 fragments, Fd' fragments, Fd fragments, and isolated CDRs or sets thereof; single chain Fvs; polypeptide- Fc fusions; single domain antibodies (e.g., shark single domain antibodies such as IgNAR or fragments thereof); cameloid antibodies; masked antibodies (e.g., Probodies®); Small Modular ImmunoPharmaceuticals (" SMIPs™"); single chain or Tandem diabodies (TandAb®); VHHs; Anticalins®; Nanobodies® minibodies; BiTE®s; ankyrin repeat proteins or DARPINs®;Avimers®; DARTs; TCR-like antibodies;, Adnectins®; Affilins®; Trans-bodies®; Affibodies®; TrimerX®;MicroProteins; Fynomers®, Centyrins®; and KALBITOR®s. In some embodiments, an antibody may lack a covalent modification (e.g., attachment of a glycan) that it would have if produced naturally. In some embodiments, an antibody may contain a covalent modification (e.g., attachment of a glycan, a payload (e.g., a detectable moiety, a therapeutic moiety, a catalytic moiety, etc.), or other pendant group (e.g., poly-ethylene glycol, etc.)).Page 23 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)
[0107] Antigen-. Those skilled in the art, reading the present specification, will appreciate that the term "antigen" refers to a molecule that is recognized by the immune system, e.g., in some embodiments, the adaptive immune system, such that it elicits an antigen-specific immune response. In some embodiments, an antigen-specific immune response may be or comprise generation of antibodies and / or antigen-specific T ceils. In some embodiments, an antigen is a peptide or polypeptide that comprises at least one epitope against which an immune response can be generated. In one embodiment, an antigen is presented by cells of the immune system such as antigen presenting cells like dendritic ceils or macrophages. In some embodiments, an antigen or a processed product thereof such as a T-cell antigen is bound by a T- or B-cell receptor, or by an immunoglobulin molecule such as an antibody. Accordingly, an antigen or a processed product thereof may react specifically with antibodies or T lymphocytes (T cells). In one embodiment, an antigen is a parasitic antigen. In accordance with the present disclosure, in some embodiments, an antigen may be delivered by RNA molecules as described herein. In some embodiments, a peptide or polypeptide antigen can be 2-100 amino acids, including for example, 5 amino acids, 10 amino acids, 15 amino acids, 20 amino acids, 25 amino acids, 30 amino acids, 35 amino acids, 40 amino acids, 45 amino acids, or 50 amino acids in length. In some embodiments, a peptide or polypeptide antigen can be greater than 50 amino acids. In some embodiments, a peptide or polypeptide antigen can be greater than 100 amino acids. In some embodiments, an antigen is recognized by an immune effector cell. In some embodiments, an antigen, if recognized by an immune effector celi, is able to induce in the presence of appropriate co-stimulatory signals, stimulation, priming and / or expansion of the immune effector cell carrying an antigen receptor recognizing the antigen. In the context of the embodiments of the present disclosure, in some embodiments, an antigen can be presented or present on the surface of a cell, e.g., an antigen presenting cell. In one embodiment, an antigen is presented by a diseased cell such as a virus-infected cell. In one embodiment, an antigen receptor is a TCR which binds to an epitope of an antigen presented in the context of MHC. In one embodiment, binding of a TCR when expressed by T cells and / or present on T cells to an antigen presented by cells such as antigen presenting cells results in stimulation, priming and / or expansion of said T celis. In one embodiment, binding of a TCR when expressed by T cells and / or present on T cells to an antigen presented on diseased cells results in cytolysis and / or apoptosis of the diseased cells, wherein said T cells preferably release cytotoxic factors, e.g., perforins and granzymes.
[0108] Associated'. Two events or entities are "associated" with one another, as that term is used herein, if the presence, level, degree, type and / or form of one is correlated with that of the other. For example, a particular entity (e.g., polypeptide, genetic signature, metabolite, microbe, etc.) is considered to be associated with a particular disease, disorder, or condition, if its presence, level and / or form correlates with incidence of, susceptibility to, severity of, stage of, etc. the disease, disorder, or condition (e.g., across a relevant popuiation). In some embodiments, two or more entities are physically "associated" with one another if they interact, directly or indirectly, so that they are and / or remain in physical proximity with one another. In some embodiments, two or more entities that are physically associated with one another are covalently linked to one another; in some embodiments, two or more entities that are physically associated with one another are not covalently linked to one another but are non-covalentiy associated, for example by means of hydrogen bonds, van der Waals interaction, hydrophobic interactions, magnetism, and combinations thereof.Page 24 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)
[0109] Binding'. Those skilled in the art, reading the present specification, will appreciate that the term "binding" typically refers to a non-covalent association between or among entities or moieties. In some embodiments, binding data are expressed in terms of "IC50". As is understood in the art, IC50 is the concentration of an assessed agent in a binding assay at which 50% inhibition of binding of reference agent known to bind the relevant binding partner is observed. In some embodiments, assays are run under conditions in which {e.g., limiting binding target and reference concentrations), IC50values approximate Ko values. Assays for determining binding are well known in the art and are described in detail, for example, in PCT publications WO 94 / 20127 and WO 94 / 03205, and other publications such Sidney et al., Current Protocols in Immunology 18.3.1 (1998); Sidney, et al., J. Immunol.154:247 (1995); and Sette, et al., Mol. Immunol. 31:813 (1994). Alternatively, binding can be expressed relative to binding by a reference standard peptide. For example, binding can be based on its IC50, relative to the IC50 of a reference standard peptide. Binding can also be determined using other assay systems including those using live cells (e.g., Ceppellini et al., Nature 339:392 (1989); Christnick et al., Nature 352:67 (1991); Busch et al., Int. Immunol.2:443 (1990); Hill et al., J. Immunol. 147:189 (1991); del Guercio et al., J. Immunol. 154:685 (1995)), cell free systems using detergent lysates (e.g., Cerundolo et al., J. Immunol 21:2069 (1991)), immobilized purified MHC (e.g., Hill et al., J. Immunol. 152, 2890 (1994); Marshall etal., J. Immunol. 152:4946 (1994)), ELISA systems (e.g., Reay et al., EMBO J. 11:2829 (1992)), surface plasmon resonance (e.g., Khilko et al., J. Biol. Chem. 268:15425 (1993)); high flux soluble phase assays (Hammer et al., J. Exp. Med. 180:2353 (1994)), and measurement of class I MHC stabilization or assembly (e.g., Ljunggren et al., Nature 346:476 (1990); Schumacher et al., Cell 62:563 (1990); Townsend et al., Cell 62:285 (1990); Parker et al., J. Immunol. 149:1896 (1992)).
[0110] Cap As used herein, the term "cap" refers to a structure comprising or essentially consisting of a nucleoside-5 '-triphosphate that is typically joined to a 5'-end of an uncapped RNA {e.g., an uncapped RNA having a 5'- diphosphate). In some embodiments, a cap is or comprises a guanine nucleotide. In some embodiments, a cap is or comprises a naturally occurring RNA 5' cap, including, e.g., but not limited to a 7- methylguanosine cap, which has a structure designated as "m7G." In some embodiments, a cap is or comprises a synthetic cap analog that resembles an RNA cap structure and possesses the ability to stabilize RNA if attached thereto, including, e.g., but not limited to anti-reverse cap analogs (ARCAs) known in the art). Those skilled in the art will appreciate that methods for joining a cap to a 5' end of an RNA are known in the art. For example, in some embodiments, a capped RNA may be obtained by in vitro capping of RNA that has a 5' triphosphate group or RNA that has a 5' diphosphate group with a capping enzyme system (including, e.g., but not limited to vaccinia capping enzyme system or Saccharomyces cerevisiae capping enzyme system). Alternatively, a capped RNA can be obtained by in vitro transcription (IVT) of a singlestranded DNA template in the presence of a dinucleotide or trinucleotide cap analog.
[0111] Cell-mediated immunity. " Cell-mediated immunity," "cellular immunity," "cellular immune response," or similar terms are meant to include a cellular response directed to cells characterized by expression of an antigen, in particular characterized by presentation of an antigen with class I or class II MHC. A cellular response relates to immune effector cells, in particular to T cells or T lymphocytes which act as either "helpers" or "killers." The helper T cells (also termed CD4+T cells or CD4 T cells) play a central role by regulating the immune response and the killer cells (also termed cytotoxic T cells, cytolytic T cells, CD8+T cells, CD8 T cells, or CTLs) kill diseased cells such as virus-infected cells, preventing the production of more diseased cells.Page 25 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)
[0112] Co-administration: As used herein, the term "co-administration" refers to use of a pharmaceutical composition (e.g, immunogenic composition, e.g,, vaccine) described herein and an additional therapeutic agent. In some embodiments, the additional therapeutic agent is an additional pharmaceutical composition described herein. The combined use of a pharmaceutical composition (e.g., immunogenic composition, e.g., vaccine) described herein and an additional therapeutic agent may be performed concurrently or separately (e.g., sequentialiy in any order). In some embodiments, a pharmaceutical composition (e.g., immunogenic composition, e.g., vaccine) described herein and an additional therapeutic agent may be combined in one pharmaceutically acceptable carrier, or they may be placed in separate carriers and delivered to a target cell or administered to a subject at different times. Each of these situations is contemplated as falling within the meaning of "co-administration'' or "combination," provided that a pharmaceutical composition (e.g., immunogenic composition, e.g., vaccine) described herein and an additional therapeutic agent are delivered or administered sufficiently close in time that there is at least some temporal overlap in biological effect(s) generated by each on a target cell or a subject being treated.
[0113] Codon -optimized-. As used herein, the term "codon-optimized" refers to alteration of codons in a coding region of a nucleic acid molecule to reflect the typical codon usage of a host organism without preferably altering the amino acid sequence encoded by the nucleic acid molecule. Within the context of the present disclosure, in some embodiments coding regions are codon-optimized for optimal expression in a subject to be treated using the RNA molecules described herein. In some embodiments, codon-optimization may be performed such that codons for which frequently occurring tRNAs are available are inserted in place of "rare codons." In some embodiments, codon¬ optimization may include increasing guanosine / cytosine (G / C) content of a coding region of RNA described herein as compared to the G / C content of the corresponding coding sequence of a wild type RNA, wherein the amino acid sequence encoded by the RNA is preferably not modified compared to the amino acid sequence.
[0114] Combination therapy. As used herein, the term "combination therapy" refers to those situations in which a subject is simultaneously exposed to two or more therapeutic regimens (e.g., two or more therapeutic agents). In some embodiments, the two or more regimens may be administered simultaneously; in some embodiments, such regimens may be administered sequentially (e.g., all "doses" of a first regimen are administered prior to administration of any doses of a second regimen); in some embodiments, such agents are administered in overlapping dosing regimens. In some embodiments, "administration" of combination therapy may involve administration of one or more agents or modalities to a subject receiving the other agents or modalities in the combination. For clarity, combination therapy does not require that individual agents be administered together in a single composition (or even necessarily at the same time), although in some embodiments, two or more agents, or active moieties thereof, may be administered together in a combination composition.
[0115] Codon Usage Quality Score As used herein the term "codon usage quality score" is used to refer to a metric that measures (e.g., quantifies) a frequency with which codons of a given polynucleotide sequence occur in a particular target organism [for example, a human (homo sapiens)] and / or a selected subset of genes thereof. For example, in certain embodiments, a given individual codon may be assigned an individual codon usage value that reflects a relative frequency with which that individual codon is used and / or appears in a given target organism. Individual codon usage values may be obtained, for example, via tabulated databases such as those of Nakamura et al., " Codon usage tabulated from the international DNA sequence database: status for the year 2000. Nucleic. Acids Res. 28:292. Individual codon usage values may account for varying numbers of synonymous codons for different Page 26 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)amino acids, for exampie via metrics such as a " Relative synonymous codon usage" (RSCU), " Relative Adaptiveness" and the like. See, e.g., Raab et al., Syst Synth Biol (2010). Individual codon usage values may, accordingly, be combined (e.g., summed and / or scaled) to determine a value of a codon usage quality score for a particular polynucleotide sequence and target organism. One example codon usage quality score is a Codon Adaptation Index (CAI), described in Raab et al., Syst Synth Biol (2010); others may be used, additionally or alternatively.
[0116] Comparable: As used herein, the term "comparable" refers to two or more agents, entities, situations, sets of conditions, etc., that may not be identical to one another but that are sufficiently similar to permit comparison there between so that one skilled in the art will appreciate that conclusions may reasonably be drawn based on differences or similarities observed. In some embodiments, comparable sets of conditions, circumstances, individuals, or populations are characterized by a plurality of substantially identical features and one or a small number of varied features. Those of ordinary skill in the art will understand, in context, what degree of identity is required in any given circumstance for two or more such agents, entities, situations, sets of conditions, etc. to be considered comparable. For example, those of ordinary skill in the art will appreciate that sets of circumstances, individuals, or populations are comparable to one another when characterized by a sufficient number and type of substantially identical features to warrant a reasonable conclusion that differences in results obtained or phenomena observed under or with different sets of circumstances, individuals, or populations are caused by or indicative of the variation in those features that are varied.
[0117] Corresponding to: As used herein, the term "corresponding to" refers to a relationship between two or more entities. For example, the term "corresponding to" may be used to designate the position / identity of a structural element in a compound or composition relative to another compound or composition e.g., to an appropriate reference compound or composition). For example, in some embodiments, a monomeric residue in a polymer (e.g., an amino acid residue in a polypeptide or a nucleic acid residue in a polynucleotide) may be identified as "corresponding to" a residue in an appropriate reference polymer. For example, those of ordinary skill will appreciate that, for purposes of simplicity, residues in a polypeptide are often designated using a canonical numbering system based on a reference related polypeptide, so that an amino acid "corresponding to" a residue at position 190, for example, need not actually be the 190thamino acid in a particular amino acid chain but rather corresponds to the residue found at 190 in the reference polypeptide; those of ordinary skill in the art readily appreciate how to identify "corresponding" amino acids. For example, those skilled in the art will be aware of various sequence alignment strategies, including software programs such as, for example, BLAST, CS-BLAST, CUSASW++, DIAMOND, fASTA, gGSEARCH / GLSEARCH, Genoogle, HMMER, HHpred / HHsearch, IDF, Infernal, KLAST, USEARCH, parasail, PSI-BLAST, PSI-Search, ScalaBLAST, Sequilab, SAM, SSEARCH, SWAPHI, SWAPHI-LS, SWIMM, or SWIPE that can be utilized, for example, to identify "corresponding" residues in polypeptides and / or nucleic acids in accordance with the present disclosure. Those of skill in the art will also appreciate that, in some instances, the term "corresponding to" may be used to describe an event or entity that shares a relevant similarity with another event or entity (e.g., an appropriate reference event or entity). To give but one example, a gene or protein in one organism may be described as "corresponding to" a gene or protein from another organism in order to indicate, in some embodiments, that it plays an analogous role or performs an analogous function and / or that it shows a particular degree of sequence identity or homology, or shares a particular characteristic sequence element.Page 27 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)
[0118] As those skilled in the art are aware, sequence alignment strategies enable consideration, for example, of "gaps" in sequences, and / or of "repeated" residues. Moreover, those skilled in the art understand that in some cases, it is not possible to unambiguously determine the exact location of a sequence change relative to a reference sequence. For example, when a reference sequence includes a stretch of two or more contiguous identical residues, and a changed sequence has one fewer of the residues, it is not possible to assign a particular singular residue in the reference sequence as the one that was deleted, as deletion of any one of the identical contiguous residues would generate the same changed sequence. Those skilled in the art therefore appreciate the convention of arbitrarily assigning one of the reference residue positions as the deleted residue. To give a specific example, SEQ ID NO:1 is a polypeptide sequence in which two adjacent Y residues are present at positions 144 and 145. If one of these amino acid residues is deleted, a person of skill in the art will not be able to determine whether amino acid 144 or 145 has been deleted in the changed sequence. They will understand, however, that either deletion describes the same polypeptide sequence, and therefore will be able to unambiguously determine the sequence of a polypeptide described as having a deletion at position 144 or 145 of SEQ ID NO: 1 (i.e., they will understand that a polypeptide described as having a deletion at a position corresponding to position 144 of SEQ ID NO: 1 and a polypeptide described as having a deletion at a position corresponding to position 145 of SEQ ID NO: 1 have the same amino acid sequence).
[0119] Derived-. In the context of an amino acid sequence (peptide or polypeptide) "derived from" a designated amino acid sequence (peptide or polypeptide), refers to a structural analogue of a designated amino acid sequence. In some embodiments, an amino acid sequence which is derived from a particular amino acid sequence has an amino acid sequence that is identical, essentially identical or homologous to that particular sequence or a fragment thereof. Amino acid sequences derived from a particular amino acid sequence may be variants of that particular sequence or a fragment thereof. For example, it will be understood by one of ordinary skill in the art that the antigens suitable for use herein may be altered such that they vary in sequence from the naturally occurring or native sequences from which they were derived, while retaining the desirable activity of the native sequences.
[0120] Designed: As used herein, the term "designed" refers to an agent (I) whose structure is or was selected by the hand of man; (ii) that is produced by a process requiring the hand of man; and / or (ill) that is distinct from natural substances and other known agents.
[0121] Disease: As used herein, the term "disease" refers to an abnormal condition that affects the body of an individual. A disease is often construed as a medical condition associated with specific symptoms and signs. A disease may be caused by factors originally from an external source, such as infectious disease, or it may be caused by internal dysfunctions, such as autoimmune diseases. In humans, "disease" is often used more broadly to refer to any condition that causes pain, dysfunction, distress, social problems, or death to the individual afflicted, or similar problems for those in contact with the individual. In this broader sense, it can include injuries, disabilities, disorders, syndromes, infections, isolated symptoms, deviant behaviors, and atypical variations of structure and function, while in other contexts and for other purposes, as will be clear to those skilled in the art from context, these may be considered distinguishable categories.
[0122] As will be familiar to those skilled in the art, the term "infectious disease" refers to a disease which can be transmitted from individual to individual or from organism to organism, and include, for example, a viral disease, a bacterial disease, or a parasitic disease, which diseases are caused by a virus, a bacterium, and a parasite,Page 28 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)respectively. In this regard, the infectious disease can be, for example, caused by a coronavirus (e.g., a betacoronaviruses, e.g., SARS-CoV-1, MERS, and SARS-CoV-2) or an influenza virus infection.
[0123] Dosing regimen-. Those skilled in the art will appreciate that the term "dosing regimen" may be used to refer to a set of unit doses (typically more than one) that are administered individually to a subject, typically separated by periods of time. In some embodiments, a given therapeutic agent has a recommended dosing regimen, which may involve one or more doses. In some embodiments, a dosing regimen comprises a plurality of doses each of wh ich is separated in time from other doses. In some embodiments, individual doses are separated from one another by a time period of the same length; in some embodiments, a dosing regimen comprises a plurality of doses and at least two different time periods separating individual doses. In some embodiments, all doses within a dosing regimen are of the same unit dose amount. In some embodiments, different doses within a dosing regimen are of different amounts. In some embodiments, a dosing regimen comprises a first dose in a first dose amount, followed by one or more additional doses in a second dose amount different from the first dose amount. In some embodiments, a dosing regimen comprises a first dose in a first dose amount, followed by one or more additional doses in a second dose amount same as the first dose amount. In some embodiments, a dosing regimen is correlated with a desired or beneficial outcome when administered across a relevant population (.e., is a therapeutic dosing regimen).
[0124] Encode As used herein, the term "encode" or "encoding" refers to sequence information of a first molecule that guides production of a second molecule having a defined sequence of nucleotides (e.g., mRNA) or a defined sequence of amino acids. For example, a DNA molecule can encode an RNA molecule (e.g., by a transcription process that includes a DNA-dependent RNA polymerase enzyme). An RNA molecule can encode a polypeptide (e.g., by a translation process). Thus, a gene, a cDNA, or an RNA molecule (e.g., an mRNA) encodes a polypeptide if transcription and translation of RNA (e.g., mRNA) corresponding to that gene produces the polypeptide in a cell or other biological system. In some embodiments, a coding region of an RNA molecule encoding a target antigen refers to a coding strand, the nucleotide sequence of which is identical to the RNA (e.g., mRNA) sequence of such a target antigen. In some embodiments, a coding region of an RNA molecule encoding a target antigen refers to a non-coding strand of such a target antigen, which may be used as a template for transcription of a gene or cDNA.
[0125] Engineered: In general, the term "engineered" refers to the aspect of having been manipulated by the hand of man. For example, a polynucleotide is considered to be "engineered" when two or more sequences that are not linked together in that order in nature are manipulated by the hand of man to be directly linked to one another in the engineered polynucleotide and / or when a particular residue in a polynucleotide is non-naturally occurring and / or is caused through action of the hand of man to be linked with an entity or moiety with which it is not linked in nature.
[0126] Epitope. As used herein, the term "epitope" refers to a moiety that is specifically recognized by an immunoglobulin (e.g., antibody or receptor) binding component. For example, an epitope may be recognized by a T cell, a B cell, or an antibody. In some embodiments, an epitope is comprised of a plurality of chemical atoms or groups on an antigen. In some embodiments, such chemical atoms or groups are surface-exposed when the antigen adopts a relevant three-dimensional conformation. In some embodiments, such chemical atoms or groups are physically near to each other in space when the antigen adopts such a conformation. In some embodiments, at least some such chemical atoms are groups that are physically separated from one another when the antigen adopts an Page 29 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)alternative conformation (e.g., is linearized). Accordingly, in some embodiments, an epitope of an antigen may include a continuous or discontinuous fragment of the antigen. In some embodiments, an epitope is or comprises a T cell epitope. In some embodiments, an epitope may have a length of about 5 to about 30 amino acids, or about 10 to about 25 amino acids, or about 5 to about 15 amino acids, or about 5 to 12 amino acids, or about 6 to about 9 amino acids.
[0127] Expression: As used herein, the term "expression" of a nucleic acid sequence refers to the generation of a gene product from the nucleic acid sequence. In some embodiments, a gene product can be a transcript. In some embodiments, a gene product can be a polypeptide. In some embodiments, expression of a nucleic acid sequence involves one or more of the following: (1) production of an RNA template from a DNA sequence (e.g., by transcription); (2) processing of an RNA transcript (e.g., by splicing, editing, etc.); (3) translation of an RNA into a polypeptide or protein; and / or (4) post-translationai modification of a polypeptide or protein.
[0128] Five prime untranslated region. As used herein, the terms "five prime untranslated region" or "5' UTR" refer to a sequence of an RNA (e.g., mRNA) molecule between a transcription start site and a start codon of a coding region of an RNA. In some embodiments, "5' UTR" refers to a sequence of an RNA (e.g., mRNA) molecule that begins at a transcription start site and ends one nucleotide (nt) before a start codon (usually AUG) of a coding region of an RNA molecule, e.g., in its natural context.
[0129] Fragment. The term "fragment" as used herein in the context of a nucleic acid sequence (e.g., RNA sequence) or an amino acid sequence may typically be a fragment of a reference sequence. In some embodiments, a reference sequence is a full-length sequence of e.g., a nucleic acid sequence or an amino acid sequence.Accordingly, a fragment, typically, refers to a sequence that is identical to a corresponding stretch within a reference sequence. In some embodiments, a fragment comprises a continuous stretch of nucleotides or amino acid residues that corresponds to at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95% of the total length of a reference sequence from which the fragment is derived. In some embodiments, the term "fragment", with reference to an amino acid sequence (peptide or polypeptide), relates to a part of an amino acid sequence, e.g., a sequence which represents the amino acid sequence shortened at the N-terminus and / or C-terminus. In some embodiments, a fragment of an amino acid sequence comprises at least 6, in particular at least 8, at least 12, at least 15, at least 20, at least 30, at least 50, or at least 100 consecutive amino acids from an amino acid sequence.
[0130] GC Content Quality Score-. As used herein, the term " GC content quality score" is used to refer to a metric that measures (e.g., quantifies) overall content of the nucleotides guanine (G) and cytosine (C) in a polynucleotide sequence and / or a variation in their (i.e., G and C) content along a sequence. For example, in certain embodiments, a GC content score may measure a total number of G and C bases within a polynucleotide sequence. In certain embodiments, a GC content score may measure a variation (e.g., a variability) in GC content along a sequence (e.g., a standard deviation, variance, in a GC content measured over a sliding window, etc.).
[0131] Homology: As used herein, the term "homology" or "homolog" refers to the overall relatedness between polynucleotide molecules (e.g., DNA molecules and / or RNA molecules) and / or between polypeptide molecules. In some embodiments, polynucleotide molecules (e.g., DNA molecules and / or RNA molecules) and / or polypeptide molecules are considered to be "homologous" to one another if their sequences are at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least Page 30 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% identical. In some embodiments, polynucleotide molecules (e.g., DNA molecules and / or RNA molecules) and / or polypeptide molecules are considered to be "homologous" to one another if their sequences are at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% similar (e.g., containing residues with related chemical properties at corresponding positions). For example, as is well known by those of ordinary skill in the art, certain amino acids are typically classified as similar to one another as "hydrophobic" or "hydrophilic" amino acids, and / or as having "polar" or "non-polar" side chains. Substitution of one amino acid for another of the same type may often be considered a "homologous" substitution.
