Coronavirus vaccines and methods of use

Abstract

Compositions and methods for the prevention and / or treatment of viral infections, in particular coronaviridae viral infections.

Description

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS

[0002] This application claims the benefit of U.S. Provisional Application No. 63 / 246,902, filed September 22, 2021, and U.S. Provisional Application No. 63 / 320,187, filed March 15, 2022, the contents of each of which are hereby incorporated herein in their entirety. Background Art

[0003] Emerging acute respiratory viral infections caused by novel coronaviruses are a major public health concern. Importantly, no vaccines or specific antiviral drugs are available at the time of an outbreak, particularly for infections such as the 2015 MERS-CoV or the 2019 SARS-CoV-2. SARS-CoV-2 claimed over 2,000 lives in less than two months after the first reported case. Therefore, new and easily scalable therapeutics are needed to combat illnesses caused by these viral infections. Summary of the Invention

[0004] Patients with compromised immune function due to autoimmunity, organ transplantation, or immunosuppressive therapy have a reduced ability to produce an antibody response to vaccination (Rousseau et al., A H1N1 v2009 vaccine in cancer patients treated with cytotoxic chemotherapy and / or targeted therapy: the VACANCE study. Ann Oncol. 2012 Feb; 23(2): 450-7). Immunocompromised patients have a reduced seropositivity rate after vaccination (Haidar et al., Immunogenicity of COVID-19 Vaccination in Immunocompromised Patients: An Observational, Prospective Cohort Study Interim Analysis. medRxiv2021.06.28.21259576). Although immunocompromised patients were excluded from the original clinical trials testing the current SARS-CoV-2 vaccines targeting the spike protein, follow-up analysis of immunocompromised patients showed that patients had a reduced ability to produce broad and lasting anti-spike antibody responses, especially in elderly patient cohorts (Boyarsky et al., Immunogenicity of a Single Dose of SARS-CoV-2 Messenger RNA Vaccine in Solid Organ Transplant Recipients. JAMA. 2021; 325(17): 1784-1786; Rincon-Arevalo et al., Impaired antigen-specific memory B cell and plasma cell responses including lack of specific IgG upon SARS-CoV-2 BNT162b2 vaccination among Kidney Transplant and Dialysis patients. medRxiv 2021.04.15.21255550). Therefore, inducing T cell responses to other SARS-CoV-2 viral proteins may be beneficial in enhancing cellular and humoral immunity. Therefore, a SARS-CoV-2 vaccine that specifically targets T cell responses is needed.Patients receiving anti-CD20 therapy have been shown to be able to generate functional T cells in response to vaccination (Apostolidis et al., Altered cellular and humoral immune responses following SARS-CoV-2 mRNA vaccination in patients with multiple sclerosis on anti-CD20 therapy. Nature Medicine, Vol. 27, pp. 1990-2001 (2021)), suggesting that patients with impaired B cells may still generate SARS-COV 2-specific T cells in response to vaccination.

[0005] Provided herein is an immunogenic composition (e.g., a vaccine) that specifically targets one or more T cell responses against a pathogen (e.g., in some embodiments, a virus), including a CD4+ T cell response and / or a CD8+ T cell response, and / or utilizes long-term persistence of T cell immunity. In some embodiments, the immunogenic compositions (e.g., vaccines) provided herein can specifically target one or more polypeptide antigens (e.g., in some embodiments, one or more viral antigens) of a pathogen, including, for example, one or more non-structural proteins, nucleocapsids, membrane proteins, and / or envelope proteins of a virus.

[0006] In one aspect, a SARS-CoV-2 immunogenic composition (e.g., a vaccine) is provided herein that specifically targets one or more T cell responses, including CD4+T cell responses and / or CD8+T cell responses, and / or utilizes the long-term persistence of T cell immunity. In some embodiments, the SARS-CoV-2 vaccine provided herein can specifically target polypeptide antigens for SARS-CoV-2, including, for example, one or more T cell responses to the nucleocapsid, membrane protein, and / or envelope protein of SARS-CoV-2. The SARS-CoV-2 immunogenic composition (e.g., a vaccine) provided herein can be used to elicit one or more T cell responses to SARS-CoV-2 in all patients. When T cell responses are present, protection against COVID19 is observed in patients with humoral immunity deficiency (Bange et al., CD8+ T cells contribute to survival in patients with COVID-19 and hematologic cancer. Nat Med 27, 1280-1289 (2021)), as well as long-term persistence of T cell responses caused by related infections from the original SARS-CoV epidemic (Le Bert et al., SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls. Nature 584, 457-462 (2020)). In some embodiments, the present disclosure provides, among other things, a particular insight that the SARS-CoV-2 immunogenic compositions (e.g., vaccines) provided herein may be particularly useful for eliciting one or more T cell responses against SARS-CoV-2 in patients whose humoral immunity has been compromised, such as in some embodiments by cancer (e.g., B-cell lymphoma), treatment with rituximab, methotrexate, or other immunosuppressive therapies targeting humoral immune responses, or in patients undergoing organ transplantation. In some embodiments, the T cell responses induced by the SARS-CoV-2 immunogenic compositions (e.g., vaccines) described herein can protect patients from severe COVID-19 and provide long-term protection through T cell immunity to the SARS-CoV-2 immunogenic compositions (e.g., vaccines) provided herein.Additionally or alternatively, in some embodiments, the SARS-CoV-2 immunogenic compositions (e.g., vaccines) provided herein can be used to overcome SARS-CoV-2 variants that may reduce the efficacy of other vaccines, such as those that do not target T cell responses (Davis et al., Reduced neutralisation of the Delta (B.1.617.2) SARS-CoV-2 variant of concern following vaccination. PLoS Pathog., 17(12):e1010022(2021); Tada et al., Comparison of. Neutralizing Antibody Titers Elicited by mRNA and Adenoviral Vector Vaccine against SARS-CoV-2 Variants.bioRxiv 2021.07.19.452771). In some embodiments, the immunogenic compositions described herein are used to treat subjects with SARS-CoV-2 B1.1.529 (omicron) variants or to immunize subjects against SARS-CoV-2 B1.1.529 (omicron) variants. In some embodiments, the SARS-CoV-2 immunogenic compositions (e.g., vaccines) provided herein can be used to supplement and / or enhance other immunogenic compositions (e.g., vaccines), such as those that do not target T cell responses. For example, in some embodiments, the SARS-CoV-2 immunogenic compositions (e.g., vaccines) provided herein can be used to enhance B cell responses by increasing CD4+ T cell activation.