[0132] Humoral immunity: As used herein, the term "humoral immunity" or "humoral immune response" refers to antibody production and the accessory processes that accompany it, including: Th2 activation and cytokine production, germinal center formation and isotype switching, affinity maturation and memory cell generation. It also refers to the effector functions of antibodies, which include pathogen neutralization, classical complement activation, and opsonin promotion of phagocytosis and pathogen elimination.
[0133] Identity: i*s used herein, the term "identity" refers to the overall relatedness between polynucleotide molecules e.g., DNA molecules and / or RNA molecules) and / or between polypeptide molecules. In some embodiments, polynucleotide molecules e.g., DNA molecules and / or RNA molecules) and / or between polypeptide molecules are considered to be "substantially identical" to one another if their sequences are at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical. Calculation of the percent identity of two nucleic acid or polypeptide sequences, for example, can be performed by aligning the two sequences for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second sequence for optimal alignment and non-identical sequences can be disregarded for comparison purposes). In certain embodiments, the length of a sequence aligned for comparison purposes is at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or substantially 100% of the length of a reference sequence. The nucleotides at corresponding positions are then compared. When a position in the first sequence is occupied by the same residue (e.g., nucleotide or amino acid) as the corresponding position in the second sequence, then the molecules are identical at that position. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which needs to be introduced for optimal alignment of the two sequences. The comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm. For example, the percent identity between two nucleotide sequences can be determined using the algorithm of Meyers and Miller, 1989, which has been incorporated into the ALIGN program (version 2.0). In some exemplary embodiments, nucleic acid sequence comparisons made with the ALIGN program use a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 4. The percent identity between two nucleotide sequences can, alternatively, be determined using the GAP program in the GCG software package using an NWSgapdna. CMP matrix.Page 31 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)
[0134] Immune response-. The term "immune response," as used herein, refers to a bodily response to an antigen (including, e.g,, a soluble antigen, an antigen bound to the surface of a cell, or an antigen included in a viral particle) and includes a humoral response and / or a cellular immune response (e.g., a cellular immune response from cells that include helper T cells (also termed CD4+ T cells) and / or killer T cells (also termed cytotoxic T cells, cytolytic T cells, CD8+ T cells or CTLs)).
[0135] Immunologically equivalent: Hie term "immunologically equivalent" means that an immunologically equivalent molecule such as the immunologically equivalent amino acid sequence exhibits the same or essentially the same immunological properties and / or exerts the same or essentially the same immunological effects, e.g., with respect to the type of the immunological effect. In the context of the present disclosure, in some embodiments, the term "immunologically equivalent" is used with respect to the immunological effects or properties of antigens or antigen variants used for immunization. For example, an amino acid sequence is immunologically equivalent to a reference amino acid sequence if said amino acid sequence when exposed to the immune system of a subject induces an immune reaction having a specificity of reacting with the reference amino acid sequence.
[0136] In one embodiment, an antigen receptor is an antibody or B cell receptor which binds to an epitope of an antigen. In one embodiment, an antibody or B cell receptor binds to native epitopes of an antigen.
[0137] Increased, Induced, or Reduced: As used herein, these terms or grammatically comparable comparative terms, indicate values that are relative to a comparable reference measurement. For example, in some embodiments, an assessed value achieved with a provided pharmaceutical composition (e.g., immunogenic composition, e.g., vaccine) may be "increased" relative to that obtained with a comparable reference pharmaceutical composition (e.g., immunogenic composition, e.g., vaccine). Alternatively or additionally, in some embodiments, an assessed value achieved in a subject may be "increased" relative to that obtained in the same subject under different conditions (e.g., prior to or after an event; or presence or absence of an event such as administration of a pharmaceutical composition (e.g., immunogenic composition, e.g., vaccine) as described herein, or in a different, comparable subject (e.g., in a comparable subject that differs from the subject of interest in prior exposure to a condition, e.g., absence of administration of a pharmaceutical composition (e.g., immunogenic composition, e.g., vaccine) as described herein.). In some embodiments, comparative terms refer to statistically relevant differences (e.g., that are of a prevalence and / or magnitude sufficient to achieve statistical relevance). Those skilled in the art will be aware, or will readily be able to determine, in a given context, a degree and / or prevalence of difference that is required or sufficient to achieve such statistical significance. In some embodiments, the term "reduced" or equivalent terms refers to a reduction in the level of an assessed value by at least 5%, at least 10%, at least 20%, at least 50%, at least 75% or higher, as compared to a comparable reference. In some embodiments, the term "reduced" or equivalent terms refers to a complete or essentially complete inhibition, i.e., a reduction to zero or essentially to zero. In some embodiments, the term "increased" or "induced" refers to an increase in the level of an assessed value by at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 80%, at least 100%, at least 200%, at least 500%, or higher, as compared to a comparable reference.
[0138] Ionizable-. The term "ionizable" refers to a compound or group or atom that is charged at a certain pH. In the context of an ionizable amino lipid, such a lipid or a function group or atom thereof bears a positive charge at a certain pH. In some embodiments, an ionizable amino lipid is positively charged at an acidic pH. In some embodiments, an ionizable amino lipid is predominately neutral at physiological pH values, e.g., in somePage 32 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)embodiments about 7.0-7.4, but becomes positively charged at lower pH values. In some embodiments, an ionizabie amino lipid may have a pKa within a range of about 5 to about 7.
[0139] Isolated: The term "isolated" means altered or removed from the natural state. For example, a nucleic acid or a peptide naturally present in a living animal is not "isolated", but the same nucleic acid or peptide partially or completely separated from the coexisting materials of its natural state is "isolated". An isolated nucleic acid or protein can exist in substantially purified form, or can exist in a non-native environment such as, for example, a host cell.
[0140] Lipid As used herein, the terms "lipid" and "lipid-like material" are broadly defined as molecules which comprise one or more hydrophobic moieties or groups and optionally also one or more hydrophilic moieties or groups. Molecules comprising hydrophobic moieties and hydrophilic moieties are also typically denoted as amphiphiles.
[0141] RNA lipid nanoparticie: As used herein, the term " RNA lipid nanoparticle" refers to a nanoparticle comprising at least one lipid and RNA molecule(s). In some embodiments, an RNA lipid nanoparticie comprises at least one ionizable amino lipid. In some embodiments, an RNA lipid nanoparticie comprises at least one ionizable amino lipid, at least one helper lipid, and at least one polymer-conjugated lipid (e.g., PEG-conjugated lipid). In various embodiments, RNA lipid nanoparticles as described herein can have an average size (e.g., Z-average) of about 100 nm to 1000 nm, or about 200 nm to 900 nm, or about 200 nm to 800 nm, or about 250 nm to about 700 nm. In some embodiments of the present disclosure, RNA lipid nanoparticles can have a particle size (e.g., Z-average) of about 30 nm to about 200 nm, or about 30 nm to about 150 nm, about 40 nm to about 150 nm, about 50 nm to about 150 nm, about 60 nm to about 130 nm, about 70 nm to about 110 nm, about 70 nm to about 100 nm, about 80 nm to about 100 nm, about 90 nm to about 100 nm, about 70 to about 90 nm, about 80 nm to about 90 nm, or about 70 nm to about 80 nm. In some embodiments, an average size of lipid nanoparticles is determined by measuring the particle diameter. In some embodiments, RNA lipid nanoparticles may be prepared by mixing lipids with RNA molecules described herein.
[0142] Lipidoid: As used herein, a "lipidoid" refers to a lipid-like molecule. In some embodiments, a lipoid is an amphiphilic molecule with one or more lipid-like physical properties. In the context of the present disclosure, the term lipid is considered to encompass lipidoids.
[0143] Nanoparticie: As used herein, the term "nanoparticie" refers to a particle having an average size suitable for parenteral administration. In some embodiments, a nanoparticie has a longest dimension (e.g., a diameter) of less than 1,000 nanometers (nm). In some embodiments, a nanoparticie may be characterized by a longest dimension (e.g., a diameter) of less than 300 nm. In some embodiments, a nanoparticie may be characterized by a longest dimension (e.g., a diameter) of less than 100 nm. In many embodiments, a nanoparticie may be characterized by a longest dimension between about 1 nm and about 100 nm, or between about 1 pm and about 500 nm, or between about 1 nm and 1,000 nm. In many embodiments, a population of nanoparticles is characterized by an average size (e.g., longest dimension) that is below about 1,000 nm, about 500 nm, about 100 nm, about 50 nm, about 40 nm, about 30 nm, about 20 nm, or about 10 nm and often above about 1 nm. In many embodiments, a nanoparticie may be substantially spherical so that its longest dimension may be its diameter. In some embodiments, a nanoparticie has a diameter of less than 100 nm as defined by the National Institutes of Health.Page 33 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)
[0144] Naturally occurring: The term "naturally occurring" as used herein refers to an entity that can be found in nature. For example, a peptide or nucleic acid that is present in an organism (including viruses) and can be isolated from a source in nature and which has not been intentionally modified by man in the laboratory is naturally occurring.
[0145] Neutralization: As used herein, the term "neutralization" refers to an event in which binding agents such as antibodies bind to a biological active site of a virus such as a receptor binding protein, thereby inhibiting the parasitic infection of cells. In some embodiments, the term "neutralization" refers to an event in which binding agents eliminate or significantly reduce ability of infecting cells.
[0146] N cleic acid particle-. A "nucleic acid particle" can be used to deliver nucleic acid to a target site of interest (e.g., cell, tissue, organ, and the like). A nucleic acid particle may comprise at least one cationic or cationically ionizable lipid or lipid-like material, at least one cationic polymer such as protamine, or a mixture thereof and nucleic acid. In some embodiments, a nucleic acid particle is a lipid nanoparticle. In some embodiments, a nucleic acid particie is a lipoplex particle.
[0147] Nucleic acid / Polynucleotide As used herein, the term "nucleic acid" refers to a polymer of at least 10 nucleotides or more. In some embodiments, a nucleic acid is or comprises DNA. In some embodiments, a nucleic acid is or comprises RNA. In some embodiments, a nucleic acid is or comprises peptide nucleic acid (PNA). In some embodiments, a nucleic acid is or comprises a single stranded nucleic acid. In some embodiments, a nucleic acid is or comprises a double-stranded nucleic acid. In some embodiments, a nucleic acid comprises both single and double¬ stranded fragments. In some embodiments, a nucleic acid comprises a backbone that comprises one or more phosphodiester linkages. In some embodiments, a nucleic acid comprises a backbone that comprises both phosphodiester and non-phosphodiester linkages. For example, in some embodiments, a nucleic acid may comprise a backbone that comprises one or more phosphorothioate or 5'-N-phosphoramidite linkages and / or one or more peptide bonds, e.g., as in a "peptide nucleic acid". In some embodiments, a nucleic acid comprises one or more, or all, natural residues (e.g., adenine, cytosine, deoxyadenosine, deoxycytidine, deoxyguanosine, deoxythymidine, guanine, thymine, uracil). In some embodiments, a nucleic acid comprises on or more, or all, non-natural residues. In some embodiments, a non-natural residue comprises a nucleoside analog (e.g., 2-aminoadenosine, 2- thiothymidine, inosine, pyrrolo-pyrimidine, 3 -methyl adenosine, 5 -methylcytidine, C-5 propynyl-cytidine, C-5 propynyl-uridine, 2-aminoadenosine, C5-bromouridine, C5-fluorouridine, C5-iodouridine, C5-propynyl-uridine, C5 -propynyl-cytidine, C5-methylcytidine, 2-aminoadenosine, 7-deazaadenosine, 7-deazaguanosine, 8-oxoadenosine, 8-oxoguanosine, 6-O-methylguanine, 2-thiocytidine, methylated bases, intercalated bases, and combinations thereof). In some embodiments, a non-natural residue comprises one or more modified sugars (e.g., 2’-fluororibose, ribose, 2'-deoxyribose, arabinose, and hexose) as compared to those in natural residues. In some embodiments, a nucleic acid has a nucleotide sequence that encodes a functional gene product such as an RNA or polypeptide. In some embodiments, a nucleic acid has a nucleotide sequence that comprises one or more introns. In some embodiments, a nucleic acid may be prepared by isolation from a natural source, enzymatic synthesis (e.g., by polymerization based on a complementary template, e.g., in vivo or in vitro, reproduction in a recombinant cell or system, or chemical synthesis. In some embodiments, a nucleic acid is at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 100,Page 34 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)at least 110, at least 120, at least 130, at least 140, at least 150, at least 160, at least 170, at least 180, at least 190, at least 200, at least 225, at least 250, at least 275, at least 300, at least 325, at least 350, at least 375, at least 400, at least 425, at least 450, at least 475, at least 500, at least 600, at least 700, at least 800, at least 900, at least 1000, at least 1500, at least 2000, at least 2500, at least 3000, at least 3500, at least 4000, at least 4500, at least 5000, at least 5500, at least 6000, at least 6500, at least 7000, at least 7500, at least 8000, at least 8500, at least 9000, at least 9500, at least 10,000, at least 10,500, at least 11,000, at least 11,500, at least 12,000, at least 12,500, at least 13,000, at least 13,500, at least 14,000, at least 14,500, at least 15,000, at least 15,500, at least 16,000, at least 16,500, at least 17,000, at least 17,500, at least 18,000, at least 18,500, at least 19,000, at least 19,500, or at least 20,000 residues or nucleotides long,
[0148] Nucleotide: As used herein, the term "nucleotide" refers to its art-recognized meaning. When a number of nucleotides is used as an indication of size, e.g., of a polynucleotide, a certain number of nucleotides refers to the number of nucleotides on a single strand, e.g., of a polynucleotide.
[0149] Patient: As used herein, the term "patient" refers to any organism who is suffering or at risk of a disease or disorder or condition. Typical patients include animals (e.g., mammals such as mice, rats, rabbits, non¬ human primates, and / or humans). In some embodiments, a patient is a human. In some embodiments, a patient is suffering from or susceptible to one or more diseases or disorders or conditions. In some embodiments, a patient displays one or more symptoms of a disease or disorder or condition. In some embodiments, a patient has been diagnosed with one or more diseases or disorders or conditions. In some embodiments, a disease or disorder or condition that is amenable to provided technologies is or includes a HSV infection. In some embodiments, a patient is receiving or has received certain therapy to diagnose and / or to treat a disease, disorder, or condition. In some embodiments, a patient is a patient suffering from or susceptible to a HSV infection.
[0150] PEG-conjugated lipid. The term " PEG-conjugated lipid" refers to a molecule comprising a lipid portion and a polyethylene glycol portion.
[0151] Pharmaceutical composition: As used herein, the term "pharmaceutical composition" refers to an active agent, formulated together with one or more pharmaceutically acceptable carriers. In some embodiments, an active agent is present in a unit dose amount appropriate for administration in a therapeutic regimen that shows a statistically significant probability of achieving a predetermined therapeutic effect when administered to a relevant population. In some embodiments, pharmaceutical compositions may be specially formulated for parenteral administration, for example, by subcutaneous, intramuscular, or intravenous injection such as, for example, a sterile solution or suspension formulation.
[0152] Pharmaceutically effective amount: The term "pharmaceutically effective amount" or "therapeutically effective amount" refers to the amount which achieves a desired reaction or a desired effect alone or together with further doses. In the case of tlie treatment of a particular disease, a desired reaction in some embodiments relates to inhibition of the course of the disease. In some embodiments, such inhibition may comprise slowing down the progress of a disease and / or interrupting or reversing the progress of the disease. In some embodiments, a desired reaction in a treatment of a disease may be or comprise delay or prevention of the onset of a disease or a condition. An effective amount of pharmaceutical compositions (e.g., immunogenic compositions, e.g., vaccines) described herein will depend, for example, on a disease or condition to be treated, the severity of such a disease or condition, individual parameters of the patient, including, e.g., age, physiological condition, size and Page 35 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)weight, the duration of treatment, the type of an accompanying therapy (if present), the specific route of administration and similar factors. Accordingly, doses of pharmaceutical compositions (e.g., immunogenic compositions, e.g., vaccines) described herein may depend on various of such parameters. In the case that a reaction in a patient is insufficient with an initial dose, higher doses (or effectively higher doses achieved by a different, more localized route of administration) may be used.
[0153] Po!y(A ) sequence: As used herein, the term "poly(A) sequence," "poly-A tail," or "poly(A) tail" refers to an uninterrupted or interrupted sequence of adenylate residues which is typically located at the 3'-end of an RNA molecule. Poly(A) sequences are known to those of skill in the art and may follow the 3'-UTR in the RNAs described herein. An uninterrupted poly(A) sequence is characterized by consecutive adenylate residues. In nature, an uninterrupted poly(A) sequence is typical. RNAs disclosed herein can have a poly(A) sequence attached to the free 3'-end of the RNA by a template-independent RNA polymerase after transcription or a poly(A) sequence encoded by DNA and transcribed by a template-dependent RNA polymerase.
[0154] Polypeptide: As used herein, the term "polypeptide" refers to a polymeric chain of amino acids. In some embodiments, a polypeptide has an amino acid sequence that occurs in nature. In some embodiments, a polypeptide has an amino acid sequence that does not occur in nature. In some embodiments, a polypeptide has an amino acid sequence that is engineered in that it is designed and / or produced through action of the hand of man. In some embodiments, a polypeptide may comprise or consist of natural amino acids, non-naturai amino acids, or both. In some embodiments, a polypeptide may comprise or consist of only natural amino acids or only non-natural amino acids. In some embodiments, a polypeptide may comprise D-amino acids, L-amino acids, or both. In some embodiments, a polypeptide may comprise only D-amino acids. In some embodiments, a polypeptide may comprise only L-amino acids. In some embodiments, a polypeptide may include one or more pendant groups or other modifications, e.g., modifying or attached to one or more amino acid side chains, at the polypeptide's N-terminus, at the polypeptide's C-terminus, or any combination thereof. In some embodiments, such pendant groups or modifications comprise acetylation, amidation, lipidation, methylation, pegylation, etc., including combinations thereof. In some embodiments, a polypeptide may be cyclic, and / or may comprise a cyclic portion. In some embodiments, a polypeptide is not cyclic and / or does not comprise any cyclic portion. In some embodiments, a polypeptide is linear. In some embodiments, a polypeptide may be or comprise a stapled polypeptide. In some embodiments, the term "polypeptide" may be appended to a name of a reference polypeptide, activity, or structure; in such instances it is used herein to refer to polypeptides that share the relevant activity or structure and thus can be considered to be members of the same ciass or family of polypeptides. For each such class, the present specification provides and / or those skilled in the art will be aware of exemplary polypeptides within the class whose amino acid sequences and / or functions are known; in some embodiments, such exemplary polypeptides are reference polypeptides for the polypeptide class or family. In some embodiments, a member of a polypeptide class or family shows significant sequence homology or identity with, shares a common sequence motif (e.g., a characteristic sequence element) with, and / or shares a common activity (in some embodiments at a comparable level or within a designated range) with a reference polypeptide of the class; in some embodiments with all polypeptides within the class). For example, in some embodiments, a member polypeptide shows an overall degree of sequence homology or identity with a reference polypeptide that is at least about 30-40%, and is often greater than about 50%, greater than about 60%, greater than about 70%, greater than about 80%, greater than about 90%, greater than about Page 36 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)91%, greater than about 92%, greater than about 93%, greater than about 94%, greater than about 95%, greater than about 96%, greater than about 97%, greater than about 98%, greater than about 99% or more and / or includes at least one region (e.g., a conserved region that may in some embodiments be or comprise a characteristic sequence element) that shows very high sequence identity, often greater than 90% or even greater than 95%, greater than 96%, greater than 97%, greater than 98%, or greater than 99%. Such a conserved region usually encompasses at least 3-4 and often up to 20 or more amino acids; in some embodiments, a conserved region encompasses at least one stretch of at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15 or more contiguous amino acids. In some embodiments, a relevant polypeptide may comprise or consist of a fragment of a parent polypeptide.
[0155] Prevent: As used herein, the term "prevent" or "prevention" when used in connection with the occurrence of a disease, disorder, and / or condition, refers to reducing the risk of developing the disease, disorder and / or condition and / or to delaying onset of one or more characteristics or symptoms of the disease, disorder or condition. Prevention may be considered complete when onset of a disease, disorder or condition has been delayed for a predefined period of time.
[0156] Recombinant: The term "recombinant" in the context of the present disclosure means "made through genetic engineering". In some embodiments, a "recombinant" entity such as a recombinant nucleic acid in the context of the present disclosure is not naturally occurring.
[0157] Reference: As used herein, the term "reference" describes a standard or control relative to which a comparison is performed. For example, in some embodiments, an agent, animal, individual, population, sample, sequence or value of interest is compared with a reference or control agent, animal, individual, population, sample, sequence or value. In some embodiments, a reference or control is tested and / or determined substantially simultaneously with the testing or determination of interest. In some embodiments, a reference or control is a historical reference or control, optionally embodied in a tangible medium. Typically, as would be understood by those skilled in the art, a reference or control is determined or characterized under comparable conditions or circumstances to those under assessment. Those skilled in the art will appreciate when sufficient similarities are present to justify reliance on and / or comparison to a particular possible reference or control.
[0158] Ribonucleic acid (RNA): As used herein, the term " RNA" refers to a polymer of ribonucleotides. In some embodiments, an RNA is single stranded. In some embodiments, an RNA is double stranded. In some embodiments, an RNA comprises both single and double stranded fragments. In some embodiments, an RNA can comprise a backbone structure as described in the definition of " Nucleic acid / Polynucleotide" above. In some embodiments where an RNA comprises at its 3' end a poly(A) region. In some embodiments, an RNA comprises at its 5' end an art-recognized cap structure, e.g., for recognizing and attachment of a mRNA to a ribosome to initiate translation. In some embodiments, a RNA is a synthetic RNA. Synthetic RNAs include RNAs that are synthesized in vitro (e.g., by enzymatic synthesis methods and / or by chemical synthesis methods).
[0159] Ribonucleotide: As used herein, the term "ribonucleotide" encompasses unmodified ribonucleotides and modified ribonucleotides. For example, unmodified ribonucleotides include the purine bases adenine (A) and guanine (G), and the pyrimidine bases cytosine (C) and uracil (U). Modified ribonucleotides may include one or more modifications including, but not limited to, for example, (a) end modifications, e.g., 5' end modifications (e.g., phosphorylation, dephosphorylation, conjugation, inverted linkages, etc.), 3' end modifications (e.g., conjugation, Page 37 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)inverted linkages, etc.), (b) base modifications, e.g., replacement with modified bases, stabilizing bases, destabilizing bases, or bases that base pair with an expanded repertoire of partners, or conjugated bases, (c) sugar modifications (e.g., at the 2' position or 4' position) or replacement of the sugar, and (d) internucleoside linkage modifications, including modification or replacement of the phosphodiester linkages. The term "ribonucleotide" also encompasses ribonucleotide triphosphates including modified and non-modified ribonucleotide triphosphates.
[0160] Risk: As will be understood from context, "risk" of a disease, disorder, and / or condition refers to a likelihood that a particular individual will develop the disease, disorder, and / or condition. In some embodiments, risk is expressed as a percentage. In some embodiments, risk is from 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90 up to 100%. In some embodiments risk is expressed as a risk relative to a risk associated with a reference sample or group of reference samples. In some embodiments, a reference sample or group of reference samples have a known risk of a disease, disorder, condition and / or event. In some embodiments a reference sample or group of reference samples are from individuals comparable to a particular individual. In some embodiments, relative risk is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more. In some embodiments, risk may reflect one or more genetic attributes, e.g., which may predispose an individual toward development (or not) of a particular disease, disorder and / or condition. In some embodiments, risk may reflect one or more epigenetic events or attributes and / or one or more lifestyle or environmental events or attributes.
[0161] RNA lipoplex particle. s used herein, the term " RNA lipoplex particle" refers to a complex comprising liposomes, in particular cationic liposomes, and RNA molecules. Without wishing to bound by a particular theory, electrostatic interactions between positively charged liposomes and negatively charged RNA results in complexation and spontaneous formation of RNA lipoplex particles. In some embodiments, positively charged liposomes may comprise a cationic lipid, such as in some embodiments DOTMA, and additional lipids, such as in some embodiments DOPE. In one embodiment, a RNA lipoplex particle is a nanoparticle.
[0162] Selective or specific: The term "selective" or "specific", when used herein in reference to an agent having an activity, is understood by those skilled in the art to mean that the agent discriminates between potential target entities, states, or cells. For example, in some embodiments, an agent is said to bind "specifically" to its target if it binds preferentially with that target in the presence of one or more competing alternative targets. In many embodiments, specific interaction is dependent upon the presence of a particular structural feature of the target entity (e.g., an epitope, a cleft, a binding site). It is to be understood that specificity need not be absolute. In some embodiments, specificity may be evaluated relative to that of a target-binding moiety for one or more other potential target entities (e.g., competitors). In some embodiments, specificity is evaluated relative to that of a reference specific binding moiety. In some embodiments, specificity is evaluated relative to that of a reference non-specific binding moiety.