[0007] Coronaviruses are single-stranded, positive-stranded RNA viruses that emerge incidentally from zoonotic sources to infect humans. Although some recent coronavirus infections over the past decade have caused significant morbidity and mortality, most human infections cause mild respiratory symptoms. These infections include severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and the ongoing SARS-CoV-2 pandemic. Infection with these viruses can lead to acute respiratory distress, resulting in high mortality. The global spread of SARS-CoV has resulted in 8,096 cases and 774 deaths. The first case of MERS-CoV was reported in Saudi Arabia in 2012, and since then, a total of 2,494 cases and 858 related deaths have been reported. As of March 8, 2020, 2019 SARS-CoV-2 has caused 118,096 cases worldwide, including 4,262 deaths. The rapid spread of 2019 SARS-CoV-2 has led to the World Health Organization declaring it a global pandemic of international concern.

[0008] All three coronaviruses, SARS-CoV, MERS-CoV and the recently emerged SARS CoV-2, belong to the genus Betacoronavirus. The genome of SARS CoV-2 is 30 kilobases in size and encodes at least four (4) structural proteins (spike protein [S], envelope protein [E], membrane protein [M] and nucleocapsid protein [N]) and at least sixteen (16) non-structural proteins (NSP 1-16). The S protein facilitates viral entry into target cells, and entry depends on the binding of the spike protein to the cell receptor ACE2 of both SARS-CoV and SARS-CoV-2. The two viruses share 76% amino acid identity in their genomes.

[0009] The field of the present disclosure relates to immunotherapeutic peptides, nucleic acids encoding the peptides, peptide binders, and their use in, for example, immunotherapy for viral diseases. In one aspect, the present disclosure provides viral epitopes expressed in virally infected cells, which are used alone or in combination with other antiviral agents or immunomodulators to treat viral infections. The present disclosure can be used for immunotherapy of coronavirus infection.

[0010] Provided herein is a method for treating or preventing viral (e.g., SARS-CoV-2) infection or treating a respiratory disease or condition associated with viral (e.g., SARS-CoV-2) infection, comprising administering to a subject with B-cell immunodeficiency a pharmaceutical composition comprising: (i) a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, (b) a sequence comprising an epitope sequence from membrane glycoprotein (M), and (c) a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); (ii) a polynucleotide encoding the polypeptide, wherein the polypeptide comprises at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, (b) a sequence comprising an epitope sequence from membrane glycoprotein (M), and (c) a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); (iii) a T cell receptor (TCR) or a T cell comprising the TCR, wherein the TCR binds to a corresponding HLA (iv) an antigen presenting cell comprising (i) or (ii); or (v) an antibody or a B cell comprising the antibody, wherein the antibody binds to the epitope sequence of the polypeptide.

[0011] In some embodiments, the subject has a reduced ability to mount an antibody response to an antigen compared to a subject that does not have a B cell immunodeficiency.

[0012] In some embodiments, the subject has a reduced ability to mount an antibody response to vaccination compared to a subject who does not have the B cell immunodeficiency.

[0013] In some embodiments, the subject has a reduced ability to generate an anti-spike protein antibody response and / or an anti-RBD antibody response compared to a subject who does not have a B cell immunodeficiency.

[0014] In some embodiments, the subject can mount a T cell response or has no reduced ability to mount a T cell response compared to a subject that does not have a B cell immunodeficiency.

[0015] In some embodiments, the pharmaceutical composition has a protective effect against variants of 2019 SARS CoV-2.

[0016] In some embodiments, the variant of 2019 SARS CoV-2 is α, β, γ, δ, ε, ζ, η, θ, ι, κ, or λ.

[0017] In some embodiments, the subject generates a T cell response to an epitope of the polypeptide.

[0018] In some embodiments, the subject generates a T cell response to an epitope sequence from ORF1ab, an epitope sequence from the membrane glycoprotein (M), and / or an epitope sequence from the nucleocapsid phosphoprotein (N).

[0019] In some embodiments, the subject is an organ transplant recipient.

[0020] In some embodiments, the organ transplant recipient is a solid organ transplant recipient, a stem cell transplant recipient, or a bone marrow transplant recipient.

[0021] In some embodiments, the subject receives an organ transplant less than 1 year, less than 6 months, or less than 3 months after administration of the pharmaceutical composition.

[0022] In some embodiments, the subject is expected to receive an organ transplant less than 1 year, less than 6 months, or less than 3 months prior to administration of the pharmaceutical composition.

[0023] In some embodiments, the subject has cancer.

[0024] In some embodiments, the cancer is a B cell cancer.

[0025] In some embodiments, the B cell cancer is a B cell lymphoma or a B cell leukemia.

[0026] In some embodiments, the subject has an autoimmune disease or disorder.

[0027] In some embodiments, the autoimmune disease or condition is Addison disease, anti-NMDA receptor encephalitis, antisynthetase syndrome, aplastic anemia, autoimmune anemia, autoimmune hemolytic anemia, autoimmune pancreatitis, Behcet's disease, bullous skin disorders, celiac sprue, chronic fatigue syndrome, chronic inflammatory demyelinating polyneuropathy, chronic lymphocytic leukemia, Crohn's disease, dermatomyositis, Devic's disease, erythroblastopenia, Evans syndrome, focal segmental glomerulosclerosis, granulomatosis with polyangiitis, Graves disease, Graves' ophthalmopathy, Guillain-Barre syndrome, Hashimoto's thyroiditis, thyroiditis), idiopathic thrombocytopenic purpura (ITP), IgA nephropathy, IgA-mediated autoimmune diseases, IgG4-related diseases, inflammatory bowel disease, juvenile idiopathic arthritis, multiple sclerosis, myasthenia gravis, myeloma, non-Hodgkin's lymphoma, opsoclonus-myoclonus syndrome (OMS), pemphigoid, pemphigus, pemphigus vulgaris, pernicious anemia, polymyositis, psoriasis, pure red cell aplasia, reactive arthritis, rheumatoid arthritis, sarcoidosis, scleroderma, Sjögren's syndrome ( syndrome), systemic lupus erythematosus, thrombocytopenic purpura, thrombotic thrombocytopenic purpura, type 1 diabetes mellitus, ulcerative colitis, vasculitis, and vitiligo.

[0028] In some embodiments, the subject does not have congenital agammaglobulinemia or congenital IgA deficiency.

[0029] In some embodiments, the subject does not have HIV or AIDS.

[0030] In some embodiments, the subject is currently receiving an immunosuppressant or has received an immunosuppressant less than 1 year, less than 6 months, or less than 3 months prior to administration of the pharmaceutical composition.

[0031] In some embodiments, the immunosuppressant is abatacept, abrilumab, acalabrutinib, adalimumab, corticosteroids, agatolimod sodium, aldesleukin, alefacept, alemtuzumab, alisertib, alvespimycin hydrochloride, alvocidib, ambrisentan, aminocamptothecin, amiselimod, anakinra, andecaliximab, andrographolide, anifrolumab, anti-thymocyte Ig, apatinib, apelisib, Asparaginase, atacicept, atezolizumab, avelumab, azacitidine, azathioprine, bafetinib, baminercept, baricitinib, basiliximab, becatecarin, begelomab, belatacept, belimumab, bemcentinib, bendamustine, betalutin with rilotomablilotomab), bevacizumab, BIIB033, BIIB059, BIIB061, bimekizumab, binimetinib, bleomycin, blinatumomab, bortezomib, brentuximab vedotin, bryostatin 1, bucillamine, buparlisib, busulfan, canakinumab, capecitabine, carboplatin, carfilzomib, carmustine, cediranib maleate maleate), cemiplimab, ceralifimod, cerdulatinib, certolizumab, cetuximab, chidamide, chlorambucil, cilengitide, cirmtuzumab, cisplatin, cladribine, clazakizumab, clemastine, clioquinol, corticosteroids, cyclophosphamide, cyclosporine, cytarabine, cytotoxic chemotherapy, daclizumab, dalfampridine, pegol-dapoxetine, daprolizumab pegol), daratumumab, dasatinib, defactinib, defibrotide, denosumab, dexamethasone, diacerein, dimethyl fumarate, dinaciclib, diroximelfumarate, doxorubicin, doxorubicin, durvalumab, duvelisib, duvortuxizumab, eculizumab, efalizumab, eftilagimod alfaalpha), the neuropeptide combination of metenkefalin and tridecactide, elezanumab, elotuzumab, encorafenib, enfuvirtida, entinostat, entospletinib, enzastaurin, epacadostat, epirubicin, epratuzumab, eritoran tetrasodium tetrasodium), etanercept, etoposide, etrolizumab, everolimus, evobrutinib, filgotinib, fingolimod, firategrast, fludarabine, fluorouracil, fontolizumab, forodesine hydrochloride, fostamatinib, galunisertib, ganetespib, ganitumab, gemcitabine, gemtuzumab ozogamicin, gerilimzumab, glasdegib, glassia, glatiramer acetate acetate), glembatumumab vedotin, glesatinib, golimumab, guadecitabine, hydrocortisone, hydroxychloroquine sulfate, hydroxyurea, ibritumomab tiuxetan, ibrutinib, ibudilast, idarubicin, idebenone, idelalisib, ifosfamide, iguratimod, imatinib, imexon, infliximab, inotuzumabozogamicin), interferon alpha-2, interferon beta-1a, interferon beta-1b, interferon gamma-1, ipilimumab, irofulven, isatuximab, ispinesib, itacitinib, ixazomib, lapatinib, laquinimod, laromustine, ld-aminopterin, leflunomide, lenalidomide, lenvatinib, letrozole, levamisole, levocabastine, lipoic acid, levitra Lirilumab, lonafarnib, lumiliximab, maraviroc, masitinib, mavrilimumab, melphalan, mercaptopurine, methotrexate, methoxsalen, methylprednisone, milatuzumab, mitoxantrone, mizoribine, mocetinostat, monalizumab, mosunetuzumab, motesanib diphosphate, moxetumomab pasudotox), muromonab-CD3, mycophenolate mofetil, mycophenolic acid, namilumab, natalizumab, navitoclax, neihulizumab, nerispirdine, neurovax, niraparib, nivolumab, obatoclax mesylate, obinutuzumab, oblimersensodium), ocrelizumab, ofatumumab, olokizumab, opicinumab, oprelvekin, osimertinib, otelixizumab, oxaliplatin, oxcarbazepine, ozanimod, paclitaxel, pacritinib, palifermin, panobinostat, pazopanib, peficitinib, pegfilgrastim, peginterferon beta-1a, pegsunercept (peg STNF-RI), pembrolizumab, pemetrexed, penclomedine, pentostatin, perifosine, pevonedistat, pexidartinib, picoplatin, pidilizumab, pivanex, pixantrone, pleneva, plovame acetate, polatuzumabvedotin), pomalidomide, ponatinib, ponesimod, prednisone / prednisolone, pyroxamide, ravulizimab-cwvz, recombinant IL-12, relatlimab, rhigf-1, rhigm22, rigosertib, rilonacept, ritonavir, rituximab, ruxolitinib, thalidomide Sarilumab, secukinumab, selumetinib, simvastatin, sintilimab, siplizumab, siponimod, sirolimus (rapamycin), sirukumab, sitravatinib, sonidegib, sorafenib, sotrastaurin acetate, sunitinib, sunphenon epigallocatechin gallate, tabalumab, tacrolimus, talabostat mesylatemesylate), talacotuzumab, tanespimycin, tegafur / gimeracil / oteracil, temozolomide, temsirolimus, tenalisib, terameprocol, teriflunomide, thalidomide, thiarabine, thiotepa, tipifarnib, tirabrutinib, tislelizumab, tivozanib, tocilizumab, tofacitinib, tregalizumab, tremelimumab, treosulfan, ublituximab, umbralisib, upadacitinib, urelumab, ustekinumab, varlilumab, vatelizumab, vedolizumab, veliparib, veltuzumab, venetoclax, vinblastine, vincristine, vinorelbine detartrate, visilizumab, vismodegib, vistusertib, voriconazole, vorinostat, vosaroxin, ziv-aflibercept, or any combination thereof.

[0032] In some embodiments, the immunosuppressant is an A2aR antagonist, an Akt inhibitor, an anti-CD20, an anti-amyloidosis (AA) agent, an anti-CD37 protein therapeutic, an anti-CTLA4 mAb, an anti-CXCR4, an anti-huCD40 mAb, an anti-LAG3 mAb, an anti-PD-1 mAb, an anti-PD-L1 agent, an anti-PD-L1 agent, an anti-PD-L1 mAb, an anti-TGFb mAb, an anti-TIGIT mAb, an anti-TIM-3 mAb, an Aurora kinase inhibitor, a Bcl-2 inhibitor, a bifunctional fusion protein targeting TGFb and PD-L1, a bispecific anti-PD-1 and anti-LAG3 mAb, CD1d ligand, CD40 agonist, complement C5a inhibitor, CSF1R inhibitor, EZH2 inhibitor, FGFR3 inhibitor, FGFR4 inhibitor, FGFrR3 inhibitor, glucocorticoid-induced tumor necrosis factor receptor-related gene agonist, glutaminase inhibitor, anti-IL-12 human monoclonal antibody, ICOS agonist, IDO1 inhibitor, IL2 mutant protein, IL2 receptor agonist, MEK inhibitor, multi-targeted receptor tyrosine kinase inhibitor, neutrophil elastase inhibitor, Notch inhibitor, p38 MAPK inhibitor, PD-1 inhibitor, recombinant human Flt3L, ROCK inhibitor, selective sphingosine-1-phosphate receptor modulator, Src kinase inhibitor, TLR4 agonist, TLR9 agonist or any combination thereof.