[0163] Stable: As used herein, the term "stable" in the context of the present disclosure refers to a pharmaceutical composition (e.g., immunogenic composition, e.g., vaccine) as a whole and / or components thereof meeting or exceeding pre-determined acceptance criteria. For example, in some embodiments, a stable pharmaceutical composition (e.g., immunogenic composition, e.g., vaccine) exhibits no unacceptable levels of microbial growth, and substantially no or no breakdown or degradation of the active biological molecule component(s). In some embodiments, a stable pharmaceutical composition (e.g., immunogenic composition, e.g., vaccine) refers to the integrity of RNA molecules being maintained at least above 90% or more. In somePage 38 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)embodiments, a stable pharmaceutical composition (e.g., immunogenic composition, e.g., vaccine) refers to at least 90% or more (including, e.g., at least 95%, at least 96%, at least 97%, or more) of RNA molecules being maintained to be encapsulated within lipid nanoparticles. In some embodiments, a stable pharmaceutical composition (e.g., immunogenic composition, e.g., vaccine) refers to a formulation that remains capable of eliciting a desired immunologic response when administered to a subject. In some embodiments, a pharmaceutical composition (e.g., immunogenic composition, e.g., vaccine) remains stable for a specified period of time under certain conditions.
[0164] Stability Quality Score-. As used herein, the term "stability quality score" is used to refer to a function or metric that measures (e.g., quantifies) a stability of a given polynucleotide sequence. In certain embodiments, a stability quality score is a predicted stability of the given polynucleotide sequence. For example, a predicted stability may be determined via computer modeling, for example as an in-silico computed mean-free energy (MFE).
[0165] Subject. As used herein, the term "subject" refers to an organism to be administered with a composition described herein, e.g., for experimental, diagnostic, prophylactic, and / or therapeutic purposes. Typical subjects include animals (e.g., mammals such as mice, rats, rabbits, non-human primates, domestic pets, etc.) and humans. In some embodiments, a subject is a human subject. In some embodiments, a subject is suffering from a disease, disorder, or condition (e.g., a coronavirus (e.g., SARS-CoV-2 and / or influenza infection). In some embodiments, a subject is susceptible to a disease, disorder, or condition (e.g., a coronavirus (e.g., SARS-CoV-2 and / or influenza infection)). In some embodiments, a subject displays one or more symptoms or characteristics of a disease, disorder, or condition (e.g., a coronavirus and / or influenza infection)). In some embodiments, a subject displays one or more non-specific symptoms of a disease, disorder, or condition (e.g., a coronavirus and / or influenza infection)). In some embodiments, a subject does not display any symptom or characteristic of a disease, disorder, or condition (e.g., a coronavirus and / or influenza infection). In some embodiments, a subject is someone with one or more features characteristic of susceptibility to or risk of a disease, disorder, or condition (e.g., an influenza and / or coronavirus infection). In some embodiments, a subject is a patient. In some embodiments, a subject is an individual to whom diagnosis and / or therapy is and / or has been administered. In some embodiments, a subject is a human or another mammal (e.g. mouse, rat, rabbit, dog, cat, cattle, swine, sheep, horse or primate) that can be afflicted with or is susceptible to a disease or disorder but may or may not have the disease or disorder. In some embodiments, the term "subject" includes humans of age of at least 50, at least 55, at least 60, at least 65, at least 70, or older. In some embodiments, the term "subject" includes humans of age of at least 65, such as 65 to 80, 65 to 75, or 65 to 70.
[0166] Suffering from-. An individual who is "suffering from" a disease, disorder, and / or condition has been diagnosed with and / or displays one or more symptoms of a disease, disorder, and / or condition.
[0167] Susceptible to-. An individual who is "susceptible to" a disease, disorder, and / or condition is one who has a higher risk of developing the disease, disorder, and / or condition than does a member of the general public. In some embodiments, an individual who is susceptible to a disease, disorder and / or condition may not have been diagnosed with the disease, disorder, and / or condition. In some embodiments, an individual who is susceptible to a disease, disorder, and / or condition may exhibit symptoms of the disease, disorder, and / or condition. In some embodiments, an individual who is susceptible to a disease, disorder, and / or condition may not exhibit symptoms of the disease, disorder, and / or condition. In some embodiments, an Individual who is susceptible to a disease,Page 39 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)disorder, and / or condition will develop the disease, disorder, and / or condition. In some embodiments, an individual who is susceptible to a disease, disorder, and / or condition will not develop the disease, disorder, and / or condition.
[0168] Synthetic:used herein, the term "synthetic" refers to an entity that is artificial, or that is made with human intervention, or that results from synthesis rather than naturally occurring. For example, in some embodiments, a synthetic nucleic acid or polynucleotide refers to a nucleic acid molecule that is chemically synthesized, e.g., in some embodiments by solid-phase synthesis. In some embodiments, the term "synthetic" refers to an entity that is made outside of biological cells. For example, in some embodiments, a synthetic nucleic acid or polynucleotide refers to a nucleic acid molecule (e.g., an RNA) that is produced by in vitro transcription using a template.
[0169] Therapy: The term "therapy" refers to an ad inistration or delivery of an agent or intervention that has a therapeutic effect and / or elicits a desired biological and / or pharmacological effect (e.g., has been demonstrated to be statistically likely to have such effect when administered to a relevant population). In some embodiments, a therapeutic agent or therapy is any substance that can be used to alleviate, ameliorate, relieve, inhibit, prevent, delay onset of, reduce severity of, and / or reduce incidence of one or more symptoms or features of a disease, disorder, and / or condition. In some embodiments, a therapeutic agent or therapy is a medical intervention (e.g., surgery, radiation, phototherapy) that can be performed to alleviate, relieve, inhibit, present, delay onset of, reduce severity of, and / or reduce incidence of one or more symptoms or features of a disease, disorder, and / or condition.
[0170] Three prime untranslated region-, s used herein, the terms "three prime untranslated region" or "3' UTR" refer to a sequence of an RNA (e.g., mRNA) molecule that begins following a stop codon of a coding region of an open reading frame sequence. In some embodiments, the 3' UTR begins immediately after a stop codon of a coding region of an open reading frame sequence, e.g., in its natural context. In other embodiments, the 3' UTR does not begin immediately after stop codon of the coding region of an open reading frame sequence, e.g., in its natural context.
[0171] Threshold level (e.g., acceptance criteria). As used herein, the term "threshold level" refers to a level that are used as a reference to attain information on and / or classify the results of a measurement, for example, the results of a measurement attained in an assay. For example, in some embodiments, a threshold level means a value measured in an assay that defines the dividing line between two subsets of a population (e.g., a batch that satisfy quality control criteria vs. a batch that does not satisfy quality control criteria). Thus, a value that is equal to or higher than the threshold level defines one subset of the population, and a value that is lower than the threshold level defines the other subset of the population. A threshold level can be determined based on one or more control samples or across a population of control samples. A threshold level can be determined prior to, concurrently with, or after the measurement of interest is taken. In some embodiments, a threshold level can be a range of values.
[0012] Treat: As used herein, the term "treat," "treatment," or "treating" refers to any method used to partially or completely alleviate, ameliorate, relieve, inhibit, prevent, delay onset of, reduce severity of, and / or reduce incidence of one or more symptoms or features of a disease, disorder, and / or condition. Treatment may be administered to a subject who does not exhibit signs of a disease, disorder, and / or condition. In some embodiments, treatment may be administered to a subject who exhibits only early signs of the disease, disorder, and / or condition, for example for the purpose of decreasing the risk of developing pathology associated with the disease, disorder, Page 40 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)and / or condition. In some embodiments, treatment may be administered to a subject at a later-stage of disease, disorder, and / or condition.
[0173] The term "therapeutic treatment" relates to any treatment which improves the health status and / or prolongs (increases) the lifespan of an individual. Said treatment may eliminate the disease in an individual, arrest or slow the development of a disease in an individual, inhibit or slow the development of a disease in an individual, decrease the frequency or severity of symptoms in an individual, and / or decrease the recurrence in an individual who currently has or who previously has had a disease.
[0174] The terms "prophylactic treatment" or "preventive treatment" relate to any treatment that is intended to prevent a disease from occurring in an individual. The terms "prophylactic treatment" or "preventive treatment" are used herein interchangeably.
[0175] Vaccination As used herein, the term "vaccination" refers to the administration of a composition intended to generate an immune response, for example to a disease-associated (e.g., disease-causing) agent. In some embodiments, vaccination can be administered before, during, and / or after exposure to a disease-associated agent, and in certain embodiments, before, during, and / or shortly after exposure to the agent. In some embodiments, vaccination includes multiple administrations, appropriately spaced in time, of a vaccine composition. In some embodiments, vaccination generates an immune response to an infectious agent.
[0176] Vaccine: As used herein, the term "vaccine" refers to a composition that induces an immune response upon administration to a subject. In some embodiments, an induced immune response provides protective immunity.
[0177] Variant: As used herein in the context of molecules, e.g., nucleic acids, proteins, or small molecules, the term "variant" refers to a molecule that shows significant structural identity with a reference molecule but differs structurally from the reference molecule, e.g., in the presence or absence or in the level of one or more chemical moieties as compared to the reference entity. In some embodiments, a variant also differs functionally from its reference molecule. In general, whether a particular molecule is properly considered to be a "variant" of a reference molecule is based on its degree of structural identity with the reference molecule. As will be appreciated by those skilled in the art, any biological or chemical reference molecule has certain characteristic structural elements. A variant, by definition, is a distinct molecule that shares one or more such characteristic structural elements but differs in at least one aspect from the reference molecule. In some embodiments, a variant polypeptide or nucleic acid may differ from a reference polypeptide or nucleic acid as a result of one or more differences in amino acid or nucleotide sequence and / or one or more differences in chemical moieties (e.g., carbohydrates, lipids, phosphate groups) that are covalently components of the polypeptide or nucleic acid (e.g., that are attached to the polypeptide or nucleic acid backbone). In some embodiments, a variant polypeptide or nucleic acid shows an overall sequence identity with a reference polypeptide or nucleic acid that is at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%. In some embodiments, a variant polypeptide or nucleic acid does not share at least one characteristic sequence element with a reference polypeptide or nucleic acid. In some embodiments, a reference polypeptide or nucleic acid has one or more biological activities. In some embodiments, a variant polypeptide or nucleic acid shares one or more of the biological activities of the reference polypeptide or nucleic acid. In some embodiments, a variant polypeptide or nucleic acid lacks one or more of the biological activities of the reference polypeptide or nucleic acid. In some embodiments, a variant polypeptide or nucleic acid shows a reduced level of one Page 41 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)or more biological activities as compared to the reference polypeptide or nucleic acid. In some embodiments, a polypeptide or nucleic acid of interest is considered to be a "variant" of a reference polypeptide or nucleic acid if it has an amino acid or nucleotide sequence that is identical to that of the reference but for a small number of sequence alterations at particular positions. Typically, fewer than about 20%, about 15%, about 10%, about 9%, about 8%, about 7%, about 6%, about 5%, about 4%, about 3%, or about 2% of the residues in a variant are substituted, inserted, or deleted, as compared to the reference. In some embodiments, a variant polypeptide or nucleic acid comprises about 10, about 9, about 8, about 7, about 6, about 5, about 4, about 3, about 2, or about 1 substituted residues as compared to a reference. Often, a variant polypeptide or nucleic acid comprises a very small number (e.g., fewer than about 5, about 4, about 3, about 2, or about 1) number of substituted, inserted, or deleted, functional residues (i.e., residues that participate in a particular biological activity) relative to the reference. In some embodiments, a variant polypeptide or nucleic acid comprises not more than about 5, about 4, about 3, about 2, or about 1 addition or deletion, and, in some embodiments, comprises no additions or deletions, as compared to the reference. In some embodiments, a variant polypeptide or nucleic acid comprises fewer than about 25, about 20, about 19, about 18, about 17, about 16, about 15, about 14, about 13, about 10, about 9, about 8, about 7, about 6, and commonly fewer than about 5, about 4, about 3, or about 2 additions or deletions as compared to the reference. In some embodiments, a reference polypeptide or nucleic acid is one found in nature.
[0178] Vector. As used herein, refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. One type of vector is a "plasmid", which refers to a circular double stranded DNA loop into which additional DNA segments may be ligated. Another type of vector is a viral vector, wherein additional DNA segments may be ligated into the viral genome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g., non-episomal mammalian vectors) can be integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. Moreover, certain vectors are capable of directing the expression of genes to which they are operatively linked. Such vectors are referred to herein as "expression vectors." In some embodiments, known techniques may be used, for example, for generation or manipulation of recombinant DNA, for oligonucleotide synthesis, and for tissue culture and transformation (e.g., electroporation, lipofection). Enzymatic reactions and purification techniques may be performed according to manufacturer’s specifications or as commonly accomplished in the art or as described herein. The foregoing techniques and procedures may be generally performed according to conventional methods well known in the art and as described in various general and more specific references that are cited and discussed throughout the present specification. See e.g., Sambrook et al,. Molecular Cloning: A Laboratory Manual (4th ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N. Y. (2012)), which is incorporated herein by reference for any purpose.Detailed Description
[0179] In some embodiments, the present provides technologies (e.g., compositions, pharmaceutical compositions, immunogenic compositions, vaccines, and methods) that can be used to induce an immune response against a coronavirus (e.g., a SARS-CoV-2 virus) and one or more influenza viruses. These technologies produce improved immune response and can be used to vaccinate subjects against both coronavirus and influenza virus using a single injection. Reducing the number of injections administered to subjects can increase vaccination rates, potentially resulting in thousands of lives being saved on an annual basis.Page 42 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)
[0180] All literature and similar material cited in this application, including, but not limited to, patents, patent applications, articles, books, treatises, and web pages, regardless of the format of such literature and similar materials, are expressly incorporated by reference in their entirety. In the event that one or more of the incorporated literature and similar materials differs from or contradicts this application, including but not limited to defined terms, term usage, described techniques, or the like, this application controls. The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described in any way.Coronavirus
[0181] Coronaviruses are enveloped, positive-sense, single-stranded RNA ((+) ssRNA) viruses. They have the largest genomes (26-32 kb) among known RNA viruses and are phylogenetically divided into four genera (a, p, y, and 6), with betacoronaviruses further subdivided into four lineages (A, B, C, and D), Coronaviruses infect a wide range of avian and mammalian species, including humans. Some human coronaviruses generally cause mild respiratory diseases, although severity can be greater in infants, the elderly, and the immunocompromised. Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus (SARS-CoV), belonging to betacoronavirus lineages C and B, respectively, are highly pathogenic. Both viruses emerged into the human population from animal reservoirs within the last 15 years and caused outbreaks with high case-fatality rates.
[0182] In general, coronaviruses have four structural proteins, namely, envelope (E), membrane (M), nucleocapsid (N), and spike (S). The E and M proteins have important functions in the viral assembly, and the N protein is necessary for viral RNA synthesis. The critical glycoprotein S is responsible for virus binding and entry into target cells. The S protein is synthesized as a single-chain inactive precursor that is cleaved by furin-like host proteases in the producing cell into two noncovalently associated subunits, SI and S2. The SI subunit contains the receptor-binding domain (RBD), which recognizes the host-cell receptor. The S2 subunit contains the fusion peptide, two heptad repeats, and a transmembrane domain, all of which are required to mediate fusion of the viral and host¬ cell membranes by undergoing a large conformational rearrangement. The SI and S2 subunits trimerize to form a large prefusion spike.SARS-CoV- 2 Overview
[0183] The outbreak of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that causes atypical pneumonia (coronavirus disease 2019; COVID-19) has developed to be a public health emergency of international concern. SARS-CoV-2 (MN908947.3) belongs to betacoronavirus lineage B. It has at least 70% sequence similarity to SARS-CoV.
[0184] SARS-CoV-2 Spike (S) protein can be proteolytically cleaved into SI (685 aa) and S2 (588 aa) subunits. SI of SARS-CoV-2 comprises a receptor-binding domain (RBD), which mediates virus entry into host cells through the host angiotensin-converting enzyme 2 (ACE2) receptor.
[0185] The presentation of COVID-19 is generally with cough and fever, with chest radiography showing ground-glass opacities or patchy shadowing. However, many patients present without fever or radiographic changes, and infections may be asymptomatic which is relevant to controlling transmission. For symptomatic subjects, progression of disease may lead to acute respiratory distress syndrome requiring ventilation and subsequent multiorgan failure and death. Common symptoms in hospitalized patients (in order of highest to lowest frequency) include Page 43 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)fever, dry cough, shortness of breath, fatigue, myalgias, nausea / vomiting or diarrhea, headache, weakness, and rhinorrhea. Anosmia (loss of smell) or ageusia (loss of taste) may be the sole presenting symptom in approximately 3% of individuals who have COVID-19.
[0186] All ages may present with the disease, but notably case fatality rates (CFR) are elevated in persons >60 years of age. Comorbidities are also associated with increased CFR, including cardiovascular disease, diabetes, hypertension, and chronic respiratory disease. Healthcare workers are overrepresented among COVID-19 patients due to occupational exposure to infected patients.
[0187] In most situations, a molecular test is used to detect SARS-CoV-2 and confirm infection. The reverse transcription polymerase chain reaction (RT-PCR) test methods targeting SARS-CoV-2 viral RNA is one method for diagnosing suspected cases of COVID-19. Samples to be tested are collected from the nose and / or throat with a swab.SARS-CoV-2 Variants
[0183] Since the initial discovery of SARS-CoV-2, a number of variants have arisen around the world. As used herein, a SARS-CoV-2 variant refers to a SARS-CoV-2 virus that has acquired one or more mutations that differentiate it from the Wuhan strain of SARS-CoV-2 that first emerged in 2019. Variants can be identified by virologists and / or health organizations using an appropriate classification system, including, e.g., the Pango or NextClade classification systems. Examples of mutations that are characteristic of certain SARS-CoV-2 variants are described herein.
[0189] The emergence of SARS-CoV-2 variants raised significant concerns about geographic and temporal efficacy of vaccine interventions. The emergence of Omicron (B.l.1.529) variants, which comprise a number of mutations in the S polypeptide, has been of particular concern. As a result, since 2022, SARS-CoV-2 vaccines have been adapted to match circulating variants of concern.
[0190] In some embodiments, the present disclosure refers to a SARS-CoV-2 variant that is prevalent and / or rapidly spreading in a relevant jurisdiction. In some embodiments, such variants may be identified based on publicly available data (e.g., data provided in the GISAID Initiative database: gisaid.org, and / or data provided by the World Health Organization (WHO) (e.g., as provided at who.int / activities / tracking-SARS-CoV-2-variants). In some embodiments, such a variant refers to a variant disclosed herein.
[0191] The Omicron BA.l variant was first reported to WHO on 24 November 24, 2021, and was detected in South Africa. Omicron and its sublineages have had a major impact on the epidemiological landscape of the COVID- 19 pandemic since their initial emergence (WHO Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE): Classification of Omicron (B.l.1.259): SARS-CoV-2 Variant of Concern (2021); WHO Headquarters (HQ), WHO Health Emergencies Programme, Enhancing Response to Omicron SARS-CoV-2 variant: Technical brief and priority actions for Member States (2022)). Significant alterations in the spike (S) glycoprotein of the first Omicron variant BA.l resulted in the loss of many neutralizing antibody epitopes (M. Hoffmann et al., " The Omicron variant is highly resistant against antibody mediated neutralization: Implications for control of the COVID-19 pandemic", Ceil 185, 447-456.ell (2022)) and rendered BA.l capable of partially escaping previously established SARS-CoV-2 wild-type strain (Wuhan-Hu-l)-based immunity (V. Servellita, et al., " Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants", Cell 185, 1539-1548.e5 (2022); Y. Cao et al., " Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies", Nature 602, 657-663 (2022)).Page 44 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)
[0192] As a result, breakthrough infection of vaccinated individuals with Omicron is more common than with previous Variants of Concern (VOCs). While Omicron BA.l was displaced by the BA.2 variant in many countries around the globe, other variants such as BA.1.1 and BA.3 temporarily and / or locally gained momentum but did not become globally dominant (S. Xia et al., " Origin, virological features, immune evasion and intervention of SARS-CoV- 2 Omicron sublineages. Signal Transduct. Target. Ther. 7, 241 (2022); H. Gruel! et al., " SARS-CoV-2 Omicron sublineages exhibit distinct antibody escape patterns, Cell Host Microbe 7, 241 (2022).). Omicron BA.2.12.1 subsequently displaced BA.2 to become dominant in the United States, whereas BA.4 and BA.5 displaced BA.2 in Europe, parts of Africa, and Asia / Pacific (H. Gruell et al., " SARS-CoV-2 Omicron sublineages exhibit distinct antibody escape patterns," Cell Host Microbe 7, 241 (2022); European Centre for Disease Prevention and Control, Weekly COVID-19 country overview -Country overview report: Week 31 2022 (2022); J. Hadfield et al., " Nextstrain: Real¬ time tracking of pathogen evolution," Bioinformatics 34, 4121-4123 (2018)).
[0193] Omicron has acquired numerous alterations (amino acid exchanges, insertions, or deletions) in the S glycoprotein, among which some are shared between all Omicron VOCs while others are specific to one or more Omicron sublineages. Antigenically, BA.2.12.1 exhibits high similarity with BA.2 but not BA.l, whereas BA.4 and BA.5 differ considerably from their ancestor BA.2 and even more so from BA.l, in line with their genealogy (A. Z. Mykytyn et al., " Antigenic cartography of SARS-CoV-2 reveals that Omicron BA.l and BA.2 are antigenically distinct," Sci. Immunol. 7, eabq4450 (2022).). Major differences of BA.l from the remaining Omicron VOCs include A143-145, L212I, or ins214EPE in the S glycoprotein N-terminal domain and G446S or G496S in the receptor binding domain (RBD). Amino acid changes T376A, D405N, and R408S in the RBD are in turn common to BA.2 and its descendants but not found in BA.l. In addition, some alterations are specific for individual BA.2-descendant VOCs, including L452Q for BA.2.12.1 or L452R and F486V for BA.4 and BA.5 (BA.4 and BA.5 encode for the same S sequence). Most of these shared and VOC-specific alterations were shown to play an important role in immune escape from monoclonal antibodies and polyclonal sera raised against the wild-type S glycoprotein. In particular, the BA.4 / BA.5-specific alterations are strongly implicated in immune escape of these VOCs (P. Wang et al., " Antibody resistance of SARS-CoV-2 variants B.1.351 and B.l.1.7. Nature 593, 130-135 (2021); Q. Wang et al., " Antibody evasion by SARS-CoV-2 Omicron subvariants BA.2.12.1, BA.4, & BA.5. Nature 608, 603-608 (2022)).
[0194] The JN.l variant emerged in August 2023, in Luxemburg. It is a descendant of the BA.2.86 variant. BA.2.86 initially drew the attention of health authorities because it had a large number of S polypeptide mutations as compared to previous variants (~30 more than other variants circulating at the time). BA.2.86 never came to dominate circulating SARS-CoV-2 variants, however. Unlike BA.2.86, the JN.l variant (and descendants thereof) can transmit efficiently between humans, an ability that is thought to be a result of the acquisition of an L455S mutation in the S polypeptide (position shown relative to SEQ ID NO: 1). The JN.l rapidly came to dominate SARS-CoV-2 variants, increasing from less than 5% in November 2023, to 60% of cases by January 2024. Since the initial emergence of the JN.l variant, descendants have continued to be identified, including the JN.1.2, JN.l.6, JN.1,7, KP.2, KP.3, and XEC variants, that have acquired further mutations relative to JN.l, and which are thought to further increase the infectivity and / or transmissibility of SARS-CoV-2 variants.
[0195] Since the emergence of JN.l, descendants of JN.l have arisen and quickly supplanted the JN.l variant. These JN.l descendants include " Slip" variants (including, e.g., JN.l.16), which include L455S and F456L mutations; and " FLIRT" variants (including, e.g., KS.1.1, KP.2), which include the mutations characteristic of SLip variants and an Page 45 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)additional R346T mutation, FLuQE variants (e.g., KP.3.3), in turn, are descendants of the FLiRT variants, and include the same mutations plus an additional Q493E mutation. The 455 position has also continued to be a mutation hot spot, with " Flip" including mutations L455F and F456L. In some embodiments, an S polypeptide or fragment thereof comprises one or more mutations characteristic of each of the Slip, FLiRT, and / or Flip variants.
[0196] The XEC variant is a hybrid of the KS.1.1 and KP.3.3 variants. A description of the emergence of the JN.l variant and descendants thereof, is provided, e.g., in E. Topol, " Are We FLiRTing With A New Covid Wave?," April 18, 2024, accessible at erictopol.substack.com / p / are-we-fiirting-with-a-new-covid; and Sankaran, V. " New Covid XEC variant starting to spread in Europe - what we know," September 4, Independent, accessible at independent.co.uk / news / science / covid-variant-xec-europe-symptoms-b2613485.html.