[0033] In some embodiments, the subject is older than 55, 56, 57, 58, 59, 60, 65, 70, 75, or 80 years old.

[0034] In some embodiments, the polypeptide comprises (a) a sequence comprising an epitope sequence from ORF1ab, (b) a sequence comprising an epitope sequence from membrane glycoprotein (M), and (c) a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N).

[0035] In some embodiments, the sequence comprising the epitope sequence from ORF1ab is C-terminal to the sequence comprising the epitope sequence from the nucleocapsid phosphoprotein (N).

[0036] In some embodiments, the sequence comprising the epitope sequence from ORF1ab is N-terminal to the sequence comprising the epitope sequence from membrane glycoprotein (M).

[0037] In some embodiments, the sequence comprising an epitope sequence from the nucleocapsid phosphoprotein (N) is N-terminal to the sequence comprising an epitope sequence from the membrane glycoprotein (M).

[0038] In some embodiments, the polypeptide comprises (a) 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more epitope sequences from ORF1ab, (b) a sequence comprising an epitope sequence from a membrane glycoprotein (M), and (c) a sequence comprising an epitope sequence from a nucleocapsid phosphoprotein (N).

[0039] In some embodiments, the epitope sequence from ORF1ab is an epitope sequence from a nonstructural protein (NSP).

[0040] In some embodiments, the nonstructural protein (NSP) is selected from the group consisting of NSP1, NSP2, NSP3, NSP4, and combinations thereof.

[0041] In some embodiments, the polypeptide comprises a sequence comprising an epitope sequence from NSP1, a sequence comprising an epitope sequence from NSP2, a sequence comprising an epitope sequence from NSP3, and a sequence comprising an epitope sequence from NSP4.

[0042] In some embodiments, the epitope sequence from ORF1ab is selected from the group consisting of YLFDESGEFKL, YLFDESGEF, FGDDTVIEV, QLMCQPILL, TTDPSFLGRY, PTDNYITTY, PSFLGRY, AEAELAKNV, KTIQPRVEK, and any combination thereof.

[0043] In some embodiments, the epitope sequence from the nucleocapsid glycoprotein (N) is LLLDRLNQL.

[0044] In some embodiments, the epitope sequence from membrane phosphoprotein (M) is VATSRTLSY.

[0045] In some embodiments, the polypeptide comprises an epitope sequence from the nucleocapsid glycoprotein (N), ie, LLLDRLNQL, and an epitope sequence from the membrane phosphoprotein (M), ie, VATSRTLSY.

[0046] In some embodiments, the polypeptide comprises (a) each of the following epitope sequences from ORF1ab: YLFDESGEFKL, YLFDESGEF, FGDDTVIEV, QLMCQPILL, TTDPSFLGRY, PTDNYITTY, PSFLGRY, AEAELAKNV, KTIQPRVEK; (b) an epitope sequence from nucleocapsid glycoprotein (N), i.e., LLLDRLNQL; and (c) an epitope sequence from membrane phosphoprotein (M), i.e., VATSRTLSY.

[0047] In some embodiments, the sequence comprising the epitope sequence from ORF1ab is selected from the group consisting of the following sequences or fragments thereof: MVTNNTFTLKVPHVGEIPVAYRKVLLKTIQPRVEKYLFDESGEFKLSEVGPEHSLAEYYIFFASFYY; MVTNNTFTLKVPHVGEIPVAYRKVLLKTIQPRVEKYLFDESGEFKLSEVGPEHSLAEY; APKEIIFLEGETLFGDDTVIEVAIILASFSAST; APKEIIFLEGETLFGDDTVIEV; HTTDPSFLGRYMSALFADDLNQLTGYHTDFSSEIIGYQLMCQPILLAEAELAKNVSLILGTVSWNL; TTDPSFLGRYMSALFADDLNQLTGYHTDFSSEIIGYQLMCQPILLAEAELAKNVSLILGTVSWNL; LLSAGIFGAITDVFYKENSYKVPTDNYITTY; and combinations thereof.

[0048] In some embodiments, the sequence comprising an epitope sequence from a membrane glycoprotein (M) is selected from the group consisting of the following sequences or fragments thereof: ADSNGTITVEELKKLLEQWNLVIGFLFLTWICLLQFAYANRNRFLYIIKLIFLWLLWPVTLACFVLAAVYRINWITGGIAIAMACLVGLMWLSYFIASFRLFARTRSMWSFNPETNILLNVPLHGTILTRPLLESELVIGAVILRGHLRIAGHHLGRCDIKDLPKEITVATSRTLSYYKLGASQRVAGDSGFAAYSRYRIGNYKLNTDHSSSSDNIALLVQ;

[0049] FAYANRNRFLYIIKLIFLWLLWPVTLACFVLAAVYRINWITGGIAIAMACLVGLMWLSYFIASFRLF;LGRCDIKDLPKEITVATSRTLSYYKLGASQRVA; KLLEQWNLVIGF; NRNRFLYIIKLIFLWLLWPVTLACFVLAAVY; SELVIGAVILRGHLRIAGHHLGR; VATSRTLSYYKLGASQRV; GLMWLSYF; and combinations thereof.

[0050] In some embodiments, the sequence comprising an epitope sequence from the nucleocapsid phosphoprotein (N) is selected from the group consisting of the following sequences or fragments thereof: KDLSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGTTLPKGFYAEGSRGGSQASSRSSSRSRNSSRNSTPGSSRGTSPARMAGNGGDAALALLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDKKKK ADETQALPQRQKKQQTVTLLPAAADLDDFSKQLQQSMSSADSTQA;RMAGNGGDAALALLLLDRLNQLESKMSGKGQQQ;YKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFP;SPARMAGNGGDAA LALLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDK and combinations thereof.

[0051] In some embodiments, the polypeptide comprises one or more linker sequences.

[0052] In some embodiments, the one or more linker sequences are selected from the group consisting of GGSGGGGSGG, GGSLGGGGSG.

[0053] In some embodiments, one or more linker sequences comprise a cleavage sequence.

[0054] In some embodiments, the one or more cleavage sequences are selected from the group consisting of FRAC, KRCF, KKRY, ARMA, RRSG, MRAC, KMCG, ARCA, KKQG, YRSY, SFMN, FKAA, KRNG, YNSF, KKNG, RRRG, KRYS, and ARYA.

[0055] In some embodiments, the polypeptide comprises a transmembrane domain sequence.

[0056] In some embodiments, the transmembrane domain sequence is C-terminal to a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N).

[0057] In some embodiments, the transmembrane domain sequence is EQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT.

[0058] In some embodiments, the polypeptide comprises a SEC sequence.

[0059] In some embodiments, the SEC sequence is N-terminal to the sequence comprising the epitope sequence from ORF1ab, the sequence comprising the epitope sequence from membrane glycoprotein (M), and the sequence comprising the epitope sequence from nucleocapsid phosphoprotein (N).

[0060] In some embodiments, the SEC sequence is MFVFLVLLPLVSSQCVNLT.

[0061] In some embodiments, the composition comprises a polynucleotide encoding a polypeptide.

[0062] In some embodiments, the polynucleotide is mRNA.

[0063] In some embodiments, the polynucleotide comprises a codon-optimized sequence for expression in humans.

[0064] In some embodiments, the polynucleotide comprises a dEarI-hAg sequence.

[0065] In some embodiments, the dEarI-hAg sequence is ATTCTTCTGGTCCCCACAGACTCAGAGAGAACCC, optionally wherein each T is U.

[0066] In some embodiments, the polynucleotide comprises a Kozak sequence.

[0067] In some embodiments, the Kozak sequence is GCCACC.

[0068] In some embodiments, the polynucleotide comprises an F element sequence.

[0069] In some embodiments, the F element sequence is the 3UTR of the amino-terminal split enhancer (AES).

[0070] In some embodiments, the F element sequence is CTGGTACTGCATGCACGCAATGCTAGCTGCCCCTTTCCCGTCCTGGGTACCCCGAGTCTCCCCCGACCTCGGGTCCCAGGTATGCTCCCACCTCCACCTGCCCCACTCACCACCTCTGCTAGTTCCAGACACCTCC, optionally wherein each T is U.

[0071] In some embodiments, the polynucleotide comprises an I element sequence.

[0072] In some embodiments, the I element sequence is the 3'UTR of the mitochondrial-encoded 12S rRNA (mtRNR1).

[0073] In some embodiments, the I element sequence is CAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACACC, optionally wherein each T is U.

[0074] In some embodiments, the polynucleotide comprises a poly A sequence.

[0075] In some embodiments, the poly A sequence is AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGCATATGACTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA, optionally wherein each T is U.

[0076] In some embodiments, each of the epitope sequences from ORF1ab, membrane glycoprotein, and nucleocapsid phosphoprotein is from 2019 SARS-CoV-2.

[0077] In some embodiments, one or more epitopes, or each epitope, elicits a T cell response.

[0078] In some embodiments, one or more epitopes, or each epitope, has been observed by mass spectrometry to be presented by an HLA molecule.

[0079] In some embodiments, the composition comprises: (i) a polypeptide having at least 70%, at least 75%, at least 80%, at least 85%, 90%, at least 95%, or 100% sequence identity to a sequence selected from the group consisting of: RSC1p1full, RS C2p1full, RS C3p1full, RS C4p1full, RS C5p1, RS C5p2, RS C5p2full, RSC6p1, RS C6p2, RS C6p2full, RS C7p1, RS C7p2, RS C7p2full, RS C7p4, RS C7p4full, RSC8p1, RS C8p2, and RS C8p2full; and (ii) a polynucleotide encoding a polypeptide having at least 70%, at least 75%, at least 80%, at least 85%, 90%, at least 95%, or 100% sequence identity to a sequence selected from the group consisting of: RSC1p1full, RS C2p1full, RS C3p1full, RS C4p1full, RS C5p1, RS C5p2, RS C5p2full, RSC6p1, RS C6p2, RS C6p2full, RS C7p1, RS C7p2, RS C7p2full, RS C7p4, RS C7p4full, RSC8p1, RS C8p2, and RS C8p2full. or (iii) a polynucleotide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% sequence identity to a sequence selected from the group consisting of SEQ ID NO: RS C1n1, RS C2n1, RS C3n1, RS C4n1, RS C5n1, RS C6n1, RS C7n1, RS C8n1, RS C5n2, RS C6n2, RS C7n2, RS C7n4, RS C7n4full, RS C8n2, RS C5n2full, RS C6n2full, RS C7n2full and RS C8n2full.

[0080] In some embodiments, the composition comprises: (i) a polypeptide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% sequence identity to a sequence selected from the group consisting of: RSC7p1, RS C7p2, RS C7p2full, RS C7p4 and RS C7p4full; or (ii) a polynucleotide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% sequence identity to a sequence selected from the group consisting of: SEQ ID NO: RS C7n1, RS C7n2, RS C7n2full, RS C7n4 and RS C7n4full.

[0081] In some embodiments, the pharmaceutical composition comprises a pharmaceutically acceptable excipient, carrier, or diluent.

[0082] Provided herein is a method for treating or preventing a viral infection, or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject having a B cell immunodeficiency a pharmaceutical composition comprising: (i) a polypeptide comprising an epitope sequence of Table 1A, Table 1B, Table 1C, Table 2Ai, Table 2Aii, Table 2B, and / or Table 16; (ii) a polynucleotide encoding a polypeptide comprising an epitope sequence of Table 1A, Table 1B, Table 1C, Table 2Ai, Table 2Aii, Table 2B, and / or Table 16; (iii) a T cell receptor (TCR) or a T cell comprising a TCR, wherein the TCR binds to the epitope sequence in complex with a corresponding HLA class I or class II molecule; (iv) an antigen presenting cell comprising (i) or (ii); or (v) an antibody or a B cell comprising the antibody, wherein the antibody binds to the epitope sequence.

[0083] In some embodiments, the epitope sequence includes one or more or each of the following: YLFDESGEFKL, YLFDESGEF, FGDDTVIEV, LLLDRLNQL, QLMCQPILL, TTDPSFLGRY, PTDNYITTY, PSFLGRY, AEAELAKNV, VATSRTLSY, and KTIQPRVEK.

[0084] In some embodiments, the epitope sequence includes one or more or each of the following: SAPPAQYEL, AVASKILGL, EYADVFHLY, DEFTPFDVV, VRIQPGQTF, SFRLFARTR, KFLPFQQF, VVQEGVLTA, RLDKVEAEV, FGADPIHSL, NYNYLYRLF, KYIKWPWYI, KWPWYIWLGF, LPFNDGVYF, QPTESIVRF, IPFAMQMAY, YLQPRTFLL, and RLQSLQTYV.

[0085] In some embodiments, the epitope sequence is from the orf1ab protein.

[0086] In some embodiments, the epitope sequence is from the orf1a protein.

[0087] In some embodiments, the epitope sequence is from a surface glycoprotein (S) or a shifted reading frame thereof.

[0088] In some embodiments, the epitope sequence is from the nucleocapsid phosphoprotein (N).

[0089] In some embodiments, the epitope sequence is from the ORF3a protein.

[0090] In some embodiments, the epitope sequence is from a membrane glycoprotein (M).

[0091] In some embodiments, the epitope sequence is from the ORF7a protein.

[0092] In some embodiments, the epitope sequence is from the ORF8 protein.

[0093] In some embodiments, the epitope sequence is from the envelope protein (E).