[0197] Exemplary mutations associated with certain SARS-CoV-2 variants are provided in Table 1, below. Unless indicated otherwise, mutation positions in Table 1 and elsewhere in the present application are indicated relative to SEQ ID NO: 1.Table 1: Omicron Variants of Concern and Characteristic MutationsSubvariant Common mutationsBA.l A67V, A69-70, T95I, G142D, A143-145, A211, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981FBA.2 T19I, A24-26, A27S, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N,N440K, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969KBA.2.12.1 T19I, A24-26, A27S, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N,N440K, L452Q, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, S704L, N764K, D796Y, Q954H, N969KBA.4 or T19I, A24-26, A27S, A69 / 70, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, BA.5 K417N, N440K, L452R, S477N, T478K, E484A. F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969KBA.2.75 T19I, A24-26, A27S, G142D, K147E, W152R, F157L, I210V, V213G, G257S, G339H, N354D, S371F,S373P, S375F, T376A, D405N, R408S, K417N, N440K, G446S, N460K, S477N, T478K, E484A, Q498R, N501Y, Y505H D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K BA.2.75.2 T19I, A24-26, A27S, G142D, K147E, W152R, F157L, I210V, V213G, G257S, G339H, R346T, N354D,S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, G446S, N460K, S477N, T478K, E484A, F486S, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K, and D1199NBJ.l T19I, A24-26, A27S, V83A, G142D, A144, H146Q, Q183E, V213E, G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, S477N, T478K, V483A, E484A, F490V, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, G798D, Q954H, N969K, and S1003IBA.4.6 or T19I, A24-26, A27S, A69 / 70, G142D, V213G, G339D, R346T, S371F, S373P, S375F, T376A, D405N, BF.7 R408S, K417N, N440K, L452R, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N658S, N679K, P681H, N764K, D796Y, Q954H, and N969KXBB T19I, A24-26, A27S, V83A, G142D, A144, H146Q, Q183E, V213E, G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486S, F490S, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969KXBB.l T19I, A24-26, A27S, V83A, G142D, A144, H146Q, Q183E, V213E, G252V, G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486S, F490S, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969KXBB.2 T19I, A24-26, A27S, V83A, G142D, A144, H146Q, Q183E, V213E, D253G, G339H, R346T, L368I,S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, N460K, S477N,Page 46 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)Subvariant Common mutationsT478K, E484A, F486S, F490S, Q493R, Q498R. N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969KXBB.1.3 T19I, A24-26, A27S, V83A, G142D, A144, H146Q, Q183E, V213E, G252V, G339H, R346T, L368I,S371F, S373P, S375F, T376A, D405N, R4O8S, K417N, N440K, V445P, G446S, N460K, S477N, T478K, A484T, F486S, F490S, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969KBA.2.3.20 T19I, A24-26, A27S, G142D, M153T, N164K, V213G, H245N, G257D, G339D, S371F, S373P, S375F,T376A, D405N, R408S, K417N, N440K, K444R, E484R N450D, L452M, N460K, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969KBQ.1.1 T19I, A24-26, A27S, A69 / 70, G142D, V213G, G339D, R346T, S371F, S373P, S375F, T376A, D405N,R408S, K417N, N440K, K444T, L452R, N460K, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969KJN.l insl6MPLF, T19I, R21T, A24-26, A27S, S50L, A69-70, V127F, G142D, A145, F157S, R158G, A211,L222I, V213G, L216F, H245N, A264D, I332V, G339H, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, N460K, S477N, T478K, N481K, A483, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, P1143LJN.l.2 insl6MPLF, T19I, R21T, A24-26, A27S, S50L, A69-70, V127F, G142D, A145, F157S, R158G, A211,L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, N460K, S477N, T478K, N481K, A483, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, P1143LJN.l.6 inslGMPLF, T19I, R21T, A24-26, A27S, S50L, A69-70, V127F, G142D, A145. F157S, R158G, A211,L212I, V213G, L216F, H245N, A264D, I332V, G339H, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, N460K, S477N, T478K, N481K, A483, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, T572I, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, P114.3L, E1150DKP.2(1) inslSMPLF, T19I, R21T, A24-26, A27S, S50L, A69-70, V127F, G142D, A145, F157S, R158G, A211,L212I, V213G, L216F, H245N, A264D, I332V, G339H, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, N460K, S477N, T478K, N481K, A483, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, P1143L, M1229IKP.2(2) insl6MPLF, T19I, R21T, A24-26, A27S, S50L, A69-70, V127F, G142D, A145, F157S, R158G, A211,L212I, V213G, L216F, H245N, A264D, I332V, G339H, R446T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456LN460K, S477N, T478K, N481K, A483, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, P1143L, M1229IXEC insl6MPLF, T19I, R21T, T22N, A24-26, A27S, S50L, A69-70, V127F, G142D, A145, F157S, R158G,A211, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, A483, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, V1104L, P1143L JN.l.7 insl6MPLF, T19I, R21T, A24-26, A27S, S50L, A69-70, V127F, G142D, A145, F157S, R158G, A211,L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, A483, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, V1104L, P1143L XBB.1.5 T19I, A24-26, A27S, V83A, G142D, A145, H146Q, Q183E, V213E, G252V, G339H, R346T, L368I,S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969KMC.l Insl6MPLF, T19I, R21T, L24del, P25del, P26dei, A27S, S31del, S50L, H69del, V70del, V127F, G142D, Y144del, F157S, R158G, N211del, L212I, V213G, L216F, H245N, A264D, I332V, G339H, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S,N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, V483del, E484K, F486P, Q493E, Page 47 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)Subvariant Common mutationsQ498R, N501Y, Y505H, E554K, A570V, T572I, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, V1104L, P1143LKP.3.1.1 Insl6MPLF, T19I, R21T, L24del, P25del, P26dei, A27S, S31dei, S50L, H69del, V70del, V127F, G142D, Y144del, F157S, R158G, N211del, L212I, V213G, L216F, H245N, A264D, I332V, G339H, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, V483del, E484K, F486P, Q493E, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, V1104L, P1143LLP.8.1 InslSMPLF, T19I, R21T, L24del, P25del, P26dei, A27S, S31del, S50L, H69del, V70del, V127F, G142D, Y144del, F157S, R158G, F186L, R190S, N211del, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445R, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, V483del, E484K, F486P, Q493E, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, K1086R, V1104L, P1143LMV.l lnsl6MPLF, T19I, R21T, T22N, L24del, P25del, P26del, A27S, S31F, S50L, H69dei, V70del, V127F,G142D, Y144del, F157S, R158G, K182N, N211del, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456V, N460K, S477N, N481K, V483del, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, P1143LLF.7 Insl6MPLF, T19I, R21T, T22N, L24dei, P25del, P26del, A27S, S31P, S50L, H69del, V70del, V127F,G142D, Y144del, F157S, R158G, K182R, R190S, N211del, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, K444R, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, V483dei, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, P1143LBA.3.2 P9L, R21T, P26L, A67V, H69del, V70del, T95I, I101T, C136del, N137del, D138dei, P139del,F140del, L141del, G142del, V143del, Y144del, Y145del, H146del, K147del, F157S, N164K, S172F, K187T, N211del, L212I, L242del, A243del, P251S, I326V, G339Y, A348P, S371F, S373P, S375F, R403K, D405N, T408S, K417N, A435S, N440R, V445A, G446D, L452W, N460K, S477N, T478N,E484K, G496S, Q498R, N501Y, K529N, A538-1210SARS-CoV-2 Variant Adaptions
[0198] In some embodiments, utilized sequences can comprise one or more mutations characteristic of a viral variant (e.g., a variant that is prevalent and / or that is predicted to be highly immune escaping). In some embodiments, utilized sequences comprise one or more mutations characteristic of a variant of concern (e.g., a variant of concern identified by WHO). In some embodiments, utilized sequences comprise one or more mutations characteristic of a viral variant that has been determined to be or has been predicted to be highly immune escaping (e.g., highly immune escaping relative to an immune response developed in subjects administered a previously approved vaccine and / or a previously prevalent viral variant).
[0199] In some embodiments, the variant is a variant of concern e.g., a variant that has been predicted to and / or has been shown to spread rapidly in a relevant jurisdiction, e.g., as identified by certain public health agencies, e.g., the Center for Disease Control and Prevention (CDC), Public Health England and the COVID-19 Genomics UK Consortium for the UK, the Canadian COVID Genomics Network (CanCOGeN), and / or the World Health Organization (WHO)). In some embodiments, a variant has been predicted to have a highly likelihood of becoming a variant of concern e.g., using sequence-based algorithms that predict the ability of a variant to escape previously developed immune responses and / or measure the ''fitness" of a given variant, such as described, e.g., in WO2022 / 235847 and WO2022 / 235853, the contents of each of which are incorporated by reference herein in their entirety). In some embodiments, a variant is a SARS-CoV-2 variant described herein, or a descendent thereof.Page 48 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)
[0200] In some embodiments, a coronavirus (e.g., SARS-CoV-2) antigen comprises an immunogenic fragment of an S polypeptide (e.g., an SI polypeptide, a fragment of an SI polypeptide, or an RBD of an S polypeptide) or a variant thereof. In some embodiments, a variant of an immunogenic fragment of a SARS-CoV-2 polypeptide comprises one or more mutations characteristic of a SARS-CoV-2 variant (e.g., a variant described herein, a variant of concern, or a variant of concern that has been recommended for seasonal adaption for a relevant governmental health authority).
[0201] As used herein, a full-length SARS-CoV-2 S polypeptide comprising a " Wild-Type" or " Wuhan" sequence has a sequence corresponding to that of the first detected SARS-CoV-2 strain, consisting of 1273 amino acids and having an amino acid sequence according to SEQ ID NO: 1:MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFD NPVLPFN DGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVN NATN WIKVCEFQFCN DPFLGVYYHKN N KSWM ESEFRVY SSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGIN1TRFQTLL ALH RSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYN ENGUTDAVDCALDPLSETKCTLKSFTVEKGIYQTSN FRVQP TESIVRFPNITN LCPFG EVFNATRFASVYAWN RKRISNCVADYSVLYNSASFSTFKCYGVSPTKLN DLCFTNVYADSFVIR GDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNG VEGFNCYFPLQSYGFQPTNGVGYQPYRVWLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPF QQFGRDIADTTDAVRDPQTLEILDrTPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSN VFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIFTNFT1SVT TEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFS QILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTrrSG WTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDWNQNAQALNTLVK QLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGK GYHLMSFPQSAPHGWFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQirTTDNTFVSG NCDWIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASWNIQKEIDRLNEVAKNLNESLIDLQELGK YEQYIKWPWYIWLGFIAGUAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT (SEQ ID NO: 1)
[0202] Unless otherwise indicated, position numberings in a SARS-CoV-2 S polypeptide given herein are in relation to the amino acid sequence of SEQ ID NO: 1. One of skill in the art reading the present disclosure will understand and be able to determine corresponding positions in a SARS-CoV-2 S polypeptide variant sequence from locations of positions provided relative to the amino acid sequence of SEQ ID NO: 1 (i.e., a person of skill in the art provided positions relative to SEQ ID NO: 1, or another variant, will be able to determine corresponding positions in the S polypeptide sequence of another SARS-CoV-2 variant or a fragment thereof). One of skill in the art will also understand that a fragment of a SARS-CoV-2 S polypeptide that comprises one or more mutations characteristic of a SARS-CoV-2 variant, comprises only those mutations that fall within the fragment region. For example, if a fragment of an SI polypeptide comprises an amino acid sequence corresponding to amino acids 20-528 of SEQ ID NO: 1 and comprises one or more mutations characteristic of a SARS-CoV-2 variant, one of skill in the art will understand that the truncated SI polypeptide comprises only those mutations located within the corresponding region of the SARS- CoV-2 variant.
[0203] In some embodiments, a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide (e.g., a truncated SI polypeptide, including, e.g., a sequence comprising amino acids 1-528, 14-528, 17-528, 20-528, 1-541, 14-541, 17-541, 20-541, 1-537, 14-527, 17-537, or 20-537 of SEQ ID NO: 1) includes 1 or more mutations characteristic of a SARS-CoV-2 variant (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, 28, 29, 30, 31, 32, 33, 34, 25, 36 or more (e.g., all)), to the extent they are present in the corresponding fragment of the S polypeptide of the SARS-CoV-2 variant.Page 49 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)
[0204] In some embodiments, a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide comprises one or more mutations (including, e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more) that are characteristic of a certain Omicron variant (e.g., one or more mutations characteristic of an Omicron variant listed in Table 1, e.g., each of the mutations characteristic of a given XBB, JN.l, KP.2, XEC, MC.l, KP.3, LP.8, MV.l, LF.7, BA3.2 variant in the above Table 1).
[0205] In some embodiments, an RNA comprises a nucleotide sequence encoding a polypeptide comprising a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide (e.g., an RBD or a truncated SI polypeptide (e.g., a region corresponding to amino acids 1-537 or 14-528 of SEQ ID NO: 1), or a variant thereof, wherein the S polypeptide or the fragment of the S polypeptide 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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, or more) mutations characteristic of a SARS-CoV-2 variant (e.g., one or more mutations characteristic of a SARS-CoV-2 variant listed in Table 1).
[0206] In some embodiments, an RNA comprises a nucleotide sequence encoding a polypeptide comprising a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide (e.g., an RBD or a truncated SI polypeptide (e.g., a region corresponding to amino acids 1-537 or 14-528 of SEQ ID NO: 1), or a variant thereof, wherein the S polypeptide or the fragment of the S polypeptide comprises at least 5% (e.g., at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95%) of the mutations characteristic of a given SARS-CoV-2 variant in the S polypeptide fragment region. For example, in some embodiments, a construct comprises at least 5% of the mutations associated a SARS-CoV-2 variant in the region corresponding to amino acids 1-537 or 14-528 of the S polypeptide.
[0207] In some embodiments, an RNA comprises a nucleotide sequence encoding a polypeptide comprising a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide (e.g., an RBD or a truncated SI polypeptide (e.g., a region corresponding to amino acids 1-537 or 14-528 of SEQ ID NO: 1), wherein the fragment of a SARS-CoV-2 S polypeptide 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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, or more) mutations characteristic of a SARS-CoV-2 variant.
[0208] In some embodiments, RNA described herein encodes a SARS-CoV-2 S polypeptide or an immunogenic fragment of a SARS-CoV-2 S polypeptide or a variant thereof comprising one or more mutations characteristic of a BA.l, BA.2, BA.2.12.1, BA.4, B.5, BA.2.75, BA.2.75.2, BJ.l, BA.4.6, BF.7, XBB, XBB.l, XBB.2, XBB.1.3, BA.2.3.20, BQ.1.1, JN.l, JN.1.2, JN.l.6, KP.2, KP.3, XEC, JN.l.7, XBB.1.5, MC.l, KP.3.1.1, LP.8.1, MV.l, LF.7, and / or BA.3.2 variant {e.g., one or more mutations described herein). In some embodiments, the one or more mutations include a mutation at a position corresponding to position 455 of SEQ ID NO: 1 (e.g., L455S). In some embodiments, the one or more mutations include mutations at a position corresponding to position 455 of SEQ ID NO: 1 (e.g., L455F). In some embodiments, the one or more mutations include a mutation at a position corresponding position 456 of SEQ ID NO: 1 (e.g., F456L). In some embodiments, the one or more mutations include mutations at positions corresponding positions 455 and 456 of SEQ ID NO: 1 (e.g., F456L and L455F). In some embodiments, the one or mutations include a mutation at a position corresponding to position 346 of SEQ ID NO: 1 (e.g., R346T). In some embodiments, the one or more mutations include a mutation at a position corresponding to position 1104 of SEQ ID Page 50 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)NO: 1 (e.g., V1104L). In some embodiments, the one or more mutations include mutations at positions corresponding to positions 346 and 1104 of SEQ ID NO: 1 (e.g., R346T and V1104L).
[0209] In some embodiments, one or more mutations characteristic of a KP.2 variant include one or more of (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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63 or more) of (e.g, aii of) insl6MPLF, T19I, R21T, A24-26, A27S, S50L, A69-70, V127F, G142D, A145, F157S, R158G, A211, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, A483, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, V1104L, and P1143L, where mutations are indicated relative to SEQ ID NO: 1. In some embodiments, one or mutations characteristic of a KP.2 variant include R346T and V1104L, where positions are indicated relative to SEQ ID NO: 1. In some embodiments, one or mutations characteristic of a KP.2 variant include R346T, F456L, and / or V1104L, where positions are indicated relative to SEQ ID NO: 1.
[0210] In some embodiments, one or more mutations characteristic of a KP.3 variant include one or more of (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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63. 64, 65 or more) of (e.g., all of) insl6MPLF, T19, A24-26, A27S, S50L, A69 / 70, V127F, G142D, A144, F157S, R158G, A211, L212I, V213G, L216F, H245N, A264D, I332V, G339H, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, A483, E484K, F486P, Q493E, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, V1104L, P1143L, or any combination thereof. In some embodiments one or more mutations characteristic of a KP.3 variant include F456L, Q493E, and / or V1104L, wherein positions are indicated relative to SEQ ID NO: 1.
[0211] In some embodiments, one or more mutations characteristic of a XEC variant include one or more of (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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 67 or more) of (e.g., aii of) insl6MPLF, T19I, R21T, T22N, A24-26, A27S, S50L, A69-70, V127F, G142D, A145, F157S, R158G, A211, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, A483, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, V1104L, P1143L, where mutations are indicated reiative to SEQ ID NO: 1. In some embodiments one or more mutations characteristic of a XEC variant include T22N, F59S, F456L, Q493E, and / or V1104L, wherein positions are indicated relative to SEQ ID NO: 1.
[0212] In some embodiments, a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide 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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, or 66 or more) of the following list of mutations: insl6MPLF, T19I, R21T, A24-26, A27S, S50L, A69-70, V127F, G142D, A145, F157S, R158G, A211, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R446T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D,Page 51 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)L452W, L455S, F456LN460K, S477N, T478K, N481K, A483, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, P1143L, or M1229I. In some embodiments, a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide 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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52 or more of the following list of mutations: insl6MPLF, T19I, R21T, A24-26, A27S, S50L, A69-70, V127F, G142D, A145, F157S, R158G, A211, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R446T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456LN460K, S477N, T478K, N481K, A483, E484K, F486P, Q498R, N501Y, Y505H,
[0213] In some embodiments, one or more mutations characteristic of a JN.l variant include one or more of {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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63 or more) of (e.g., all of) insl6MPLF, T19I, R21T, A24-26, A27S, S50L, A69-70, V127F, G142D, A145, F157S, R158G, A211, L212I, V213G, L216F, H245N, A264D, I332V, G339H, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, N460K, S477N, T478K, N481K, A483, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, P1143L, or any combination thereof, where mutations are indicated relative to SEQ ID NO: 1. In some embodiments, one or more mutations characteristic of a JN.l variant include insl6MPLF, T19I, R21T, A24-26, A27S, S50L, A69-70, V127F, G142D, A145. F157S, R158G, A211, L212I, V213G, L216F, H245N, A264D, I332V, G339H, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, N460K, S477N, T478K, N481K, A483, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, and P1143L, relative to SEQ ID NO: 1. In some embodiments, one or mutations characteristic of a JN.l variant include L455S.
[0214] In some embodiments, a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide (e.g., an RBD or a truncated SI polypeptide described herein) or a variant thereof comprises one or more mutations characteristic of a JN.2 variant. In some embodiments, a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide 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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, or more) of the following list of mutations: insl6MPLF, T19I, R21T, A24-26, A27S, S50L, A69-70, V127F, G142D, A145, F157S, R158G, A211, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, N460K, S477N, T478K, N481K, A483, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, and P1143L. In some embodiments, a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide 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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, or more of the following list of mutations: insl6MPLF, T19I, R21T, A24-26, A27S, S50L, A69-70, V127F, G142D, A145, F157S, R158G, A211, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, N460K, S477N, T478K, N481K, A483, E484K, F486P, Q498R, N501Y, and Y505H.Page 52 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)
[0215] In some embodiments, one or more mutations characteristic of a JN.1.2 variant include one or more of {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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63 or more of) (e.g., all of) insl6MPLF, T19I, R21T, A24-26, A27S, S50L, A69-70, V127F, G142D, A145, F157S, R158G, A211, L212I, V213G, L216F, H245N, A264D, I332V, G339H, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, N460K, S477N, T478K, N481K, A483, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, P1143L, and M1229I, where mutations are indicated relative to SEQ ID NO: 1. In some embodiments, one or more mutations characteristic of a JN.1.2 variant include M1229I, where position is indicated relative to SEQ ID NO: 1.
[0216] In some embodiments, one or more mutations characteristic of a JN.1.6 variant include one or more of {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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63 or more of) (e.g., all of) insl6MPLF, T19I, R21T, A24-26, A27S, S50L, A69-70, V127F, G142D, A145. F157S, R158G, A211, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, N460K, S477N, T478K, N481K, A483, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, and P1143L, where mutations are indicated relative to SEQ ID NO: 1. In some embodiments, one or more mutations characteristic of a JN.1.6 variant include R346T.
[0217] In some embodiments, one or more mutations characteristic of a JN.1.7 variant include one or more of 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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63 or more of) (e.g., all of) insl6MPLF, T19I, R21T, A24-26, A27S, S50L, A69-70, V127F, G142D, A145. F157S, R158G, A211, L212I, V213G, L216F, H245N, A264D, I332V, G339H, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, N460K, S477N, T478K, N481K, A483, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, T572I, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, P1143L, and E1150D, where mutations are indicated relative to SEQ ID NO: 1.
[0218] In some embodiments, a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide (e.g., an RBD or a truncated SI polypeptide described herein) or a variant thereof comprises one or more mutations characteristic of a JN.6 variant. In some embodiments, a fragment of a SARS-CoV-2 S polypeptide 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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, or more) of the following list of mutations: insl6MPLF, T19I, R21T, A24-26, A27S, S50L, A69-70, V127F, G142D, A145. F157S, R158G, A201, L202I, V203G, L206F, H245N, A264D, I332V, G339H, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, N460K, S477N, T478K, N481K, A483, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, T572I, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, P1143L, and E1150D. In some embodiments, a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide 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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44,Page 53 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)45, 46, 47, 48, or more of the following list of mutations: insl6MPLF, T19I, R21T, A24-26, A27S, S50L, A69-70, V127F, G142D, A145. F157S, R158G, A201, L202I, V203G, L206F, H245N, A264D, I332V, G339H, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, N460K, S477N, T478K, N481K, A483, E484K, F486P, Q498R, N501Y, Y505H.
[0219] In some embodiments, a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide (e.g., an RBD or a truncated SI polypeptide described herein) or a variant thereof comprises one or more mutations characteristic of a JN.6 variant. In some embodiments, a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide 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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, or more) of the following mutations: insl6MPI_F, T19I, R21T, A24-26, A27S, S50L, A69-70, V127F, G142D, A145, F157S, R158G, A201, L202I, V203G, L206F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, A483, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, V1104L, and / or P1143L. In some embodiments, a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide 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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or more) of the following mutations: insl6MPLF, T19I, R21T, A24-26, A27S, S50L, A69-70, V127F, G142D, A145, F157S, R158G, A201, L202I, V203G, L206F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, A483, E484K, F486P, Q498R, N501Y, and / or Y505H.
[0220] In some embodiments, a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide (e.g., an RBD or a truncated SI polypeptide described herein) or a variant thereof comprises one or more mutations characteristic of an XBB.1.5 variant. In some embodiments, a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide 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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, or more) of the following mutations: T19I, A24-26, A27S, V83A, G142D, A145, H146Q, Q183E, V213E, G252V, G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and / or N969K. In some embodiments, a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide 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, 28, 29, 30, 31, 32, 33, or more) of the following mutations: T19I, A24-26, A27S, V83A, G142D, A145, H146Q, Q183E, V213E, G252V, G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, and / or Y505H.
[0221] In some embodiments, a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide encoded by an RNA molecule comprises a majority of mutations characteristic of a KP.2, KP.3, or XEC variant and one or more additional mutations. In some embodiments a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide comprises 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63 or more of (e.g., all of) mutations characteristic of a KP.2, KP.3, or XEC variant {e.g., Page 54 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)mutations provided herein) and one or more additional mutations. In some embodiments, a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide comprises a majority of mutations characteristic of a JN.l variant (e.g., as described herein) and one or more additional mutations. In some embodiments, a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide comprises a majority of mutations characteristic of a JN.l variant (e.g., as described herein) and one or more additional mutations characteristic of a descendent of a JN.l variant (e.g., a descendant described herein). In some embodiments, a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide comprises a majority of mutations characteristic of a JN.l variant (e.g., as described herein) and one or more additional mutations characteristic of increased spread of a descendent of a JN.l variant (e.g., a descendant described herein).
[0222] In some embodiments, a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide comprises a majority of mutations characteristic of a JN.l variant (e.g., as described herein) and:(a) a mutation at a position corresponding to position 346 of SEQ ID NO: 1 (e.g., R346T);(b) a mutation at a position corresponding to position 456 of SEQ ID NO: 1 (e.g., F456L);(c) mutations at positions corresponding to positions 455 and 456 of SEQ ID NO: 1 (e.g., L455S and F456L); or (d) a mutation at a position corresponding to position 1104 of SEQ ID NO: 1 (e.g., V1104L).
[0223] In some embodiments, a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide comprises a majority of mutations characteristic of a KP.2 and / or JN.l variant and one or more additional mutations. In some embodiments, a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide comprises a majority of mutations characteristic of a KP.2 and / or JN.l variant and a mutation at a position corresponding to position 493 of SEQ ID NO: 1 (e.g., Q493E).