[0094] In some embodiments, the epitope sequence is from the ORF6 protein.

[0095] In some embodiments, the epitope sequence is from the ORF7b protein.

[0096] In some embodiments, the epitope sequence is from the ORF10 protein.

[0097] In some embodiments, the epitope sequence is from the ORF9b protein.

[0098] Provided herein is a method for treating or preventing viral infection, or treating a respiratory disease or condition associated with a viral infection, comprising administering a pharmaceutical composition to a subject with B-cell immunodeficiency, the pharmaceutical composition comprising: a polypeptide having an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% identical to the sequence of any one of the sequences depicted in column 2 of Table 11, column 2 of Table 12, or column 3 of Table 15; or a recombinant polynucleotide encoding a polypeptide having an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% identical to the sequence of any one of the sequences depicted in column 2 of Table 11, column 2 of Table 12, or column 3 of Table 15.

[0099] In some embodiments, the pharmaceutical composition comprises: a polypeptide having at least 70%, at least 75%, at least 80%, at least 85%, 90%, at least 95%, or 100% sequence identity to a sequence selected from the group consisting of: RSC1p1full, RS C2p1full, RS C3p1full, RS C4p1full, RS C5p1, RS C5p2, RS C5p2full, RSC6p1, RS C6p2, RS C6p2full, RS C7p1, RS C7p2, RS C7p2full, RS C7p4, RS C7p4full, RSC8p1, RS C8p2, and RS C8p2full; or a polynucleotide encoding a polypeptide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% sequence identity to a sequence selected from the group consisting of: RSC1p1full, RS C2p1full, RS C3p1full, RS C4p1full, RS C5p1, RS C5p2, RS C5p2full, C2p1full, RS C3p1full, RS C4p1full, RS C5p1, RS C5p2, RS C5p2full, RSC6p1, RS C6p2, RS C6p2full, RS C7p1, RS C7p2, RS C7p2full, RS C7p4, RS C7p4full, RSC8p1, RS C8p2, and RS C8p2full.

[0100] In some embodiments, the pharmaceutical composition comprises a polynucleotide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% sequence identity to a sequence selected from the group consisting of SEQ ID NO: RS C1n1, RS C2n1, RS C3n1, RS C4n1, RS C5n1, RS C6n1, RS C7n1, RS C8n1, RSC5n2, RS C6n2, RS C7n2, RS C8n2, RS C5n2full, RS C6n2full, RS C7n2full, RS C8n2full, RS C7n4, and RS C7n4full.

[0101] In some embodiments, the polynucleotide is mRNA.

[0102] In some embodiments, the pharmaceutical composition further comprises one or more lipid components.

[0103] In some embodiments, the one or more lipid components comprise lipid nanoparticles (LNPs).

[0104] In some embodiments, the LNP encapsulates the recombinant polynucleotide construct.

[0105] In some embodiments, the polypeptide is synthetic.

[0106] In some embodiments, the polypeptide is recombinant.

[0107] In some embodiments, the polypeptide is 8-1000 amino acids in length.

[0108] In some embodiments, the epitope sequence binds or is predicted to bind to an HLA class I or class II molecule with a KD of 1000 nM or less.

[0109] In some embodiments, the epitope sequence binds or is predicted to bind to an HLA class I or class II molecule with a KD of 500 nM or less.

[0110] In some embodiments, the epitope sequence comprises the sequence of a viral protein expressed by a virus-infected cell of the subject.

[0111] In some embodiments, the virus is a coronavirus.

[0112] In some embodiments, the virus is 2019 SARS-CoV 2.

[0113] In some embodiments, at the time of administration, the HLA molecules expressed by the subject are unknown.

[0114] In some embodiments, the ability of a virus to avoid recognition by a subject's immune system is lower than the ability of a virus to avoid recognition by the immune system of a subject who has been administered a pharmaceutical composition containing epitopes from a single protein or from fewer proteins than in a pharmaceutical composition administered according to the methods described herein.

[0115] In some embodiments, the subject expresses an HLA molecule encoded by an HLA allele of any one of Table 1A, Table 1B, Table 1C, Table 2Ai, Table 2Aii, Table 2B, and Table 16, and the epitope sequence is an HLA allele-matched epitope sequence.

[0116] In some embodiments, the epitope sequence comprises one or more or each of the following: SAPPAQYEL, AVASKILGL, EYADVFHLY, DEFTPFDVV, VRIQPGQTF, SFRLFARTR, KFLPFQQF, VVQEGVLTA, RLDKVEAEV, and FGADPIHSL.

[0117] In some embodiments, the method further comprises administering to the subject an additional therapy for 2019 SARS-CoV 2 viral infection.

[0118] In some embodiments, the method further comprises administering to the subject (a) a polypeptide having the amino acid sequence of a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; (b) a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; or a 2019 SARS-CoV 2 spike protein pharmaceutical composition comprising (a) or (b).

[0119] In some embodiments, the vaccine or therapeutic agent of (a) or (b) is administered to the subject once.

[0120] In some embodiments, the vaccine or therapeutic agent of (a) or (b) is administered to the subject more than once.

[0121] In some embodiments, the vaccine or therapeutic agent is administered at least twice, wherein the first administered dose is a priming dose, and the second and subsequent doses are boosting doses.

[0122] In some embodiments, the priming dose and the boosting dose are administered at least 21 days apart.

[0123] In some embodiments, the interval between two booster doses is at least 30 days, at least 60 days, or at least 90 days.

[0124] In some embodiments, the vaccine or therapeutic agent is administered annually.

[0125] In some embodiments, the vaccine or therapeutic agent is administered twice per year.

[0126] In some embodiments, the vaccine or therapeutic agent is administered as a high priming or loading dose as a first dose, and as decreasing boosting or maintenance doses as subsequent doses.

[0127] In some embodiments, the subject receives a SARS-CoV spike vaccine at a dose or frequency lower than the dose or frequency the subject receives the SARS-CoV spike vaccine alone.

[0128] Provided herein is a method for treating or preventing viral infection or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject in need thereof a pharmaceutical composition comprising: (i) a recombinant polynucleotide encoding a polypeptide comprising at least two of the following: a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; wherein the ratio (e.g., mass ratio) of (i):(ii) is greater than 20:1 or less than 1:20.

[0129] In some embodiments, the ratio (e.g., mass ratio) of (i):(ii) is greater than 20:1, 30:1, 40:1, 50:1, 60:1, 70:1, 80:1, 90:1, or 100:1.

[0130] In some embodiments, the ratio (e.g., mass ratio) of (i):(ii) is less than 1:20, 1:30, 1:40, 1:50, 1:60, 1:70, 1:80, 1:90, or 1:100.

[0131] Provided herein is a method for treating or preventing viral infection or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject in need thereof: (i) a first pharmaceutical composition comprising a first recombinant polynucleotide encoding a polypeptide comprising at least two of the following: a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a second pharmaceutical composition comprising a second recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; wherein the ratio (e.g., mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is 1:50 to 50:1.

[0132] In some embodiments, the ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:25 to 25:1.

[0133] In some embodiments, the ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:10 to 10:1.

[0134] In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:10, 1:9, 1:8, 1:7, 1:6, 1:5, 1:4, 1:3, 1:2, 1:1, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 1:9.5, 1:8.5, 1:7.5, 1:6.5, 1:5.5, 1:4.5, 1:3.5, 1:2.5, 1:1.5, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 1:9.5, 1:8.5, 1:7.5, 1:6.5, 1:5.5, 1:4.5, 1:3.5, 1:2.5, 1:1.5, 2:1, 3:1, 4:1, 5:1 In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:6. In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1: 3. In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1: 2.

[0135] In some embodiments, the recombinant polynucleotide in (i) is present in the pharmaceutical composition at a dose of 0.1 μg to 100 μg, or 1 μg to 50 μg, or 1 μg to 30 μg, or 1 μg to 20 μg, or 3 μg to 20 μg, or 5 μg to 15 μg. In some embodiments, the recombinant polynucleotide in (i) is present in the pharmaceutical composition at a dose of 0.05 μg to 10 μg, or 0.1 μg to 5 μg, or 0.3 μg to 5 μg. In some embodiments, the recombinant polynucleotide in (i) is present in the pharmaceutical composition at a dose of 0.1 μg to 20 μg or 0.5 μg to 15 μg.

[0136] In some embodiments, the recombinant polynucleotide in (ii) is present in the pharmaceutical composition at a dose of 0.1 microgram to 100 micrograms, or 1 microgram to 100 micrograms, or 1 microgram to 30 micrograms, or 1 microgram to 20 micrograms, or 3 micrograms to 30 micrograms.

[0137] In some embodiments, the recombinant polynucleotide in (i) is present in the pharmaceutical composition at a dose of about 5 micrograms, and the recombinant polynucleotide in (ii) is present in the pharmaceutical composition at a dose of about 30 micrograms. In some embodiments, the recombinant polynucleotide in (i) is present in the pharmaceutical composition at a dose of about 10 micrograms, and the recombinant polynucleotide in (ii) is present in the pharmaceutical composition at a dose of about 30 micrograms. In some embodiments, the recombinant polynucleotide in (i) is present in the pharmaceutical composition at a dose of about 15 micrograms, and the recombinant polynucleotide in (ii) is present in the pharmaceutical composition at a dose of about 30 micrograms.

[0138] In some embodiments, the recombinant polynucleotide in (ii) encompasses at least two separate recombinant polynucleotides, each encoding a SARS-CoV-2 S protein or an immunogenic variant or fragment thereof (e.g., in some embodiments, an RBD) of a different strain or variant thereof. For example, in some embodiments, the recombinant polynucleotide in (ii) encompasses a recombinant polynucleotide encoding a SARS-CoV-2 S protein or an immunogenic variant or fragment thereof (e.g., in some embodiments, an RBD) of a previous strain (e.g., the Wuhan strain) and a recombinant polynucleotide encoding a SARS-CoV-2 S protein of a SARS-CoV-2 variant that is prevalent or rapidly spreading at the time of administration. For example, in some embodiments, the recombinant polynucleotides in (ii) encompass recombinant polynucleotides encoding a SARS-CoV-2 S protein or an immunogenic variant or fragment thereof (e.g., in some embodiments, an RBD) of a previous strain (e.g., a Wuhan strain) and a recombinant polynucleotide encoding a SARS-CoV-2 S protein or an immunogenic variant or fragment thereof of a variant strain having one or more mutations characteristic of a SARS-CoV-2 variant (e.g., in some embodiments, an Omicron variant, such as an Omicron BA.1, BA.2, BA.4, or BA.5 variant). In some embodiments, at least two recombinant polynucleotides (each encoding a SARS-CoV-2 S protein or an immunogenic variant or fragment thereof of a different strain or variant thereof) can be present in the pharmaceutical composition at a ratio (e.g., mass ratio) of 3:1 to 1:3, or 2:1 to 1:2, or 1:1.

[0139] In some embodiments, the pharmaceutical compositions described herein may further comprise (iii) a recombinant polynucleotide encoding a peptide or polypeptide antigen from a pathogen associated with a non-SARS-CoV-2 respiratory disease. In some embodiments, such a non-SARS-CoV-2 respiratory disease may be influenza (influenza) and / or respiratory syncytial virus.

[0140] Provided herein is a method for treating or preventing viral infection or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject in need thereof a pharmaceutical composition comprising nanoparticles, wherein the nanoparticles comprise: (i) a first recombinant polynucleotide encoding a polypeptide comprising at least two of the following: a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a second recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof. In some embodiments, the first recombinant polynucleotide encodes a polypeptide comprising all of the following: a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N).

[0141] In some embodiments, the nanoparticles are present in the pharmaceutical composition at a dose of 100 ng to 500 micrograms.

[0142] In some embodiments, the nanoparticles are present in the pharmaceutical composition at a dose of 1 microgram to 100 micrograms.

[0143] In some embodiments, the nanoparticles are present in the pharmaceutical composition at a dose of 1 microgram to 30 micrograms, 5 micrograms to 40 micrograms, or 10 micrograms to 50 micrograms.

[0144] In some embodiments, the nanoparticles are present in the pharmaceutical composition at a dose of 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1,000 micrograms.

[0145] In some embodiments, the ratio (eg, mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:50 to 50:1.

[0146] In some embodiments, the ratio (eg, mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:25 to 25:1.

[0147] In some embodiments, the ratio (eg, mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:10 to 10:1.

[0148] In some embodiments, the ratio of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:10, 1:9, 1:8, 1:7, 1:6, 1:5, 1:4, 1:3, 1:2, 1:1, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 1:9.5, 1:8.5, 1:7.5, 1:6.5, 1:5.5, 1:4.5, 1:3.5, 1:2.5, 1:1.5, 2.5:1, 3.5:1, 4.5:1, 5.5:1, 6. In some embodiments, the ratio of the first recombinant polynucleotide to the second recombinant polynucleotide (e.g., mass ratio) is about 1:6. In some embodiments, the ratio of the first recombinant polynucleotide to the second recombinant polynucleotide (e.g., mass ratio) is about 1:3. In some embodiments, the ratio (eg, mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:2.