[0224] In some embodiments, a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide of a XEC variant includes a majority of mutations characteristic of a KP.2, KP.3 and / or JN.l variant and one or more additional mutations. In some embodiments, a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide comprises a majority of mutations characteristic of a KP.2, KP.3 and / or JN.l variant and a mutation at a position corresponding to position 22 of SEQ ID NO: 1 (e.g., T22N). In some embodiments, a SARS-CoV-2 S polypeptide or a fragment of a SARS-CoV-2 S polypeptide comprises a majority of mutations characteristic of a KP.2, KP.3 and / or JN.l variant and a mutation at a position corresponding to position 592 of SEQ ID NO: 1 (e.g., F592).
[0225] As used herein, a change to each amino acid position in a sequence is counted as a single mutation. For example, insl6MPLF would be counted as 4 mutations.
[0226] In some embodiments, one or more mutations characteristic of an MV.l variant include one or more of (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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67 or more of (e.g., all of) insl6MPLF, T19I, R21T, T22N, A24-26, A27S, S31F, S50L, A69-70, V127F, G142D, A144, F157S, R158G, K182N, A211, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456V, N460K, S477N, N481K, A483, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, or P1143L, where mutations are indicated relative to SEQ ID NO: 1.Page 55 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)
[0227] In some embodiments, one or more mutations characteristic of an MC.l variant include one or more of (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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68 or more of (e.g, all of) Insl6MPLF, T19I, R21T, A24-26, A27S, A31, S50L, A69-70, V127F, G142D, A144, F157S, R158G, A211, L212I, V213G, L216F, H245N, A264D, I332V, G339H, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, A483, E484K, F486P, Q493E, Q498R, N501Y, Y505H, E554K, A570V, T572I, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, V1104L, or P1143L, where mutations are indicated relative to SEQ ID NO: 1.
[0228] In some embodiments, one or more mutations characteristic of an LP.8.1 variant include one or more of (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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 67, 68, 69, 70, 71 or more of (e.g., all of) Insl6MPLF, T19I, R21T, A24-26, A27S, A31, S50L, A69-70, V127F, G142D, A144, F157S, R158G, F186L, R190S, A211, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445R, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, A483, E484K, F486P, Q493E, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, K1086R, V1104L, or PU43L, where mutations are indicated relative to SEQ ID NO: 1. In some embodiments one or more mutations characteristic of an LP.8.1 variant include A31, F186L, R190S, R346T, V445R, F456L, Q493E, K1086R, and / or V1104L, wherein positions are indicated relative to SEQ ID NO: 1.
[0229] In some embodiments, one or more mutations characteristic of an LF.7 variant include one or more of (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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70 or more of (e.g., all of) Insl6MPLF, T19I, R21T, T22N, A24-26, A27S, S31P, S50L, A69-70, V127F, G142D, A144, F157S, R158G, K182R, R190S, A211, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, K444R, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, A483, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, or P1143L, where mutations are indicated relative to SEQ ID NO: 1.
[0230] In some embodiments, one or more mutations characteristic of an BAS, 2 variant include one or more of (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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70 or more of (e.g., all of) P9L, R21T, P26L, A67V, H69del, V70del, T95I, I101T, C136del, N137del, D138del, P139del, F140del, L141del, G142del, V143del, Y144del, Y145del, H146del, K147del, F157S, N164K, S172F, K187T, N211del, L212I, L242del, A243del, P251S, I326V, G339Y, A348P, S371F, S373P, S375F, R403K, D405N, T408S, K417N, A435S, N440R, V445A, G446D, L452W, N460K, S477N, T478N, E484K, G496S, Q498R, N501Y, K529N, or A538-1210, where mutations are indicated relative to SEQ ID NO: 1.
[0231] As used herein, every change in an amino acid is counted as a single mutation. For example, insl6MPLF would be counted as 4 mutations.Page 56 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)Immunogenic Portions of a Coronavirus S Polypeptide
[0232] As noted elsewhere in the present disclosure, in some embodiments, compositions described herein deliver an immunogenic portion of a full-length SARS-CoV-2 S protein. As used herein, "immunogenic portion of a full-length SARS-CoV-2 S protein" is synonymous with an "immunogenic fragment o a full length SARS-CoV-2 S protein).
[0233] The SARS-CoV-2 Spike (S) protein comprises an extracellular N-terminus, a transmembrane (TM) domain anchored in the viral membrane, and a short intracellular C-terminal segment. The S protein normally exists in a metastable, prefusion conformation. Once the virus interacts with the host cell, extensive structural rearrangement of the S protein occurs, allowing the virus to fuse with the host cell membrane.
[0234] An immunogenic portion of a SARS-CoV-2 S protein lacks certain features that are present in the full- length polypeptide. In some embodiments, an immunogenic portion of a SARS-CoV-2 S protein lacks certain features that are in the full length polypeptide e.g., features that have been shown or predicted to interfere with induction of a naive immune response). For example, in some embodiments, an immunogenic portion of a SARS-CoV-2 lacks regions that have (I) a low number or density of B cell neutralization epitopes and / or (ii) a high number or density of B cell epitopes not associated with neutralization. For example, in some embodiments, an immunogenic portion of a SARS-CoV-2 S protein lacks a full 52 domain. In some embodiments, a SARS-CoV-2 S protein lacking a full 52 domain lacks regions of 52 that have (i) a low number or density of B cell epitopes associated with neutralization or (ii) a high number of B cell epitopes not associated with neutralization but retains other portions of 52. In some embodiments, an immunogenic portion of a SARS-CoV-2 S protein lacks the entire 52 domain. In some embodiments, an immunogenic portion of a SARS-CoV-2 S protein lacks a full 52 domain, but comprises certain sequences that can improve immunogenicity and / or stability of an immunogenic portion (e.g., in some embodiments, an immunogenic portion lacks a full S2 domain but retains a TM sequence and optionally a sequence that is endogenously C-terminally adjacent to the TM sequence in a SARS-CoV-2 S protein). In some embodiments, an immunogenic portion of a SARS-CoV-2 S protein includes fragments of the 52 subdomain that are highly conserved and which have been shown to include one or more neutralization epitopes. Examples of such regions include the fusion peptide (FP), stem helix (SH), and heptad repeat 2 (HR2) regions of the 52 subdomain, e.g., as described herein. Among other things, the present disclosure provides an insight that a polypeptide comprising a (1) one or more NTDs, one or more RBDs, and / or one or more truncated SI subdomains, and (2) one or more fragments of an 52 subdomain that are highly conserved and comprise one or more neutralization epitopes, can provide improved immune responses (e.g., higher neutralization titers, increased cross-neutralization, and / or a more broadly neutralizing T cell response) as compared to a reference (e.g., as compared to polypeptides comprising an immunogenic portion of a SARS-CoV-2 S protein that is conserved and lacks one or more neutralization epitopes).
[0235] A person of skill in the art reading the present disclosure will be able to identify B cell epitopes in a SARS-CoV-2 S protein (e.g., a SARS-CoV-2 S protein) and determine which epitopes are or are not associated with neutralization. For example, a person of skill in the art will be aware of numerous studies that have identified such regions using antibody binding studies (e.g., studies characterizing antibodies produced in subjects infected with or vaccinated against SARS-CoV-2).
[0236] In some embodiments, an immunogenic portion of a SARS-CoV-2 S protein (e.g., SARS-CoV-2 S protein comprises certain regions that have been determined to have a high number or density of neutralization epitopes and Page 57 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)optionally a high mutation rate. In some embodiments, an immunogenic portion of a SARS-CoV-2 S protein comprises an N-temninal domain (NTD) of the S protein. In some embodiments, an immunogenic portion of a SARS- CoV-2 S protein comprises a receptor binding domain (RBD) of the S protein. In some embodiments, an immunogenic portion of a SARS-CoV-2 S protein comprises an SI domain of the S protein or a truncated SI subdomain or a variant thereof.
[0237] In some embodiments, an immunogenic portion of a SARS-CoV-2 S protein comprises an RBD and an NTD and omits other features of the SI domain, optionally wherein the endogenous secretory signal peptide in the NTD is replaced with a heterologous secretory signal peptide.
[0238] SARS-CoV-2 S proteins are well characterized, and a person of skill in the art will be able to determine which portions of an S protein sequence correspond to immunogenic portions discussed herein (e.g., which portions of an S protein sequence correspond to the NTD, the RBD, the SI, and the S2 domains).SI Polypeptide
[0239] In some embodiments, an SI polypeptide of a SARS-CoV-2 S polypeptide comprises amino acids 1 to 678 of SEQ ID NO: 1, or a corresponding region in an S polypeptide of a SARS-CoV-2 variant. In some embodiments, an SI polypeptide of a SARS-CoV-2 S polypeptide comprises amino acids 1 to 683 of SEQ ID NO: 1, or a corresponding region in an S polypeptide of a SARS-CoV-2 variant. In some embodiments, an SI polypeptide of a SARS-CoV-2 S polypeptide comprises amino acids 1 to 685 of SEQ ID NO: 1, or a corresponding region in an S polypeptide of a SARS-CoV-2 variant.
[0240] In some embodiments, an SI polypeptide of a SARS-CoV-2 S polypeptide comprises an amino acid sequence according to SEQ ID NO: 10 or an amino acid sequence at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical thereto.MFVFLVLLPLVSSQCVNUTRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPAL PFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNWIKVCEFQFCNDPFLDVYQKNNKSWMESEFRVYSSANN CTFEYVSQPFLMDLEGKEGNFKNLREFVFKNIDGYFKIYSKHTPINLERDLPQGFSALEPLVDLPIGINITRFQTLLALHRSY LTPVDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFP NITN LCPFH EVFNATTFASVYAWN RKRISNCVADYSVIYNFAPFFAFKCYGVSPTKLN DLCFTNVYADSFVIRGN EVSQIAP GQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKPSGNYNYLYRLFRKSKLKPFERDISTEIYQAGNKPCNGVAGPNCYSPL QSYGFRPTYGVGHQPYRWVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADT TDAVRDPQTLEHDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIG AEYVNNSYECDIPIGAGICASYQTQT (SEQ ID NO: 10)
[0241] In some embodiments, an SI polypeptide of a SARS-CoV-2 S polypeptide comprises an amino acid sequence according to SEQ ID NO: 11 or an amino acid sequence at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical thereto.MFVFLVLLPLVSSQG / NLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDN PVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSS ANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINrTRFQTLLALH RSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTrTDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESI VRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEV RQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFN CYFPLQSYGFQPTNGVGYQPYRVWLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGR DIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRA GCLIGAEHVNNSYECDIPIGAGICASYQTQT (SEQ ID NO: 11).Page 58 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)Receptor Binding Domain (RBD)
[0242] The Spike receptor binding domain (RBD) has been researched extensively since the onset of tine pandemic because of its role in the host ceil invasion process, during which it binds the angiotensin-converting enzyme 2 (ACE2) receptor on the host cell surface. This process is similar to invasion by SARS-CoV and HCoV-NL63. The RBD comprises two domains: a large core domain, which folds as a twisted five-stranded antiparallel p-sheet, and an receptor binding motif (RBM), a 69-residue long insertion of two short a-helices and p-strands between the 4 and P7 strands.
[0243] RBD is the main site of mutations that characterize SARS-CoV- 2 variants, some of which have spread rapidly throughout human populations and are thus called variants of concern (VOC). Specific mutations can alter the properties of the RBD, influencing its interaction with ACE2 and contribute to the virus's ability to evade host immune responses and vaccine induced immunity.
[0244] In some embodiments, the N-terminal residue of an RBD corresponds to about position 317 in SEQ ID NO: 1, or a corresponding amino acid in an S polypeptide of a SARS-CoV-2 variant. In some embodiments, the N- terminal residue of an RBD corresponds to about position 319 in SEQ ID NO: 1, or a corresponding amino acid in an S polypeptide of a SARS-CoV-2 variant. In some embodiments, the N-terminal residue of an RBD corresponds to about position 327 in SEQ ID NO: 1, or a corresponding amino acid in an S polypeptide of a SARS-CoV-2 variant. In some embodiments, the N-terminal residue of an RBD corresponds to about position 328 in SEQ ID NO: 1, or a corresponding amino acid in an S polypeptide of a SARS-CoV-2 variant. In some embodiments, the N-terminal residue of an RBD corresponds to about position 330 of SEQ ID NO: 1, or a corresponding amino acid in an S polypeptide of a SARS-CoV-2 variant.
[0245] In some embodiments, the C-terminal residue of an RBD corresponds to about position 528 of SEQ ID NO: 1, or a corresponding residue in an S polypeptide of a SARS-CoV-2 variant. In some embodiments, the C-terminal residue of an RBD corresponds to about position 530 of SEQ ID NO: 1, or a corresponding residue in an S protein of a SARS-CoV-2 variant. In some embodiments, the C-terminal residue of an RBD corresponds to about position 531 of SEQ ID NO: 1, or a corresponding residue in an S protein of a SARS-CoV-2 variant. In some embodiments, the C-terminal residue of an RBD corresponds to about position 537 of SEQ ID NO: 1, or a corresponding residue in an S protein of a SARS-CoV-2 variant. In some embodiments, the C-terminal residue of an RBD corresponds to about position 541 of SEQ ID NO: 1, or a corresponding residue in an S polypeptide of a SARS-CoV- 2 variant.
[0246] In some embodiments, an RBD comprises amino acids 319-528, 327-528, 328-528, 330-528, 319-530, 327-530, 328-530, 330-530, 319-531, 327-531, 328-531, 330-531, 319-537, 327-537, 328-537, 330-537, 330-537, 319-541, 327-541, 328-541, or 330-541 of SEQ ID NO: 1, or a corresponding region of any of the foregoing of a SARS-CoV-2 variant.
[0247] In some embodiments, an RBD comprises a portion of SEQ ID NO: 1 corresponding to the amino acid sequence between (I) about amino acid 317 to about amino acid 330 (inclusive) of SEQ ID NO: 1, and (ii) about amino acid 528 and about amino acid 541 (inclusive) of SEQ ID NO: 1, or a corresponding region in an S polypeptide of a SARS-CoV-2 variant.Page 59 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)
[0248] In some embodiments, an RBD of SARS-CoV-2 comprises an amino acid sequence according to SEQ ID NO: 2, or an amino acid sequence at least 80%, at ieast 85%, at least 90%, at least 91%, at ieast 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical thereto.VRFPNITNLCPFHEVFNATTFASVYAWNRKRISNCVADYSVIYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVS QIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKPSGNYNYLYRLFRKSKLKPFERDISTEIYQAGNKPCNGVAGPNCY SPLQSYGFRPTYGVGHQPYRWVLSFELLHAPATVCGPK (SEQ ID NO: 2)
[0249] In some embodiments, an RBD of SARS-CoV-2 comprises an amino acid sequence according to SEQ ID NO: 3, or an amino acid sequence at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical thereto.PNITNLCPFHEVFNATTFASVYAWNRKRISNCVADYSVIYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIA PGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKPSGNYNYLYRLFRKSKLKPFERDISTEIYQAGNKPCNGVAGPNCYSPL QSYGFRPTYGVGHQPYRWVLSFELLHAPATVCGPK (SEQ ID NO: 3)
[0250] In some embodiments, an RBD of SARS-CoV-2 comprises an amino acid sequence according to SEQ ID NO: 4, or an amino acid sequence at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical thereto.VRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEV RQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFN CYFPLQSYGFQPTNGVGYQPYRVWLSFELLHAPATVCGPK (SEQ ID NO: 4)
[0251] In some embodiments, an RBD of SARS-CoV-2 comprises an amino acid sequence according to SEQ ID NO: 5, or an amino acid sequence at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical thereto.VRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEV RQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSK (SEQ ID NO: 5)N -Term Inal Domain
[0252] The N-terminal domain (NTD) of the SARS-CoV-2 Spike protein has a galectin-like fold, and several authors have suggested that the domain can bind sialoside moieties of cell surface components. It may also bind other accessory cell receptors, such as several lectin receptors and / or the extracellular immunoglobulin domain of AXL f anexelekto') receptor tyrosine kinase. It is known that the Spike NTD of other coronaviruses can bind specific receptors or sugar receptors. For example, the mouse hepatitis coronavirus NTD interacts with the carcinoembryonic antigen related cell adhesion molecule 1 (CEACAM1) that contains two or four immunoglobulin domains. The NTDs of the bovine and the human OC43 coronaviruses recognize the sugar 5-N-acetyl-9-O-acetylneuraminic acid (Neu5, 9Ac2). The NTDs of the Spike protein of other coronavirus genera (a, y and 5) are evolutionary and structurally related to those of the p -coronaviruses and recognize, with diverse specificities, sugar receptors different from Neu5, 9Ac2. Interaction with accessory receptors may influence host selection, tissue tropism and pathogenicity.
[0253] Moreover, the NTD is an important target for host immune responses and for selective gene pressure, as suggested by numerous mutations that have occurred in the NTDs of VOCs, some of which confer evasion from protective antibody responses. Indeed, an NTD electropositive supersite targeted by neutralizing antibodies has been described. A recently published work reports a comprehensive study on the structural and functional properties of the NTD loops (Canton!, Diego, et al. " Evolutionary remodeling of N-terminal domain loops fine-tunes SARS-CoV-2 spike." EMBO reports 23.10 (2022): e54322, incorporated by reference herein in its entirety).Page 60 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)
[0254] In some embodiments, an immunogenic fragment of a SARS-CoV-2 S polypeptide comprises an NTD polypeptide ( / .e., a polypeptide that includes a Spike NTD polypeptide, an immunogenic fragment thereof, or a variant thereof, e.g., as described herein). In some embodiments, an NTD lacks an endogenous SARS-CoV-2 secretory signal peptide, and a polypeptide instead comprises a heterologous secretory signal peptide (i.e., a secretory signal peptide that is not from a SARS-CoV-2 S polypeptide). As used herein, an NTD encompasses both domains comprising a SARS-CoV-2 S polypeptide secretory signal peptide, and domains in which the SARS-CoV-2 S polypeptide secretory signai peptide has been replaced by a heterologous secretory signal peptide.
[0255] In some embodiments, an NTD comprises a portion of a SARS-CoV-2 S polypeptide corresponding to the amino acid sequence between about amino acid 1 and about amino acid 21 of SEQ ID NO: 1 and about amino acid 302 to 318 (inclusive) of SEQ ID NO: 1, or a corresponding region in an S polypeptide of a SARS-CoV-2 variant.
[0256] In some embodiments, the N-terminal residue of an NTD corresponds to about position 1 in SEQ ID NO: 1, or a corresponding amino acid in an S polypeptide of a SARS-CoV-2 variant. In some embodiments, the N-terminal residue of an NTD corresponds to about position 14 of SEQ ID NO: 1, or a corresponding amino acid in an S polypeptide of a SARS-CoV-2 variant. In some embodiments, the N-terminal residue of an NTD corresponds to about position 15 of SEQ ID NO: 1, or a corresponding amino acid in an S polypeptide of a SARS-CoV-2 variant. In some embodiments, the C-terminal residue of an NTD corresponds to about position 17 of SEQ ID NO: 1, or a corresponding residue in an S polypeptide of a SARS-CoV-2 variant. In some embodiments, the N-terminal residue of an NTD corresponds to about position 19 of SEQ ID NO: 1, or a corresponding amino acid in an S polypeptide of a SARS-CoV-2 variant. In some embodiments, the C-terminal residue of an NTD corresponds to about position 20 of SEQ ID NO: 1, or a corresponding residue in an S polypeptide of a SARS-CoV-2 variant. In some embodiments, the N-terminal residue of an NTD corresponds to about position 21 of SEQ ID NO: 1, or a corresponding amino acid in an S poiypeptide of a SARS-CoV-2 variant.
[0257] In some embodiments, the C-terminal residue of an NTD corresponds to about position 302 of SEQ ID NO: 1, or a corresponding residue in an S polypeptide of a SARS-CoV-2 variant. In some embodiments, the C- terminal residue of an NTD corresponds to about position 303 of SEQ ID NO: 1, or a corresponding residue in an S polypeptide of a SARS-CoV-2 variant. In some embodiments, the C-terminal residue of an NTD corresponds to about position 305 of SEQ ID NO: 1, or a corresponding residue in an S polypeptide of a SARS-CoV-2 variant. In some embodiments, the C-terminai residue of an NTD corresponds to about position 311 of SEQ ID NO: 1, or a corresponding residue in an S polypeptide of a SARS-CoV-2 variant. In some embodiments, the C-terminal residue of an NTD corresponds to about position 318 of SEQ ID NO: 1, or a corresponding residue in an S polypeptide of a SARS-CoV-2 variant.
[0258] In some embodiments the N-terminal residue of an NTD corresponds to an amino acid between amino acids 1 and 20 (inclusive) of SEQ ID NO: 1 and the C-terminal residue of an NTD corresponds to an amino acid between amino acids 302-318 (inclusive) of SEQ ID NO: 1. In some embodiments, an NTD of a SARS-CoV-2 S polypeptide comprises residues 1-209, 14-209, 15-209, 19-209, 20-209, 21-209, 1-302, 14-302, 15-302, 19-302, 20-302, 21-302, 1-303, 14-303, 15-303, 19-303, 20-303, 21-303, 1-305, 14-305, 15-305, 19-305, 20-305, 21-305, 1-311, 14-311, 15-311, 19-311, 20-311, 21-311, 1-318, 14-318, 15-318, 19-318, 20-318, 21-318, 1-302, 14-302, 15- 302, 19-302, 20-302, or 21-302 of SEQ ID NO: 1, or a corresponding region of any of the foregoing of an S protein of a SARS-CoV-2 variant.Page 61 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)
[0259] In some embodiments, an RNA comprising a nucieotide sequence that encodes a polypeptide comprising an NTD polypeptide can be administered in combination with an RNA comprising a nucleotide sequence that encodes a polypeptide comprising an RBD polypeptide (e.g., as described herein). For example, in some embodiments, one or more RNAs encoding a polypeptide comprising an RBD polypeptide can be administered in combination with one or more RNAs encoding a polypeptide comprising an NTD polypeptide, wherein the one or more RNAs encoding a polypeptide comprising an RBD polypeptide and the one or more RNAs encoding a polypeptide comprising an NTD polypeptide can be formulated in the same or separate nanoparticles.
[0260] In some embodiments, an NTD polypeptide comprises a sequence provided in Table 2, below, a variant thereof, or an immunogenic fragment thereof. In some embodiments, an RNA construct encodes a polypeptide comprising an NTD polypeptide that is depicted in Fig. 6.Table 2: Exemplary NTD sequencesNTD Amino Acid SequenceWuhan TRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFA NTD (long) STEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCrF EYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALH RSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTTTDAVDCALDPLSETKCTLKSFTVEKGIYQTSNF(SEQ ID NO: 6)Wuhan TRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFA NTD (short) STEKSNIIRGWIFGTTLDSKTQSLLIVN NATN WIKVCEFQFCN DPFLGVYYH KNN KSWM ESEFRVYSSAN NCTF EYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALH RSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTTTDAVDCALDPLSETKCT (SEQ ID NO: 7) Omicron TRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIE KSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQ BA.l NTDPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPnVREPEDLPQGFSALEPLVDLPIGINrTRFQTLLALHRSY (long) LTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTnTDAVDCALPLSETKCTLKSFTVEKGIYQTSNF (SEQ ID NO: 8)Omicron TRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIE KSNIIRGWIFGTTLDSKTQSLLIVN NATN WIKVCEFQFCN DPFLDHKN N KSWM ESEFRVYSSAN NCTFEYVSQ BA.l NTD PFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSY(short) LTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENG 111 DAVDCALDPLSETKCT (SEQ ID NO: 9)
[0261] In some embodiments, an NTD of SARS-CoV-2 comprises an amino acid sequence according to SEQ ID NO: 6, or an amino acid sequence at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical thereto.
[0262] In some embodiments, an NTD of SARS-CoV-2 comprises an amino acid sequence according to SEQ ID NO: 7, or an amino acid sequence at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical thereto.
[0263] In some embodiments, an NTD of SARS-CoV-2 comprises an amino acid sequence according to SEQ ID NO: 8, or a sequence at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical thereto.
[0264] In some embodiments, an NTD of SARS-CoV-2 comprises an amino acid sequence according to SEQ ID NO: 9, or a sequence at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical thereto.Page 62 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)Truncated SI Subdomain
[0265] In some embodiments, a fragment of a SARS-CoV-2 S polypeptide comprises a fragment of an SI polypeptide or a variant thereof. As used herein, a "fragment of an SI polypeptide" refers to a polypeptide comprising the NTD and the RBD of the SI polypeptide, where the NTD and RBD are connected via an endogenous linker, and wherein at least one amino acid C-terminal to the RBD in the SI polypeptide has been deleted. In some embodiments, a fragment of an SI polypeptide comprises an RBD at its C-terminus (e.g., an RBD as described herein). In some embodiments, a fragment of an SI polypeptide comprises an NTD and an RBD, wherein the RBD is at the C-terminus of the fragment of an Si polypeptide, and wherein the endogenous secretory signa! peptide in the NTD is optionally replaced with a heterologous secretory signal peptide.
[0266] In some embodiments, the C-terminal residue of a fragment of a SARS-CoV-2 S polypeptide corresponds to about position 528 of SEQ ID NO: 1, or a corresponding residue in an S protein of a SARS-CoV-2 variant. In some embodiments, the C-terminal residue of a fragment of a SARS-CoV-2 S polypeptide corresponds to about position 530 of SEQ ID NO: 1, or a corresponding residue in an S protein of a SARS-CoV-2 variant. In some embodiments, the C-terminal residue of a fragment of a SARS-CoV-2 S polypeptide corresponds to about position 531 of SEQ ID NO: 1, or a corresponding residue in an S protein of a SARS-CoV-2 variant. In some embodiments, the C-terminal residue of a fragment of a SARS-CoV-2 S polypeptide corresponds to about position 537 of SEQ ID NO: 1, or a corresponding residue in an S protein of a SARS-CoV-2 variant. In some embodiments, the C-terminal residue of a fragment of a SARS-CoV-2 S polypeptide corresponds to about position 541 of SEQ ID NO: 1, or a corresponding residue in an S protein of a SARS-CoV-2 variant.
[0267] In some embodiments, the N-terminal residue of a fragment of a SARS-CoV-2 S polypeptide corresponds to about position 1 in SEQ ID NO: 1, or a corresponding amino acid in an S protein of a SARS-CoV-2 variant. In some embodiments, the N-terminal residue of a fragment of a SARS-CoV-2 S polypeptide corresponds to about position 14 of SEQ ID NO: 1, or a corresponding amino acid in an S protein of a SARS-CoV-2 variant. In some embodiments, the N-terminal residue of a fragment of a SARS-CoV-2 S polypeptide corresponds to about position 15 of SEQ ID NO: 1, or a corresponding amino acid in an S protein of a SARS-CoV-2 variant. In some embodiments, the N-terminal residue of a fragment of a SARS-CoV-2 S polypeptide corresponds to about position 19 of SEQ ID NO: 1, or a corresponding amino acid in an S protein of a SARS-CoV-2 variant. In some embodiments, the N-terminal residue of a fragment of a SARS-CoV-2 S polypeptide corresponds to about position 20 of SEQ ID NO: 1, or a corresponding amino acid in an S protein of a SARS-CoV-2 variant. In some embodiments, the N-terminal residue of a fragment of a SARS-CoV-2 S polypeptide corresponds to about position 21 of SEQ ID NO: 1, or a corresponding amino acid in an S protein of a SARS-CoV-2 variant.
[0268] In some embodiments, a fragment of a SARS-CoV-2 S polypeptide comprises an amino acid sequence corresponding to the region between (1) about 14 to 21 of SEQ ID NO: 1, and (2) about 528-541 of SEQ ID NO: 1, or a corresponding region of an S protein of a SARS-CoV-2 variant.
[0269] In some embodiments, a fragment of a SARS-CoV-2 S polypeptide comprises or consists of amino acids 1-528, 14-528, 15-528, 19-528, 20-528, 21-528, 1-530, 14-530, 15-530, 19-530, 20-530, 21-530, 1-531, 14-531, 15-531, 19-531, 20-531, 21-531, 1-537, 14-537, 15-537, 19-537, 20-537, 21-537, 1-541, 14-541, 15-541, 19-541, 20- 541, or 21-541 of SEQ ID NO: 1, or a corresponding region in an S protein in a SARS-CoV-2 variant, or a variant of any of the foregoing.Page 63 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)
[0270] In some embodiments, a fragment of an SI polypeptide comprises or consists of amino acids 20 to 528 of SEQ ID NO: 1 (e.g., amino acids 14 to 528 or 17 to 528 of SEQ ID NO: 1), or a corresponding region in an S polypeptide in a SARS-CoV-2 variant, or a variant of either of the foregoing. In some embodiments, a fragment of an SI polypeptide comprises or consists of amino acids 20 to 541 (e.g., amino acids 14 to 541 or 17 to 541) of SEQ ID NO: 1, or a corresponding region in a SARS-CoV-2 variant, or a variant of either of tine foregoing.
[0271] In some embodiments, a fragment of an SI polypeptide of a SARS-CoV-2 S polypeptide comprises an amino acid sequence according to SEQ ID NO: 12, or an amino acid sequence at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical thereto.MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDN PVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSS ANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALH RSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESI VRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEV RQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFN CYFPLQSYGFQPTNGVGYQPYRWVLSFELLHAPATVCGPK (SEQ ID NO: 12)
[0272] In some embodiments, a fragment of an SI polypeptide of a SARS-CoV-2 S polypeptide comprises an amino acid sequence according to SEQ ID NO: 13, or an amino acid sequence at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical thereto.MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDN PVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSS ANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALH RSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESI VRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEV RQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFN CYFPLQSYGFQPTNGVGYQPYRVWLSFELLHAPATVCGPKKSTNLVKNKCVNF (SEQ ID NO: 13)
[0273] In some embodiments, a fragment of an SI polypeptide of a SARS-CoV-2 S polypeptide comprises an amino acid sequence according to SEQ ID NO: 14, or a sequence at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical thereto.QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFA STEKSNIIRGWIFGTTLDSKTQSLLIVN NATNWIKVCEFQFCNDPFLGVYYH KN N KSWM ESEFRVYSSAN NCTFEYVSQP FLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSG WTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFG EVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIAD YNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPT NGVGYQPYRVWLSFELLHAPATVCGPK (SEQ ID NO:14)
[0274] In some embodiments, a fragment of an SI polypeptide of a SARS-CoV-2 S polypeptide comprises an amino acid sequence according to SEQ ID NO: 15, or an amino acid sequence at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical thereto.QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFA STEKSNIIRGWIFGTTLDSKTQSLLIVN NATNWIKVCEFQFCNDPFLGVYYH KN N KSWM ESEFRVYSSAN NCTFEYVSQP FLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSG WTAGAAAYYVGYLQPRTFLLKYNENGHTDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNrTNLCPFG Page 64 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)EVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIAD YNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPT NGVGYQPYRWVLSFELLHAPATVCGPKKSTNLVKNKCVNF (SEQ ID NO: 15)
[0275] In some embodiments, a fragment of an SI polypeptide of a SARS-CoV-2 S polypeptide comprises an amino acid sequence according to SEQ ID NO: 16, or an amino acid sequence at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical thereto.VNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNLXjVYFASTE KSNIIRGWIFGTTLDSKTQSLLTV NATNWIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLM DLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWr AGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEV FNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSFTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYN YKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNG VGYQPYRVWLSFELLHAPATVCGPK (SEQ ID NO: 16)
[0276] In some embodiments, a fragment of an SI polypeptide of a SARS-CoV-2 S polypeptide comprises the amino acid sequence according to SEQ ID NO: 17, or an amino acid sequence at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical thereto.VNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTE KSNIIRGWIFGTTLDSKTQSLLIVNNATNWIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLM DLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWT AGAAAYYVGYLQPRTFLLKYNENGTETDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEV FNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYN YKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNG VGYQPYRWVLSFELLHAPATVCGPKKSTNLVKNKCVNF (SEQ ID NO: 17)
[0277] In some embodiments, a fragment of an SI polypeptide of a SARS-CoV-2 S polypeptide comprises the amino acid sequence according to SEQ ID NO: 18, or an amino acid sequence at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical thereto.TTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNnRGWIFGTTLDSKTQSLUVN NATN WIKVCEFQFCN DPFLGVYYH KN N KSWM ESEFRVYSSAN NCTFEYVSQPFLM DLE GKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGIN1TRFQTLLALHRSYLTPGDSSSGWTAGA AAYYVGYLQPRTFLLKYNENGTTTDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQFTESIVRFPN1TNLCPFGEVFNA TRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKL PDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGY QPYRVWLSFELLHAPATVCGPK(SEQ ID NO: 18)
[0278] In some embodiments, a fragment of an SI polypeptide of a SARS-CoV-2 S polypeptide comprises the amino acid sequence according to SEQ ID NO: 19, or an amino acid sequence at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical thereto.TTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSN IIRGWIFGTTLDSKTQSLLIVN NATN WIKVCEFQFCN DPFLGVYYH KN N KSWM ESEFRVYSSAN NCTFEYVSQPFLM DLE GKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGIN1TRFQTLLALHRSYLTPGDSSSGWTAGA AAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSnVEKGIYQTSNFRVQPTESIVRFPNrrNLCPFGEVFNA TRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKL PDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGY QPYRVWLSFELLHAPATVCGPKKSTNLVKNKCVNF (SEQ ID NO: 19)Page 65 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)
[0279] In some embodiments, a fragment of an SI polypeptide of a SARS-CoV-2 S polypeptide comprises the amino acid sequence according to SEQ ID NO: 20, or an amino acid sequence at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical thereto.QCVMPLFNLITTrQSYTNSFTRGVYYPDKVFRSSVLHLTQDLFLPFFSNVTWFHAISGTNGTKRFDNPVLPFNDGVYFAST EKSNIIRGWIFGTTLDSKTQSLLIVNNATNVFIKVCEFQFCNDPFLDVYHKNNKSWMESESGVYSSANNCTFEYVSQPFLM DLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIGRDFPQGFSALEPLVDLPIGINITRFQTLLALNRSYLTPGDSSSGWTA GAADYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNVTNLCPFHEVF NATTFASVYAWNRTRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIKGNEVSQIAPGQTGNIADYNY KLPDDFTGCVIAWNSNKLDSKHSGNYDYWYRSLRKSKLKPFERDISTEIYQAGNKPCKGKGPNCYFPLQSYGFRPTYGVG HQPYRVWLSFELLHAPATVCGPK (SEQ ID NO: 20)
[0280] In some embodiments, a fragment of an SI polypeptide of a SARS-CoV-2 S polypeptide comprises the amino acid sequence according to SEQ ID NO: 21, or an amino acid sequence at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical thereto.QCVNLTTRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPALPFNDGVYFASTE KSNIIRGWIFGTTLDSKTQSLLIVNNATNWIKVCEFQFCNDPFLDVYQKNNKSWMESEFRVYSSANNCTFEYVSQPFLM DLEGKEGNFKNLREFVFKNIDGYFKIYSKHTPINLERDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPVDSSSGWr AGAAAYYVGYLQPRTFLLKYN ENGTHDAVDCALDPLSETKCTLKSFTVEKGIYQTSN FRVQPTESIVRFPNITN LCPFH E VFNATTFASVYAWNRKRISNCVADYSVIYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIAD YNYKLPDDFTGCVIAWNSNKLDSKPSGNYNYLYRLFRKSKLKPFERDISTEIYQAGNKPCNGVAGPNCYSPLQSYGFRPT YGVGHQPYRVWLSFELLHAPATVCGPK (SEQ ID NO:21)52 Subdomain Fragments
[0281] Among other things, the present application provides an insight that, in some embodiments, an RNA encoding a polypeptide comprising one of more of certain immunogenic fragments of an S2 polypeptide, or a variant thereof can produce an improved immune response as compared to a reference (e.g., an RNA encoding a full-length SARS-CoV-2 S protein). In particular, in some embodiments, such an RNA can produce a more broadly cross¬ neutralizing immune response as compared to an appropriate reference (including, e.g., as compared to RNA encoding a full-length SARS-CoV-2 S protein), wherein such a broader immune response can comprise, e.g., higher neutralization titers against a larger number of and / or more diverse set of SARS-CoV-2 variants, betacoronaviruses and / or sarbecoronaviruses.
[0282] Without wishing to be bound by theory, certain regions of the S2 domain are highly conserved among pan-betacoronaviruses and comprise neutralizing epitopes. Thus, in some embodiments, an RNA encoding a polypeptide comprising certain immunogenic fragments of an S2 domain can elicit production of antibodies that can bind conserved neutralization epitopes, therefore resuiting in an immune response that is more broadly cross¬ neutralizing as compared to RNA encoding an appropriate reference antigen (e.g., an RNA that encodes a polypeptide comprising a full-length S protein and / or an RNA that encodes a polypeptide comprising an S2 domain). Without wishing to be bound by theory, in some embodiments, certain immunogenic fragments can induce an improved immune response as compared to RNA encoding a full length S protein and / or a full S2 protein at least in part because solvent accessibility of the fragments is increased when not part of the S2 domain or full length S protein.
[0283] The S2 domain comprises, from N- to C-terminus, a fusion peptide (FP), a heptad repeat 1 (HR1), a heptad repeat 2 (HR2), a transmembrane domain (TMD), and a C-terminal, membrane proximal region.Page 66 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)
[0284] In some embodiments, an S2 domain of a SARS-CoV-2 S protein comprises amino acids 679 to 1273 of SEQ ID NO: 1, or a corresponding region in an S protein of a SARS-CoV-2 variant. In some embodiments, an S2 domain of a SARS-CoV-2 S protein comprises amino acids 684 to 1273 of SEQ ID NO: 1, or a corresponding region in an S protein of a SARS-CoV-2 variant. In some embodiments, an S2 domain of a SARS-CoV-2 S protein comprises amino acids 686 to 1273 of SEQ ID NO: 1, or a corresponding region in an S protein of a SARS-CoV-2 variant.
[0285] In some embodiments, an S2 domain of a SARS-CoV-2 S protein comprises amino acids 679 to 1273 of SEQ ID NO: 1, or a corresponding region in an S protein of a SARS-CoV-2 variant. In some embodiments, an S2 domain of a SARS-CoV-2 S protein comprises amino acids 684 to 1273 of SEQ ID NO: 1, or a corresponding region in an S protein of a SARS-CoV-2 variant. In some embodiments, an S2 domain of a SARS-CoV-2 S protein comprises amino acids 686 to 1273 of SEQ ID NO: 1, or a corresponding region in an S protein of a SARS-CoV-2 variant.
[0286] In some embodiments, an RNA encodes a polypeptide comprising a stem helix (SH), fusion peptide (FP) region, heptad repeat 1 (HR1), central helix (CH), and / or heptad repeat 2 (HR2) region of a SARS-CoV-2 S protein.Fusion Peptide Region
[0287] The Fusion Peptide (FP) region of a SARS-CoV-2 S protein comprises a short (~20-40 amino acid) segment of conserved amino acids, comprising mainly hydrophobic residues, such as glycine (G) or alanine (A), which can anchor to the target membrane when a full length S protein in an infectious SARS-CoV-2 viral particle adopts the pre-hairpin conformation. Previous research has shown that FP plays an important role in mediating membrane fusion by disrupting and connecting lipid bilayers of the host cell membrane (see, e.g., Millet, Jean Kaoru, and Gary R. Whittaker. " Physiological and molecular triggers for SARS-CoV membrane fusion and entry into host cells." Virology 517 (2018): 3-8).
[0288] In some embodiments, a fusion peptide region comprises amino acids 809-832 of SEQ ID NO: 1 (PSKPSKRSFIEDLLFNKVTLADAG (SEQ ID NO: 833)), or an amino acid sequence of a corresponding region of an S protein of a SARS-CoV-2 variant. In some embodiments, a fusion peptide region comprises an amino acid sequence that is 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more identical to SEQ ID NO: 833. In some embodiments, a fusion peptide region comprises an amino acid sequence having 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid modifications relative to SEQ ID NO: 833.
[0289] In some embodiments, a fusion peptide region comprises amino acids 809-843 of SEQ ID NO: 1 (PSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGD (SEQ ID NO: 823)), or an amino acid sequence of a corresponding region of an S protein of a SARS-CoV-2 variant. In some embodiments, a fusion peptide region comprises an amino acid sequence that is 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more identical to SEQ ID NO: 823. In some embodiments, a fusion peptide region comprises an amino acid sequence having 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid modifications relative to SEQ ID NO: 823.Stem Helix Region
[0290] The SARS-CoV-2 stem helix comprises ~21 amino acid residues in a region corresponding to around amino acids 1141-1161 of SEQ ID NO: 1 (LQPELDSFKEELDKYFKNHTS (SEQ ID NO: 834)), and, in the full length S protein, forms a central triple-helix under the spike bundle to connect with the HR2 region. During conformational transition, a helical motif of the upstream helix (amino acids 737-783 of SEQ ID NO: 1) runs parallel to the Central Helix (CH) groove via hydrophobic interactions, effectively forming a short six-helix bundle in post-S trimer. Due to the rotation of the connector domain, the extended SH-HR2 element aligns with the long-axis formed by the CH-HR1Page 67 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)domain, thus inducing the subsequent binding of SH to the outer region of the 6-HB-l, and HR2 to the hydrophobic groove formed by HR1. Specifically, a portion of SH (a region corresponding to amino acids 1147-1154 of SEQ ID NO: 1) maintains the helicai state, while the remaining segments of SH (regions corresponding to amino acids 1140- 1146 and 1155-1161 of SEQ ID NO: 1) extend from the helix into a iong loop to fit the extended post-fusion S2 state. Correct refolding of SH contributes to the formation of HR1-HR2 fusion bundle and the overall stability of the S2 fusion subunit. Thus, the SH region, especially in light of its relative conservation across SARS-CoV-2 variants, represents a promising target for the design of SARS-CoV-2 vaccines.
[0291] In some embodiments, a stem heiix region comprises amino acids 1140-1162 of SEQ ID NO: 1 (PLQPELDSFKEELDKYFKNHTSP (SEQ ID NO: 825)), or an amino acid sequence of a corresponding region of an S protein of a SARS-CoV-2 variant. In some embodiments, a stem heiix region comprises an amino acid sequence that is 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more identical to SEQ ID NO: 825. In some embodiments, a stem helix region comprises an amino acid sequence having 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid modifications relative to SEQ ID NO: 825.
[0292] In some embodiments, a stem heiix region comprises amino acids 1141-1164 of SEQ ID NO: 1 (LQPELDSFKEELDKYFKNHTSPDV SEQ ID NO: 824), or an amino acid sequence of a corresponding region of an S protein of a SARS-CoV-2 variant. In some embodiments, a stem helix region comprises an amino acid sequence that is 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more identical to SEQ ID NO: 824. In some embodiments, a stem helix region comprises an amino acid sequence having 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid modifications relative to SEQ ID NO: 824.
[0293] In some embodiments, a polypeptide comprises amino acids 1136-1167 of SEQ ID NO: 1 (TVYDPLQPELDSFKEELDKYFKNHTSPDVDLG (SEQ ID NO: 826)) or an amino acid sequence of a corresponding region of an S protein of a SARS-CoV-2 variant. In some embodiments, a polypeptide comprises a fragment of an S protein that has an amino acid sequence that is 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more identical to SEQ ID NO: 826. In some embodiments, a fragment of an S protein has an amino acid sequence having 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid modifications relative to SEQ ID NO: 826.
[0294] In some embodiments, a polypeptide comprises amino acids 1136-1168 of SEQ ID NO: 1 (TVYDPLQPELDSFKEELDKYFKNHTSPDVDLGD (SEQ ID NO: 827)) or an amino acid sequence of a corresponding region of an S protein of a SARS-CoV-2 variant. In some embodiments, a poiypeptide comprises a fragment of an S protein that has an amino acid sequence that is 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more identical to SEQ ID NO: 827. In some embodiments, a fragment of an S protein has an amino acid sequence having 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid modifications relative to SEQ ID NO: 827.Heptad Repeat Regions 1 and 2
[0295] HR1 and HR2 regions of a SARS-CoV-2 S protein comprise a repetitive heptapeptide: HPPHCPC, where H is a hydrophobic or traditionally bulky residue, P is a polar or hydrophilic residue, and C is another charged residue. HR1 and HR2 can form a six-helical bundle (6-HB), which is important for viral fusion and entry of the SARS-CoV-2 viral particle. In the native S protein, HR1 is located at the C-terminus of a hydrophobic FP, and HR2 is iocated at the N-terminus of the TM domain.
[0296] During membrane fusion, the RBD of the S protein binds to ACE2, and S2 changes conformation by inserting FP into the target cell membrane, exposing the prehairpin coiled-coil of the HR1 domain and triggering Page 68 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)interaction between the HR2 domain and HR1 trimer to form 6-HB, thus bringing the viral envelope and cell membrane into proximity for viral fusion and entry, HR1 forms a homotrimeric assembly in which three highly conserved hydrophobic grooves on the surface that bind to HR2 are exposed. The HR2 domain forms both a rigid heiix and a flexible loop to interact with the HR1 domain. In the postfusion hairpin conformation of CoVs, there are many strong interactions between the HR1 and HR2 domains inside the helical region, which is designated the "fusion core region" (HRlcore and HR2core regions, respectively). Overall, HR1 and HR2 can provide the promising therapeutic targets for the design of fusion inhibitors and vaccines.
[0297] In some embodiments, a polypeptide comprises an HR1 region of a SARS-CoV-2 S protein, or a fragment thereof.
[0298] In some embodiments, an HR1 region of a SARS-CoV-2 S protein comprises amino acids 910-985 of SEQ ID NO: 1, or an amino acid sequence of a corresponding region of an S protein of a SARS-CoV-2 variant. In some embodiments, an HR1 region comprises an amino acid sequence that is 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more identical to amino acids 910-985 of SEQ ID NO: 1. In some embodiments, a stem helix comprises an amino acid sequence having 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid modifications relative to amino acids 910-985 of SEQ ID NO: 1.
[0299] In some embodiments, a polypeptide comprises a Central Helix (CH) region or a fragment thereof. In full length S protein, the segment between HR1 and HR2 is the central helix region. There is a transitional bend between HR1 and the central helix which, when fixed with two consecutive proline residues, prevents structural transitions from prefusion to postfusion, and consequently contributes to the stabilization of the spike protein at the prefusion state, which is important for vaccine development. Spike proteins with these two proline replacements are known as S-2P, which is encoded in the mRNA vaccine from both Pfizer / BioNTech (BNT162b2) and Modema (mRNA-1273). A new spike protein variant (HexaPro) that includes four additional amino acid replacements by proline (F817P, A892P, A899P, and A942P) is even more stable and expressed more than the original S-2P.[O3OO] in some embodiments, a polypeptide comprises an HR2 region of a SARS-CoV-2 S protein, or a fragment thereof.
[0301] In some embodiments, an HR2 region of a SARS-CoV-2 S protein comprises amino acids 1163-1211 of SEQ ID NO: 1, or an amino acid sequence of a corresponding region of an S protein of a SARS-CoV-2 variant. In some embodiments, an HR2 region comprises a sequence that is 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more identical to amino acids 1163-1211 of SEQ ID NO: 1. In some embodiments, an HR2 region comprises a sequence having 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid modifications relative to amino acids 1163-1211 of SEQ ID NO: 1.
[0302] In some embodiments, a HR2 region or a fragment thereof comprises amino acids 1162-1200, 1162- 1207, 1165-1200, 1168-1200, 1169-1200, 1165-1207, 1168-1207, or 1169-1207 of SEQ ID NO: 1, a corresponding region of an S protein of a SARS-CoV-2 variant, or an amino acid sequence that is 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more identical to any one of amino acids 1162-1200, 1162-1207, 1165- 1200, 1168-1200, 1169-1200, 1165-1207, 1168-1207, or 1169-1207 of SEQ ID NO: 1.
[0303] In some embodiments, a polypeptide comprises a fragment of a SARS-CoV-2 S protein that comprises a fragment of an HR1 region and a CH region. In some embodiments, a polypeptide comprises amino acids 975-995 of Page 69 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)SEQ ID NO: 1 (SVLNDILSRLDKVEAEVQIDR (SEQ ID NO: 828)) or a corresponding region of an S protein of a SARS-CoV-2 variant. In some embodiments, a fragment of an HR1 region comprises an amino acid sequence that is 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more identical to SEQ ID NO: 828. In some embodiments, a fragment of an HR1 region comprises an amino acid sequence having 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid modifications relative to SEQ ID NO: 828.
[0304] In some embodiments, an HR2 region comprises amino acids 1136-1168 of SEQ ID NO: 1, or a corresponding region of an S protein of a SARS-CoV-2 variant. In some embodiments, an HR2 region comprises an amino acid sequence that is 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more identical to amino acids 1136-1168 of SEQ ID NO: 1. In some embodiments, an HR2 region comprises an amino acid sequence having 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid modifications relative to amino acids 1136-1168 of SEQ ID NO: 1.
[0305] In some embodiments, a fragment of an S2 subdomain comprises a plurality of regions of an S2 subdomain or fragments thereof. For example, in some embodiments, a fragment of an S2 subdomain comprises two or more of:(a) a fusion peptide (FP) region,(b) a stem helix (SH) region,(c) an HR1 region or a fragment thereof,(d) a central helix (CH) region or a fragment thereof, and(e) an HR2 region or a fragment thereof.
[0306] In some embodiments, a fragment of an S2 subdomain comprises an SH region and an HR2 region or a fragment thereof.
[0307] In some embodiments, a fragment of an S2 subdomain comprising an SH region and an HR2 region or a fragment thereof comprises amino acids 1136-1200, 1136-1205, 1136-1206, 1140-1200, 1140-1205, 1140-1206, 1141-1200, 1141-1205, or 1141-1206 of SEQ ID NO: 1, a sequence of a corresponding region of an S protein of a SARS-CoV-2 variant, or an amino acid sequence that is at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at ieast 92%, at least 93%, at least 94%, at least 95%, at least 96%, at ieast 97%, at least 98%, or at least 99% identical to amino acids 1136-1200, 1136-1205, 1136-1206, 1140-1200, 1140-1205, 1140- 1206, 1141-1200, 1141-1205, 1141-1206 of SEQ ID NO: 1, IVYDPLQPELDSFKEELDKYFKNHTSPDVSDLGDISGINASWNIQKEIDRLNEVAKNLNESLIDL (SEQ ID NO: 829) or TVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASWNIQKEIDRLNEVAKNLNESLIDL (SEQ ID NO: 830).
[0308] In some embodiments, a fragment of an S2 subdomain comprises an SH region, an HR2 region or a fragment thereof, and a transmembrane domain of the SARS-CoV-2 S protein. In some embodiments, a fragment of an S2 subdomain comprising an SH region, an HR2 region or a fragment thereof, and a transmembrane domain of a SARS-CoV-2 S protein comprises amino acids 1140-1254, 1141-1254, 1136-1254, 1140-1273, 1141-1273, or 1136-1273 of SEQ ID NO: 1, a corresponding region of an S protein of a SARS-CoV-2 variant, or a sequence is at ieast 70%, at ieast 71%, at ieast 72%, at least 73%, at least 74%, at least 75%, at ieast 76%, at ieast 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at ieast Page 70 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% or more identical to amino acids 1140-1254, 1141-1254, 1136-1254, 1140-1273, 1141-1273, or 1136-1273 of SEQ ID NO: 1;
[0309] In some embodiments, a fragment of an S2 subdomain comprises an HR2 region or a fragment thereof and a transmembrane domain of a SARS-CoV-2 S protein. In some embodiments, a fragment of an S2 subdomain comprising an HR2 region or a fragment thereof and a transmembrane domain of a SARS-CoV-2 S protein comprises amino acids 1162-1254, 1162-1273, 1165-1254, 1165-1273, 1168-1254, 1168-1273, 1169-1254, or 1169-1273 of SEQ ID NO: 1, a corresponding region of an S protein of a SARS-CoV-2 variant, or a sequence that is at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to amino acids 1136-1254, 1136-1273, 1165-1254, 1165-1273, 1168-1254, 1168-1273, 1169-1254, or 1169-1273 of SEQ ID NO: 1.Polypeptides Comprising a Plurality of Immunogenic Fragments of an S protein
[0310] In some embodiments, a poiypeptide comprises two or more fragments of an S protein. In some embodiments, a polypeptide comprises two or more fragments of an SI subdomain (e.g., two or more RBDs, two or more NTDs, or one or more RBDs and one or more NTDs). In some embodiments, the two or more fragments of an S protein are each from the same SARS-CoV-2 strain or variant. In some embodiments, two or more of the two or more fragments of an S protein are from different SARS-CoV-2 strains or variants (e.g., in some embodiments, a polypeptide comprises three RBDs, where two RBDs are from a first SARS-CoV-2 strain or variant, and the third RBD is from a SARS-CoV-2 strain or variant that is different from the first SARS-CoV-2 strain or variant).
[0311] In some embodiments, a polypeptide comprises:(a) an NTD and an RBD, wherein the N- to C-terminal orientation of the NTD and the RBD is NTD-RBD or RBD- NTD, and wherein the NTD and the RBD are from the same or different SARS-CoV-2 strains or variants.(b) two RBDs, wherein the two RBDs are from the same or different SARS-CoV-2 strains or variants;(c) two NTDs and an RBD, wherein the N- to C-terminal orientation of the two NTDs and the RBD is NTD-NTD- RBD, NTD-RBD-NTD, or RBD-NTD-NTD, and wherein one, two, or three of the two NTDs and the RBD are from the same SARS-CoV-2 strain or variant (optionally wherein, if the C-terminal to N-terminal orientation is NTD-RBD-NTD, the first NTD and the RBD are from a first SARS-CoV-2 strain or variant and the second NTD is of a different SARS- CoV-2 strain or variant than the first SARS-CoV-2 strain or variant);(d) two RBDs and one NTD, wherein the N- to C- terminal orientation of the two RBDs and one NTD is RBD RBD-NTD, RBD-NTD-RBD, or NTD-RBB-RBD, and wherein one, two, or all three of the two RBDs and the NTD are from the same SARS-CoV-2 strain or variant (optionally wherein, if the C-terminal to N-terminal orientation is NTD- RBD-RBD, the NTD and the first RBD are from a first SARS-CoV-2 strain or variant, and the second RBD is from a second SARS-CoV-2 strain or variant that is different from the first SARS-CoV-2 strain or variant); or(e) two NTDs and two RBDs, wherein the N-terminal to C-terminal orientation of the two NTDs and two RBDs is NTD-NTD-RBD-RBD, NTD-RBD-NTD-RBD, NTD-RBD-RBD-NTD, RBD-NTD-RBD-NTD, or RBD-RBD-NTD-NTD, and wherein one, two, three, or all four of the NTDs and the two RBDs are from the same SARS-CoV-2 strains or variants Page 71 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)(and optionally, if the N-terminal to C-terminal orientation of the polypeptide is NTD-RBD-NTD-RBD, the first NTD and the first RBD are of a different SARS-CoV-2 strain or variant than the second NTD and the second RBD).
[0312] In some embodiments, a polypeptide comprises:(a) an RBD and an NTD, wherein the RBD and NTD are directly adjacent via a flexible linker (e.g., a flexible linker described herein);(b) two RBDs, wherein the two RBDs are connected via a flexible linker or are directly adjacent to one another; (c) an NTD and two RBDs, wherein the NTDs and the RBDs are each directedly adjacent to one another or are each connected to one another by a sequence that comprises a flexible linker.(d) two NTDs and two RBDs, wherein the NTDs and the RBDs are each connected to one another by a sequence that comprises a flexible linker, optionally wherein one or more of the sequences that connect the NTDs and RBDs further comprises a multimerization domain (e.g., a fibritin trimerization domain).
[0313] In some embodiments, a polypeptide comprises two or more fragments of an S2 subdomain. In some embodiments, each of the two or more fragments of an S2 domain are immediately adjacent to one another. In some embodiments, each of the two or more fragments of an S2 domain are connected to one another via a I inker (e.g., a flexible linker, including, e.g., a flexible linker described herein).
[0314] In some embodiments, a polypeptide comprises an SH region and an FP region. In some embodiments, an SH region and an FP region are directly adjacent to one another. In some embodiments, an SH region and an FP region are connected via an endogenous sequence (i.e., a sequence that connects the SH region and FP region in a native S protein). In some embodiments, an SH region and an FP region are connected via a non- endogenous sequence (i.e., a sequence that does not connect an SH region and an FP region in the native S protein). In some embodiments, an SH region and an FP region are connected via a sequence that comprises a linker, including, e.g., a flexible linker. In some embodiments, the flexible linker comprises one or more Gly residues and / or one of more Ser residues (e.g., a linker described in Table 8 of the present disclosure). In some embodiments, the flexible linker comprises 1-10, about 3, about 5, about 7 or about 10 Gly or Ser residues.
[0315] In some embodiments, an RNA encodes a polypeptide comprises:(a) an SH region and a fragment of an HR2 region;(b) an FP region, an SH region, and a fragment of an HR2 region, wherein the FP region, the SH region, and the fragment of the HR2 region are directed adjacent to one another or have one or more intervening sequences; (c) an FP region and an SH region, wherein the FP region and the SH region are directed adjacent to one another or are connected to one another via one or more intervening sequences;(d) an FP region, an SH region, and a fragment of an HR2 region, wherein the FP region, the SH region, and tiie fragment of the HR2 region are directly adjacent to one another or are connected via an intervening sequence that comprises one or more additional antigenic regions.
[0316] In some embodiments, an RNA encodes a polypeptide comprising two or more fragments of an S2 subdomain, wherein the two or more fragments are each independently (a) immediately adjacent to one another, (b) connected to one another via a sequence that comprises a flexible linker, and / or (c) connected to one another via a sequence that comprises one or more NTDs and / or one or more RBDs of a SARS-CoV-2 S protein.
[0317] In some embodiments, an RNA described herein encodes a polypeptide comprising one or more fragments of an SI subdomain (e.g., an NTD, RBD, and / or truncated SI subdomain) and one or more fragments of Page 72 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)an S2 subdomain (e.g., an FP region, SH region, HR1 region or a fragment thereof, HR2 region or a fragment thereof, a CH region or a fragment thereof, or a combination of any of the foregoing).
[0318] In some embodiments, an RNA encodes a polypeptide comprising:(a) an RBD and an SH region;(b) two RBDs and an SH region;(c) an NTD, an RBD, and an SH region;(d) an NTD, two RBDs, and an SH region;(e) an NTD, two RBDs, and an FP region;(f) an NTD, an RBD, an FP region, and an SH region;(g) three RBDs, an FP region, an SH region, and an HR2 region;(h) three RBDs, an FP region, and an SH region; or(i) three RBDs, and NTD, an FP region, and an SH region.
[0319] In some embodiments, an RNA encodes a polypeptide comprising two or more fragments of an S protein, wherein the two or more fragments comprise:(a) an RBD and an SH region, wherein the N-temninal to C-terminal orientation of the RBD and the SH region is RBD-SH, and wherein the RBD and the SH region are either directly adjacent to one another or connected to one another via a sequence that comprises a flexible linker;(b) two RBDs and an SH region, wherein the N-terminal to C-terminal orientation of the two RBDs and the SH region is RBD-RBD-SH, and wherein the two RBDs and the SH region are each independently either directly adjacent to one another or connected to one another via a sequence that comprises a flexible linker;(c) an NTD, an RBD, and an SH region, wherein the N-terminal to C-terminal orientation of the NTD, RBD, and SH region is NTD-RBD-SH, and wherein the NTD, RBD, and SH region are each independently either directly adjacent to one another or connected to one another via a sequence that comprises a flexible linker;(d) an NTD, two RBDs, and an SH region, wherein the N-terminal to C-terminal orientation of the NTD, two RBDs, and SH region is NTD-RBD-RBD-SH, and wherein the NTD, RBDs, and SH region are each independently either directly adjacent to one another or are connected to one another via a sequence that comprises a flexible linker; (e) an NTD, an RBD, an FP region, an SH region, and a fragment of an HR2 region, wherein the N-terminal to C-terminal orientation of the NTD, RBD, FP region, SH region, and fragment of an HR2 region is NTD-FP-RBD-SH-RBD-HR2, and wherein the NTD, RBD, FP region, SH region, and fragment of an HR2 region are each independently either directly adjacent to one another or connected to one another via a sequence that comprises a flexible linker; (f) an NTD, an FP region, two RBDs, and an SH region, wherein the N-terminal to C-terminal orientation of the NTD, FP region, two RBDs, and SH region is NTD-FP-RBD-SH-RBD, and wherein the NTD, FP region, two RBDs, and SH region are each independently either directly adjacent to one another or connected to one another via a sequence that comprises a flexible linker;(g) three RBDs, an FP region, an SH region, and a fragment of an HR2 region, wherein the N-terminal to C-terminal orientation of the three RBDs, FP region, SH region, and fragment of an HR2 region is RBD-FP-RBD-SH-RBD-HR2, and wherein the three RBDs, FP region, SH region, and fragment of an HR2 region are each independently either directly adjacent to one another or are connected to one another via a sequence that comprises a flexible linker;Page 73 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)(h) three RBDs, an FP region, and an SH region, wherein the N-terminal to C-terminal orientation of the three RBDs, the FP region, and the SH region is RBD-FP-RBD-SH-RBD, and wherein the three RBDs, FP region, and SH region are each independently either directly adjacent to one another or are connected to one another via a sequence that comprises a flexible linker;(i) an NTD, an FP region, two SH regions, and three RBDs, wherein the N-terminal to C-terminal orientation of the NTD, FP region, two SH regions, and three RBDs is NTD-FP-RBD-SH-RBD-SH-RBD, and wherein the NTD, FP region, three RBDs, and two SH regions are each either independently directly adjacent to one another or connected to one another via a sequence that comprises a flexible linker;(j) an NTD, an FP region, a fragment of an HR1 region, an SH region, three RBDs, and a fragment of an HR2 region, wherein the N-terminal to C-terminal orientation of the NTD, FP region, fragment of an HR1 region, SH region, fragment of an HR2 region and three RBDs is NTD-FP-RBD-HR1-RBD-SH-RBD-HR2, and wherein the NTD, FP region, three RBDs, SH region, and fragment of an HR2 region are each either independently directly adjacent to one another or connected to one another via a sequence that compris...
Claims
Attorney Docket No. 2013237-1556 (P2037W001)CLAIMSWhat is claimed is:
1. A combination comprising:(a) an RNA encoding a hemagglutinin (HA) polypeptide of a first influenza virus or variant thereof; and (b) an RNA encoding a polypeptide comprising a fragment of a coronavirus S polypeptide or variant thereof.
2. The combination of claim 1, wherein the HA polypeptide of the first influenza virus or variant thereof comprises one or more mutations at an HA cleavage site as compared to a respective wild-type HA polypeptide of the first influenza virus, and wherein the HA cleavage site is within a region of the HA polypeptide corresponding to amino acids 352-382 of SEQ ID NO: 325.
3. The combination of claim 1 or 2, wherein the combination further comprises an RNA encoding a polypeptide comprising a coronavirus S polypeptide or variant thereof.
4. The combination of claim 2 or 3, wherein the one or more mutations at the HA cleavage site comprise a deletion of three to ten amino acid residues as compared to a respective wild-type HA polypeptide of the first influenza virus.
5. The combination of claim 3 or 4, wherein the coronavirus S polypeptide or variant thereof is a prefusion stabilized S polypeptide comprising at least two proline substitutions at positions corresponding to residues 986 and 987 of SEQ ID NO: 1.
6. The combination of claim 5, wherein the prefusion stabilized S polypeptide further comprises proline substitutions at positions corresponding to residues 817, 892, 899, and 942 of SEQ ID NO: 1.
7. The combination of claim 5 or 6, wherein the coronavirus S polypeptide further comprises one or more mutations in a region corresponding to amino acids 682-685 of SEQ ID NO: 1.
8. The combination of any one of claims 4-7, wherein:(a) the RNA encoding the polypeptide comprising the coronavirus S polypeptide or variant thereof comprises (i) a nucleotide sequence according to SEQ ID NO: 286 or a sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at ieast 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 286, (ii) a nucleotide sequence according to SEQ ID NO: 288 or a sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 288, and / or (iii) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence according to SEQ ID NO: 285 or an amino acid sequence that is at least 70%, at ieast 80%, at least 85%, at least 90%, at Page 336 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 285;(b) the RNA encoding the polypeptide comprising the coronavirus S polypeptide or variant thereof comprises (I) a nucleotide sequence according to SEQ ID NO: 291 or a sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 291, (II) a nucleotide sequence according to SEQ ID NO: 293 or a sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 293, and / or (iii) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence according to SEQ ID NO: 290 or an amino acid sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 290; or(c) the RNA encoding the polypeptide comprising the coronavirus S polypeptide or variant thereof comprises (I) a nucleotide sequence according to SEQ ID NO: 296 or a sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 296, (ii) a nucleotide sequence according to SEQ ID NO: 298 or a sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 298, and / or (iii) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence according to SEQ ID NO: 295 or an amino acid sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 295.
9. The combination of any one of claims 1-8, wherein the fragment of the coronavirus S polypeptide or variant thereof comprises a receptor binding domain (RBD).
10. The combination of claim 9, wherein the RBD comprises:(a) an amino acid sequence corresponding to amino acids 319-528, 327-528, 328-528, 330-528, 319-530, 327-530, 328-530, 330-530, 319-531, 327-531, 328-531, 330-531, 319-537, 327-537, 328-537, 330-537, 330-537, 319-541, 327-541, 328-541, or 330-541 of SEQ ID NO: 1;(b) an amino acid sequence of a region of an S polypeptide of a SARS-CoV-2 variant that corresponds to amino acids 319-528, 327-528, 328-528, 330-528, 319-530, 327-530, 328-530, 330-530, 319-531, 327-531, 328-531, 330-531, 319-537, 327-537, 328-537, 330-537, 330-537, 319-541, 327-541, 328-541, or 330-541 of SEQ ID NO: 1;(c) an amino acid sequence according to SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 325, or SEQ ID NO: 326, or an amino acid sequence of a region of an S polypeptide of a SARS-CoV-2 variant that corresponds to any one of SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 325, or SEQ ID NO: 326; orPage 337 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)(d) an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at ieast 90%, at least 91%, at least 92%, at least 93%, at least 94%, at ieast 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any one of the amino acid sequences recited in (a)-(c).
11. The combination of any one of claims 1-10, wherein the fragment of the coronavirus S polypeptide or variant thereof comprises an N-Terminai Domain (NTD).
12. The combination of claim 11, wherein the NTD comprises:(a) an amino acid sequence corresponding to amino acids 1-209, 14-209, 15-209, 19-209, 20-209, 21-209, 1-305, 14-305, 15-305, 19-305, 20-305, 21-305, 1-311, 14-311, 15-311, 19-311, 20-311, 21-311, 1-318, 14-318, 15- 318, 19-318, 20-318, 21-318, 1-302, 14-302, 15-302, 19-302, 20-302, or 21-302 of SEQ ID NO: 1;(b) an amino acid sequence of a region of an S polypeptide of a SARS-CoV-2 variant that corresponds to amino acids 1-209, 14-209, 15-209, 19-209, 20-209, 21-209, 1-305, 14-305, 15-305, 19-305, 20-305, 21-305, 1-311, 14-311, 15-311, 19-311, 20-311, 21-311, 1-318, 14-318, 15-318, 19-318, 20-318, 21-318, 1-302, 14-302, 15-302, 19-302, 20-302, or 21-302 of SEQ ID NO: 1; or(c) an amino acid sequence that is at least 70%, at least 75%, at least 80%, at ieast 85%, at ieast 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any one of the amino acid sequences recited in (a)-(b).
13. The combination of any one of claims 1-12, wherein the fragment of the coronavirus S polypeptide or variant thereof comprises a fragment of an SI polypeptide comprising:(a) an amino acid sequence corresponding to amino acids 1-528, 14-528, 15-528, 19-528, 20-528, 21-528, 1-530, 14-530, 15-530, 19-530, 20-530, 21-530, 1-531, 14-531, 15-531, 19-531, 20-531, 21-531, 1-537, 14-537, 15-537, 19-537, 20-537, 21-537, 1-541, 14-541, 15-541, 19-541, 20-541, or 21-541 of SEQ ID NO: 1;(b) an amino acid sequence of QCVMPLFNLnTTQSYTNSFTRGVYYPDKVFRSSVLHLTQDLFLPFFSNVTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIR GWIFGTTLDSKTQSLUVNNATNVFIKVCEFQFCNDPFLDVYHKNNKSWMESESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNL REFVFKNIDGYFKIYSKHTPnGRDFPQGFSALEPLVDLPIGINITRFQTLLALNRSYLTPGDSSSGWTAGAADYYVGYLQPRTFLLKYN ENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNVTNLCPFHEVFNATTFASVYAWNRTRISNCVADYSVL YNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIKGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKHSGNYDYWYRS LRKSKLKPFERDISTEIYQAGNKPCKGKGPNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPK (SEQ ID NO: 20);(c) an amino acid sequence of QCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPALPFNDGVYFASTEKSNIIRG WIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYQKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKEGNFKNLRE FVFKNIDGYFKIYSKHTPINLERDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPVDSSSGWrAGAAAYYVGYLQPRTFLLKYNE NGTFTDAVDCALDPLSETKCTLKSFTVEKGIYQTSN FRVQPTESIVRFPNITN LCPFH EVFNATTFASVYAWN RKRISNCVADYSVIYN FAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKPSGNYNYLYRLFRK SKLKPFERDISTEIYQAGNKPCNGVAGPNCYSPLQSYGFRPTYGVGHQPYRVWLSFELLHAPATVCGPK (SEQ ID NO: 21);Page 338 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)(d) an amino acid sequence of a region of an S polypeptide of a SARS-CoV-2 variant that corresponds to any one of the amino acid sequences recited in (a)-(c); or(e) an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any one of the amino acid sequences recited in (a)-(d).
14. The combination of any one of claims 1-13, wherein the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises a secretory signal peptide, wherein the secretory signal peptide is at the N-terminus of the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof.
15. The combination of claim 14, wherein the secretory signal peptide is a secretory signal peptide of a coronavirus S polypeptide or a heteroiogous secretory signal peptide.
16. The combination of claim 14 or 15, wherein the secretory signal peptide is a SARS-CoV-2 S poiypeptide secretory signal peptide comprising:(a) an amino acid sequence corresponding to amino acids 1-13 of SEQ ID NO: 1;(b) an amino acid sequence corresponding to amino acids 1-16 of SEQ ID NO: 1;(c) an amino acid sequence corresponding to amino acids 1-19 of SEQ ID NO: 1; or(d) an amino acid sequence of a region of an S polypeptide of a SARS-CoV-2 variant corresponding to any one of the amino acid sequences recited in (a)-(c).
17. The combination of claim 14 or 15, wherein the secretory signal peptide is an HSV-1 gD protein secretory signal polypeptide comprising an amino acid sequence of MGGAAARLGAVILFWIVGLHGVRG (SEQ ID NO: 27) or an amino acid sequence having 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more amino acid alterations relative to SEQ ID NO: 27.
18. The combination of any one of claims 1-17, wherein the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises a transmembrane region, wherein the transmembrane region is at the C-terminus of the fragment of the coronavirus S polypeptide or variant thereof.
19. The combination of claim 18, wherein the transmembrane region is a SARS-CoV-2 S polypeptide transmembrane region.
20. The combination of claim 18 or 19, wherein the transmembrane region comprises:(a) an amino acid sequence of EQYIKWPWYIWLGFIAGLIAIVMVnMLCCMTSCCSCLKGCCSCGSCC (SEQ ID NO: 90), or an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 90;Page 339 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)(b) an amino acid sequence of EQYIKWPWYIWLGFIAGUAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT (SEQ ID NO: 89), or an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 89;(c) an amino acid sequence corresponding to amino acids 1200-1254 or 1200-1273 of SEQ ID NO: 1, an amino acid sequence of a region of a S polypeptide of a SARS-CoV-2 variant that corresponds to amino acids 1200-1254 or 1200-1273 of SEQ ID NO: 1, or an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to amino acids 1200-1254 or 1200-1273 of SEQ ID NO: 1;(d) an amino acid sequence corresponding to amino acids 1206-1254 or 1206-1273 of SEQ ID NO: 1, an amino acid sequence of a region of a S polypeptide of a SARS-CoV-2 variant that corresponds to amino acids 1206-1254 or 1206-1273 of SEQ ID NO: 1, or an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to amino acids 1206-1254 or 1206-1273 of SEQ ID NO: 1;(e) an amino acid sequence corresponding to amino acids 1211-1254 or 1211-1273 of SEQ ID NO: 1, an amino acid sequence of a region of a S polypeptide of a SARS-CoV-2 variant that corresponds to amino acids 1211-1254 or 1211-1273 of SEQ ID NO: 1, or an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to amino acids 1211-1254 or 1211-1273 of SEQ ID NO: 1; or(f) an amino acid sequence corresponding to amino acids 1207-1254 or 1207-1273 of SEQ ID NO: 1, an amino acid sequence of a region of a S polypeptide of a SARS-CoV-2 variant that corresponds to amino acids 1207- 1254 or 1207-1273 of SEQ ID NO: 1, or an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at ieast 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to amino acids 1207-1254 or 1207-1273 of SEQ ID NO: 1.
21. The combination of any one of claims 1-16 or 18-20, wherein the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises, from N-terminus to C-terminus:(a) a secretory signal peptide of a SARS-CoV-2 S polypeptide comprising an amino acid sequence corresponding to amino acids 1-13, 1-16, or 1-19 of SEQ ID NO: 1, or an amino acid sequence of a region of an S polypeptide of a SARS-CoV-2 variant corresponding to amino acids 1-13, 1-16, or 1-19 of SEQ ID NO: 1;(b) a fragment of an SI polypeptide comprising an amino acid sequence corresponding to amino acids 1-537 of SEQ ID NO: 1, or an amino acid sequence of a region of an S polypeptide of a SARS-CoV-2 variant corresponding to amino acids 1-537 of SEQ ID NO: 1; and(c) a transmembrane region of an S polypeptide of a SARS-CoV-2 virus comprising an amino acid sequence according to SEQ ID NO: 183, SEQ ID NO: 193, SEQ ID NO: 351, SEQ ID NO: 352, or SEQ ID NO: 353, or an amino acid sequence of a region of an S polypeptide of a SARS-CoV-2 variant that corresponds to SEQ ID NO: 183, SEQ ID NO: 193, SEQ ID NO: 351, SEQ ID NO: 352, or SEQ ID NO: 353.Page 340 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)22. The combination of claim 21, wherein the fragment of the SI polypeptide and the transmembrane region are connected to one another by a linker.
23. The combination of any one of claims 1-14 or 17-20, wherein the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises, from N-terminus to C-terminus:(a) a secretory signal peptide of an HSV-1 gD protein;(b) a fragment of an SI polypeptide comprising an amino acid sequence corresponding to amino acids 14-528 of SEQ ID NO: 1, or an amino acid sequence of a region of an S polypeptide of a SARS-CoV-2 variant that corresponds to amino acids 14-528 of SEQ ID NO; 1; and(c) a transmembrane region of an S polypeptide of a SARS-CoV-2 virus comprising an amino acid sequence according to SEQ ID NO: 183, SEQ ID NO: 193, SEQ ID NO: 351, SEQ ID NO: 352, or SEQ ID NO: 353, or an amino acid sequence of a region of an S polypeptide of a SARS-CoV-2 variant that corresponds to SEQ ID NO: 183, SEQ ID NO: 193, SEQ ID NO: 351, SEQ ID NO: 352, or SEQ ID NO: 353.
24. The combination of claim 23, wherein (1) the secretory signal peptide and the fragment of the SI polypeptide; and / or (2) the fragment of the SI polypeptide and the transmembrane region are connected to one another by a linker.
25. The combination of any one of claims 1 to 24, wherein the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises one or more mutations characteristic of a SARS-CoV-2 Omicron variant, a SARS-CoV-2 XBB.1.5 variant, a SARS-CoV-2 JN.l variant, a SARS-CoV-2 KP.2 variant, a SARS- CoV-2 XEC variant, a SARS-CoV-2 XBB1.5 variant, a SARS-CoV-2 MC.l variant, a SARS-CoV-2 KP.3.1.1 variant, or a SARS-CoV-2 LP.8.1 variant.
26. The combination of any one of claims 1-14, 17-20, or 22-25, wherein the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises (i) a nucleotide sequence according to SEQ ID NO: 301 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at ieast 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 301; (ii) a nucleotide sequence according to SEQ ID NO: 303 or a sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 303; and / or (iii) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence according to SEQ ID NO: 300 or an amino acid sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 300.
27. The combination of any one of claims 1-14, 17-20, or 22-25, wherein the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises (i) a nucleotide sequence according to SEQ ID NO: 306 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least Page 341 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 306; (ii) a nucleotide sequence according to SEQ ID NO: 308 or a sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 308; and / or (iii) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence according to SEQ ID NO: 305 or an amino acid sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 305.
28. The combination of any one of claims 1-16, 19-22, or 25, wherein the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises (i) a nucleotide sequence according to SEQ ID NO: 311 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 311; (ii) a nucleotide sequence according to SEQ ID NO: 313 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 313; and / or (iii) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence according to SEQ ID NO: 310 or an amino acid sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 310.
29. The combination of any one of claims 1-16, 19-22, or 25, wherein the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises (I) a nucleotide sequence according to SEQ ID NO: 316 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 316; (ii) a nucleotide sequence according to SEQ ID NO: 318 or a nucleotide sequence that is at least 70%, at least 80%, at ieast 85%, at least 90%, at least 91%, at least 92%, at least 93%, at ieast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 318; and / or (iii) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence according to SEQ ID NO: 315 or an amino acid sequence that is at least 70%, at ieast 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 315.
30. The combination of any one of claims 1-14, 17-20, or 22-25, wherein:(a) the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises (i) a nucleotide sequence according to SEQ ID NO: 813 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 813, (ii) a nucleotide sequence according to SEQ ID NO: 815 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at Page 342 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 815, and / or (ill) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence according to SEQ ID NO: 812, or an amino acid sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 812;(b) the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises (I) a nucleotide sequence according to SEQ ID NO: 721 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 721, (ii) a nucleotide sequence according to SEQ ID NO: 723 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 723, and / or (ill) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence according to SEQ ID NO: 817, or an amino acid sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 817;(c) the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises (i) a nucleotide sequence according to SEQ ID NO: 362 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 362, (ii) a nucleotide sequence according to SEQ ID NO: 364 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 364, and / or (iii) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence according to SEQ ID NO: 817, or an amino acid sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 817;(d) the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises (i) a nucleotide sequence according to SEQ ID NO: 803 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 803, (ii) a nucleotide sequence according to SEQ ID NO: 805 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 805, and / or (iii) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence according to SEQ ID NO: 802, or an amino acid sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 802;(e) the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises (i) a nucleotide sequence according to SEQ ID NO: 808 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 808, (ii) a nucleotide Page 343 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)sequence according to SEQ ID NO: 810 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at ieast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 810, and / or (ill) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence according to SEQ ID NO: 807, or an amino acid sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 807; or(f) the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof comprises (i) a nucleotide sequence according to SEQ ID NO: 819 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 819, (ii) a nucleotide sequence according to SEQ ID NO: 820 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 820, and / or (ill) a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence according to SEQ ID NO: 818, or an amino acid sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at ieast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 818.
31. The combination of any one of claims 1-30, wherein the first influenza virus or variant thereof is predicted by a health authority and / or based on human serology data from the Northern and / or Southern hemisphere to circulate during a flu season.
32. The combination of any one of claims 1-31, wherein the first influenza virus or variant thereof is an H1N1, H1N2, H2N2, H3N1, H3N2, H3N8, H5N1, H5N2, H5N3, H5N8, H5N9, H7N1, H7N2, H7N3, H7N4, H7N7, H7N9, H9N2, H10N7, or H10N8 type A influenza virus.
33. The combination of any one of claims 1-32, wherein the first influenza virus or variant thereof is an A / Wisconsin / 588 / 2019 H1N1 virus, and wherein the HA polypeptide comprises an amino acid sequence according to SEQ ID NO: 331, or an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 331.
34. The combination of claim 33, wherein the RNA encoding the HA polypeptide of A / Wisconsin / 588 / 2019 comprises a nucleotide sequence according to SEQ ID NO: 333 or SEQ ID NO: 335, or a nucleotide sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 333 or SEQ ID NO: 335.
35. The combination of any one of claims 1-32, wherein the first influenza virus is:Page 344 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)(a) an A / Cambodia / e0826360 / 2020 H3N2 virus, and wherein the HA polypeptide comprises an amino acid sequence according to SEQ ID NO: 336, or an amino acid sequence that is at ieast 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 336; or(b) an A / Darwin / 6 / 2021 H3N2 virus, and wherein the HA polypeptide comprises an amino acid sequence according to SEQ ID NO: 320 or an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 320.
36. The combination of claim 35, wherein:(a) the RNA encoding the HA polypeptide of A / Cambodia / e0826360 / 2020 H3N2 comprises a nucleotide sequence according to SEQ ID NO: 338 or SEQ ID NO: 337 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 338 or SEQ ID NO: 337; or(b) the RNA encoding the HA polypeptide of A / Darwin / 6 / 2021 comprises a nucleotide sequence according to SEQ ID NO: 322 or SEQ ID NO: 324 or a nucleotide sequence that is at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 322 or SEQ ID NO: 324.
37. The combination of any one of claims 1-32, wherein the first influenza virus or variant thereof is:(a) a B / Washington / 02 / 2019 virus, and wherein the HA polypeptide comprises an amino acid sequence according to SEQ ID NO: 341 or an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 341;(b) a B / Austria / 1359417 / 2021 virus, and wherein the HA polypeptide comprises an amino acid sequence according to SEQ ID NO: 325, or an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 325; or(c) a B / Phuket / 3073 / 2013 virus, and wherein the HA polypeptide comprises an amino acid sequence according to SEQ ID NO: 346, or an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 346.
38. The combination of claim 37, wherein:(a) the RNA encoding the HA polypeptide of B / Washington / 02 / 2019 comprises a nucleotide sequence according to SEQ ID NO: 343 or SEQ ID NO: 345, or a nucleotide sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 343 or SEQ ID NO: 345;Page 345 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)(b) the RNA encoding the HA polypeptide of B / Austria / 1359417 / 2021 comprises a nucleotide sequence according to SEQ ID NO: 327 or SEQ ID NO: 329, or a nucleotide sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at ieast 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 327 or SEQ ID NO: 329; or(c) the RNA encoding the HA polypeptide of B / Phuket / 3073 / 2013 comprises a nucleotide sequence according to SEQ ID NO: 348 or SEQ ID NO: 350, or a nucleotide sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 348 or SEQ ID NO: 350,39. The combination of any one of claims 1-32, wherein the first influenza virus or variant thereof is a B / Austria / 1359417 / 2021 virus, and wherein the HA polypeptide comprises an amino acid sequence according to SEQ ID NO: 330 or an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 330, and comprises one or more mutations at an HA cleavage site within the region of the HA polypeptide corresponding to amino acids 352-382 of SEQ ID NO: 325.
40. The combination of any one of claims 1-39, further comprising an RNA encoding an HA polypeptide of a second influenza virus or variant thereof, wherein:(a) the first influenza virus or variant thereof is a type A influenza virus and the second influenza virus or variant thereof is a type B influenza virus;(b) the first influenza virus or variant thereof is a type A influenza virus and the second influenza virus or variant thereof is a type A influenza virus;(c) the first influenza virus or variant thereof is a type B influenza virus and the second influenza virus influenza virus or variant thereof is a type A influenza virus; or(d) the first influenza virus or variant thereof is a type B influenza virus and the second influenza virus or variant thereof is a type B influenza virus.
41. The combination of claim 40, wherein the ratio of the amount of RNA encoding the HA polypeptide of the first influenza virus or variant thereof to the amount of RNA encoding the HA poiypeptide of the second influenza virus or variant thereof is 1:1, 1:2, 1:3, 1:4, or 1:5,42. The combination of claim 40 or 41, further comprising an RNA encoding an HA poiypeptide of a third influenza virus or variant thereof, wherein:(a) the first influenza virus or variant thereof is a type A influenza virus, the second influenza virus or variant thereof is a type A influenza virus, and the third influenza virus or variant thereof is a type A influenza virus;(b) the first influenza virus or variant thereof is a type A influenza virus, the second influenza virus or variant thereof is a type A influenza virus, and the third influenza virus or variant thereof is a type B influenza virus;(c) the first influenza virus or variant thereof is a type A influenza virus, the second influenza virus or variant thereof Is a type B influenza virus, and the third influenza virus or variant thereof is a type B influenza virus;Page 346 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)(d) the first influenza virus or variant thereof is a type B influenza virus, the second influenza virus or variant thereof is a type A influenza virus, and the third influenza virus or variant thereof is a type A influenza virus;(e) the first influenza virus or variant thereof is a type B influenza virus, the second influenza virus or variant thereof is a type A influenza virus, and the third influenza virus or variant thereof is a type A influenza virus; or (f) the first influenza virus or variant thereof is a type B influenza virus, the second influenza virus or variant thereof is a type A influenza virus, and the third influenza virus or variant thereof is a type B influenza virus.
43. The combination of claim 42, wherein the ratio of the amount of RNA encoding the HA polypeptide of the first influenza virus or variant thereof to the amount of RNA encoding the HA polypeptide of the second influenza virus or variant thereof to the amount of RNA encoding the HA polypeptide of the third influenza virus or variant thereof is 1:1:1, 2:1:1, 3:1:1, 4:1:1, or 5:1:1.
44. The combination of claim 42 or 43, further comprising an RNA encoding an HA polypeptide of a fourth influenza virus or variant thereof, wherein:(a) the first influenza virus or variant thereof is a type A influenza virus, the second influenza virus or variant thereof is a type A influenza virus, the third influenza virus or variant thereof is a type A influenza virus, and the fourth influenza virus or variant thereof is a type A influenza virus;(b) the first influenza virus or variant thereof is a type A influenza virus, the second influenza virus or variant thereof is a type A influenza virus, the third influenza virus or variant thereof is a type A influenza virus, and the fourth influenza virus or variant thereof is a type B influenza virus;(c) the first influenza virus or variant thereof is a type A influenza virus, the second influenza virus or variant thereof is a type A influenza virus, the third influenza virus or variant thereof is a type A influenza virus, and the fourth influenza virus or variant thereof is a type B influenza virus;(d) the first influenza virus or variant thereof is a type A influenza virus, the second influenza virus or variant thereof is a type B influenza virus, the third influenza virus or variant thereof is a type A influenza virus, and the fourth influenza virus or variant thereof is a type B influenza virus;(e) the first influenza virus or variant thereof is a type B influenza virus, the second influenza virus or variant thereof is a type B influenza virus, the third influenza virus or variant thereof is a type B influenza virus, and the fourth influenza virus or variant thereof is a type B influenza virus;(f) the first influenza virus or variant thereof is a type B influenza virus, the second influenza virus or variant thereof is a type B influenza virus, the third influenza virus or variant thereof is a type B influenza virus, and the fourth influenza virus or variant thereof is a type B influenza virus;(g) the first influenza virus or variant thereof is a type B influenza virus, the second influenza virus or variant thereof is a type B influenza virus, the third influenza virus or variant thereof is a type A influenza virus, and the fourth influenza virus or variant thereof is a type A influenza virus; or(h) the first influenza virus or variant thereof is a type B influenza virus, the second influenza virus or variant thereof is a type A influenza virus, the third influenza virus or variant thereof is a type A influenza virus, and the fourth influenza virus or variant thereof is a type A influenza virus.Page 347 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)45. The combination of claim 44, wherein the ratio of the amount of RNA encoding the HA polypeptide of the first influenza virus or variant thereof to the amount of RNA encoding the HA polypeptide of the second influenza virus or variant thereof to the amount of RNA encoding the HA polypeptide of the third influenza virus or variant thereof to the amount of RNA encoding the HA polypeptide of the fourth influenza virus or variant thereof is 1:1: 1:1, 2:1:1:1, 3:1:1:1, 4:1:1:1, 5:1:1:1, 2:2:1:1, 3:3:1:1, 4:4:1:1, or 5:5:l:l.
46. The combination of any one of claims 40-45, wherein:(a) the total amount of RNA encoding an HA polypeptide of an influenza type A virus is equal to the total amount of RNA encoding an HA polypeptide of an influenza type B virus; or(b) the total amount of RNA encoding an HA polypeptide of an influenza type B virus is 2, 3, 4, or 5 times greater than the total amount of RNA encoding an HA polypeptide of an influenza type A virus.
47. The combination of any one of claims 1-46, wherein each RNA comprises a 5' cap, a cap proximal sequence, a 5' UTR sequence, a 3' UTR sequence, and a poly(A) sequence.
48. The combination of any one of claims 1-47, wherein each RNA in the combination comprises a single modified uridine in place of each uridine, wherein the modified uridine is Nl-methyl-pseudouridine.
49. A composition comprising the combination of any one of claims 1-48, wherein each RNA is formulated in a nanoparticle.
50. The composition of claim 49, wherein:(a) the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof, and, if present, the RNA encoding the HA polypeptide of tlie second influenza virus or variant thereof, the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and the RNA encoding the HA polypeptide of the fourth influenza virus or variant thereof are each formulated in separate nanoparticles;(b) the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof, and, if present, the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and the RNA encoding the HA polypeptide of the fourth influenza virus are co-formulated or variant thereof; or(c) the RNA encoding the fragment of the coronavirus S polypeptide or variant thereof is formulated in a first nanoparticle, and the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, and, if present the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and the RNA encoding the HA polypeptide of the fourth influenza virus or variant thereof are co-formulated in a second nanoparticle.Page 348 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)51. The composition of ciaim 49 or 50, wherein the nanoparticle is a lipid nanoparticle (LNP), a polypiex (PLX), a lipidated polypiex (LPLX), a liposome, or a polysaccharide nanoparticle.
52. The composition of claim 51, wherein the nanoparticle is an LNP comprising a cationically ionizable lipid, a sterol, a neutral iipid, and a polymer-conjugated lipid.
53. The composition of claim 52, wherein the polymer-conjugated iipid comprises a PEG-conjugated lipid.
54. The composition of any one of claims 51-53, wherein each RNA is encapsulated in an LNP, and wherein the LNP comprises molar ratios of 20-60% ionizable cationic iipid, 5-25% neutral lipid, 25-55% sterol, and 0.5-15% PEG-modified iipid.
55. The composition of any one of claims 49-54, wherein each nanoparticle has an average diameter of about 50-150 nm.
56. The composition of any one of claims 49-55, comprising a cryoprotectant.
57. The composition of any one of claims 49-56, comprising one or more of Tris base, Tris HCI, NaCI, KCI, Na2HPO, and KH2PCh.
58. The composition of any one of claims 49-57, comprising about 10 mM Tris buffer, about 10% sucrose, about 0.1 mg / mL total RNA, and a pH of about 7.4.
59. The composition of any one of claims 49-58, wherein the composition is formulated to provide one or more unit doses, wherein each unit dose comprises 100 pg or less or 90 pg or less of total RNA.
60. The composition of any one of claims 49-59, wherein the composition is formulated to provide one or more unit doses, wherein:(a) the total amount of RNA encoding the HA polypeptide of the first influenza virus or variant thereof in each unit dose is about 60 pg, about 45 pg, or about 30 pg; and / or the total amount of RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof in each unit dose is about 30 pg, about 25 pg, about 20 pg, about 15 pg, about 10 pg, about 6 pg, about 5 pg, about 3 pg, or about 1 pg;(b) the total amount of RNA encoding the HA polypeptide of the first influenza virus or variant thereof in each unit dose is about 60 pg and the total amount of RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof in each unit dose is about 20 pg;(c) the total amount of RNA encoding the HA polypeptide of the first influenza virus or variant thereof in each unit dose is about 60 pg and the total amount of RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof in each unit dose is about 10 pg;Page 349 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)(d) the total amount of RNA encoding the HA polypeptide of the first influenza virus or variant thereof in each unit dose is about 60 pg and the total amount of RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof in each unit dose is about 5 pg;(e) the total amount of RNA encoding the HA polypeptide of the first influenza virus or variant thereof in each unit dose is about 45 pg and the total amount of RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof in each unit dose is about 10 pg;(f) the total amount of RNA encoding the HA polypeptide of the first influenza virus or variant thereof in each unit dose is about 45 pg and the total amount of RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or a variant thereof in each unit dose is about 30 pg; or(g) the total amount of RNA encoding the HA polypeptide of the first influenza virus or variant thereof in each unit dose is about 30 pg and the total amount of RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof in each unit dose is about 10 pg.
61. The composition of any one of claims 49-60, wherein the composition is formulated to provide one or more unit doses, wherein each unit dose comprises:(a) about 20 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof and, if present, about 5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, and about 5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof;(b) about 30 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof and, if present, about 7.5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, and about 7.5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof; or(c) about 40 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof and, if present, about 10 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, and about 10 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof,wherein the first influenza virus or variant thereof is a type B influenza virus and, if present, the second influenza virus or variant thereof is a type A influenza virus, and the third influenza virus is a type A influenza virus.
62. The composition of any one of claims 49-60, wherein the composition is formulated to provide one or more unit doses, wherein each unit dose comprises:(a) about 7.5 pg of the RNA encoding the HA polypeptide of the first influenza virus and, if present, about 7.5 pg of the RNA encoding the HA polypeptide of the second influenza virus, about 7.5 pg of the RNA encoding the HA polypeptide of the third influenza virus, and about 7.5 pg of the RNA encoding the HA polypeptide of the fourth influenza virus;(b) about 11.25 pg of the RNA encoding the HA polypeptide of the first influenza virus and, if present, about 11.25 pg of the RNA encoding the HA polypeptide of the second influenza virus, about 11.25 pg of the RNA encoding the HA polypeptide of the third influenza virus, and about 11.25 pg of the RNA encoding the HA polypeptide of the fourth influenza virus;(c) about 2,5 pg of the RNA encoding the HA polypeptide of the first influenza virus and, if present, about 2.5 pg of the RNA encoding the HA polypeptide of the second Influenza virus, about 12.5 pg of the RNA encoding the Page 350 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)HA polypeptide of the third influenza virus, and about 12.5 pg of the RNA encoding the HA polypeptide of the fourth influenza virus;(d) about 25 pg of the RNA encoding the HA polypeptide of the first influenza virus and, if present, about 25 pg of the RNA encoding the HA polypeptide of the second influenza virus, about 5 pg of the RNA encoding the HA polypeptide of the third influenza virus, and about 5 pg of the RNA encoding the HA polypeptide of the fourth influenza virus; or(e) about 15 pg of the RNA encoding the HA polypeptide of the first influenza virus and, if present, about 15 pg of the RNA encoding the HA polypeptide of the second influenza virus, about 15 pg of the RNA encoding the HA polypeptide of the third influenza virus, and about 15 pg of the RNA encoding the HA polypeptide of the fourth influenza virus;wherein: (i) the first influenza virus is a type B influenza virus and, if present, the second influenza virus is a type B influenza virus, the third influenza virus is a type A influenza virus, and the fourth influenza virus is a type A influenza virus; or (ii) the first influenza virus is a type B influenza virus and, if present, the second influenza virus is a type A influenza virus, the third influenza virus is a type A influenza virus, and the fourth influenza virus is a type A influenza virus.
63. The composition of any one of claims 49-62, wherein the composition is formulated to provide one or more unit doses, wherein each unit dose comprises:(a) about 20 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 5 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof;(b) about 30 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 5 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof;(c) about 40 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 5 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof;(d) about 20 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 10 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof;(e) about 30 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 10 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof;Page 351 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)(f) about 40 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 10 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof;(g) about 20 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 20 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof;(h) about 30 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 20 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof;(i) about 40 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 20 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof;(j) about 20 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 10 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof;(k) about 20 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 15 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof;(l) about 20 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 20 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof;(m) about 20 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 30 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof;(n) about 30 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 10 pg of the RNA encoding the polypeptide comprising the coronavirus S polypeptide or variant thereof;(o) about 30 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 7.5 pg of thePage 352 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 15 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof;(p) about 30 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 20 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof;(q) about 30 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 7.5 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 30 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof;(r) about 40 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 10 pg of the RNA encoding The HA polypeptide of the third influenza virus or variant thereof, and about 10 pg of the RNA encoding the polypeptide comprising the coronavirus S polypeptide or variant thereof;(s) about 40 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 15 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof;(t) about 40 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 20 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof; or(u) about 40 pg of the RNA encoding the HA polypeptide of the first influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the second influenza virus or variant thereof, about 10 pg of the RNA encoding the HA polypeptide of the third influenza virus or variant thereof, and about 30 pg of the RNA encoding the polypeptide comprising the fragment of the coronavirus S polypeptide or variant thereof;wherein the first influenza virus is a type B influenza virus, the second influenza virus is a type A influenza virus, and the third influenza virus is a type A influenza virus.
64. A pharmaceutical composition comprising (I) a combination of any one of claims 1-48, or a composition of any one of claims 49-63, and (ii) a pharmaceutically acceptable excipient.
65. The pharmaceutical composition of claim 64, formulated as: (i) a multi-dose formulation in a vial, (ii) a single-dose formulation in a vial, or (ill) a prefilled syringe.
66. A method of inducing an immune response against a coronavirus and an influenza virus in a subject comprising administering the combination of any one of claims 1-48, the composition of any one of claims 49-63, or the pharmaceutical composition of claim 64 or 65 to the subject.Page 353 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)67. The method of claim 66, wherein the subject is 18 to 64 years old.
68. The method of claim 66, wherein the subject is 65 years or oider.
69. The method of any one of claims 66-68, wherein the combination, composition, or pharmaceutical composition is administered in a volume of about 200 pl to about 300 pL.
70. The method of any one of claims 66-69, wherein the subject has previously been administered a composition that delivers a coronavirus antigen.
71. The method of any one of claims 66-70, wherein the method comprises administering a single dose of the combination, composition, or pharmaceutical composition to the subject.
72. The method of any one of claims 66-70, wherein the method comprises administering two or more doses of the combination, composition, or pharmaceutical composition to the subject, wherein the two doses are administered about 21 days apart; or wherein the subject has previously been administered (i) a composition that delivers a coronavirus antigen and an influenza antigen or (ii) a composition that delivers a coronavirus antigen and a composition that delivers an influenza antigen, and wherein the combination, composition, or pharmaceutical composition is administered about 21 days after the subject has been administered (I) or (ii).
73. The method of any one of claims 66-70,wherein the method comprises administering three or more doses of the combination, composition, or pharmaceutical composition to the subject, wherein the first dose and the second dose are administered about 21 days apart and the third dose is administered at least about 2 months after the second dose; orwherein the subject has previously been administered two doses of (i) a composition that delivers a coronavirus antigen and an influenza antigen or (ii) a composition that delivers a coronavirus antigen and a composition that delivers an influenza antigen wherein the combination, composition, or pharmaceutical composition is administered at least about 2 months after the subject has been administered (I) or (ii).
74. The method of any one of claims 66-73, further comprising administering one or more vaccines against a non-coronavirus and non-infiuenza disease, wherein the one or more vaccines comprise a vaccine against a respiratory virus.
75. The method of any one of claims 66-74, wherein the method results in induction of an immune response against a coronavirus and an influenza virus in the subject, wherein the immune response comprises production of antibodies and / or a T cell response directed against one or more coronaviruses and one or more influenza viruses.
76. The method of any one of claims 66-75, wherein the method prevents or reduces the chance of a coronavirus and / or an influenza infection in the subject, prevents or mitigates deleterious symptoms associated with Page 354 of 35613222610vlAttorney Docket No. 2013237-1556 (P2037W001)a coronavirus and / or an influenza infection in tine subject, increases the likelihood of experiencing an asymptomatic coronavirus and / or influenza infection In the subject, and / or treats a coronavirus and / or influenza infection.Page 355 of 35613222610vl