[0149] In some embodiments, the first recombinant polynucleotide is present in the pharmaceutical composition at a dose of 0.1 microgram to 100 micrograms, or 1 microgram to 50 micrograms, or 1 microgram to 30 micrograms, or 1 microgram to 20 micrograms, or 3 micrograms to 20 micrograms, or 5 micrograms to 15 micrograms. In some embodiments, the first recombinant polynucleotide is present in the pharmaceutical composition at a dose of 0.05 micrograms to 10 micrograms, or 0.1 microgram to 5 micrograms, or 0.3 micrograms to 5 micrograms. In some embodiments, the first recombinant polynucleotide is present in the pharmaceutical composition at a dose of 0.1 microgram to 20 micrograms or 0.5 micrograms to 15 micrograms.

[0150] In some embodiments, the second recombinant polynucleotide is present in the pharmaceutical composition at a dose of 0.1 microgram to 100 micrograms, or 1 microgram to 100 micrograms, or 1 microgram to 30 micrograms, or 1 microgram to 20 micrograms, or 3 micrograms to 30 micrograms.

[0151] In some embodiments, the second recombinant polynucleotide encompasses at least two separate recombinant polynucleotides, each encoding a SARS-CoV-2 S protein or immunogenic variant or fragment thereof (e.g., in some embodiments, an RBD) of a different strain or variant thereof. For example, in some embodiments, the second recombinant polynucleotide encompasses a recombinant polynucleotide encoding a SARS-CoV-2 S protein or immunogenic variant or fragment thereof (e.g., in some embodiments, an RBD) of a previous strain (e.g., the Wuhan strain) and a recombinant polynucleotide encoding a SARS-CoV-2 S protein of a SARS-CoV-2 variant that is prevalent or rapidly spreading at the time of administration. For example, in some embodiments, the second recombinant polynucleotide encompasses a recombinant polynucleotide encoding a SARS-CoV-2 S protein or an immunogenic variant or fragment thereof (e.g., in some embodiments, an RBD) of a previous strain (e.g., the Wuhan strain) and a recombinant polynucleotide encoding a SARS-CoV-2 S protein or an immunogenic variant or fragment thereof of a variant strain having one or more mutations characteristic of a SARS-CoV-2 variant (e.g., in some embodiments, an Omicron variant, such as an Omicron BA.1, BA.2, BA.4, or BA.5 variant). In some embodiments, the two recombinant polynucleotides (each encoding a SARS-CoV-2 S protein or an immunogenic variant or fragment thereof of a different strain or variant thereof) can be present in the pharmaceutical composition in a ratio (e.g., mass ratio) of 3:1 to 1:3, or 2:1 to 1:2, or 1:1.

[0152] In some embodiments, the pharmaceutical compositions described herein may comprise a third recombinant polynucleotide encoding a peptide or polypeptide antigen from a pathogen associated with a non-SARS-CoV-2 respiratory disease. In some embodiments, such non-SARS-CoV-2 respiratory disease may be, but is not limited to, influenza (influenza) and / or respiratory syncytial virus.

[0153] Provided herein is a method for treating or preventing viral infection or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject in need thereof: (i) a first pharmaceutical composition comprising a first nanoparticle, wherein the first nanoparticle comprises a recombinant polynucleotide encoding a polypeptide comprising at least two of the following: a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a second pharmaceutical composition comprising a second nanoparticle, wherein the second nanoparticle comprises a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof. In some embodiments, the first pharmaceutical composition comprises a first nanoparticle, wherein the first nanoparticle comprises a recombinant polynucleotide encoding a polypeptide comprising all of the following: a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N).

[0154] In some embodiments, the ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:50 to 50:1.

[0155] In some embodiments, the ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:25 to 25:1.

[0156] In some embodiments, the ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:10 to 10:1.

[0157] In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:10, 1:9, 1:8, 1:7, 1:6, 1:5, 1:4, 1:3, 1:2, 1:1, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 1:9.5, 1:8.5, 1:7.5, 1:6.5, 1:5.5, 1:4.5, 1:3.5, 1:2.5, 1:1.5, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 1:9.5, 1:8.5, 1:7.5, 1:6.5, 1:5.5, 1:4.5, 1:3.5, 1:2.5, 1:1.5, 2:1, 3:1, 4:1, 5:1 In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:6. In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1: 3. In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1: 2.

[0158] In some embodiments, the recombinant polynucleotide in (i) is present in the pharmaceutical composition at a dose of 0.1 μg to 100 μg, or 1 μg to 50 μg, or 1 μg to 30 μg, or 1 μg to 20 μg, or 3 μg to 20 μg, or 5 μg to 15 μg. In some embodiments, the recombinant polynucleotide in (i) is present in the pharmaceutical composition at a dose of 0.05 μg to 10 μg, or 0.1 μg to 5 μg, or 0.3 μg to 5 μg. In some embodiments, the recombinant polynucleotide in (i) is present in the pharmaceutical composition at a dose of 0.1 μg to 20 μg or 0.5 μg to 15 μg.

[0159] In some embodiments, the recombinant polynucleotide in (ii) is present in the pharmaceutical composition at a dose of 0.1 microgram to 100 micrograms, or 1 microgram to 100 micrograms, or 1 microgram to 30 micrograms, or 1 microgram to 20 micrograms, or 3 micrograms to 30 micrograms.

[0160] In some embodiments, the recombinant polynucleotide in (ii) encompasses at least two separate recombinant polynucleotides, each encoding a SARS-CoV-2 S protein or an immunogenic variant or fragment thereof (e.g., in some embodiments, an RBD) of a different strain or variant thereof. For example, in some embodiments, the recombinant polynucleotide in (ii) encompasses a recombinant polynucleotide encoding a SARS-CoV-2 S protein or an immunogenic variant or fragment thereof (e.g., in some embodiments, an RBD) of a previous strain (e.g., the Wuhan strain) and a recombinant polynucleotide encoding a SARS-CoV-2 S protein of a SARS-CoV-2 variant that is prevalent or rapidly spreading at the time of administration. For example, in some embodiments, the recombinant polynucleotides in (ii) encompass recombinant polynucleotides encoding a SARS-CoV-2 S protein or an immunogenic variant or fragment thereof (e.g., in some embodiments, an RBD) of a previous strain (e.g., a Wuhan strain) and a recombinant polynucleotide encoding a SARS-CoV-2 S protein or an immunogenic variant or fragment thereof of a variant strain having one or more mutations characteristic of a SARS-CoV-2 variant (e.g., in some embodiments, an Omicron variant, such as an Omicron BA.1, BA.2, BA.4, or BA.5 variant). In some embodiments, at least two recombinant polynucleotides (each encoding a SARS-CoV-2 S protein or an immunogenic variant or fragment thereof of a different strain or variant thereof) can be present in the pharmaceutical composition at a ratio (e.g., mass ratio) of 3:1 to 1:3, or 2:1 to 1:2, or 1:1.

[0161] In some embodiments, a third pharmaceutical composition (iii) comprising a third nanoparticle may be administered to a subject in need thereof, wherein the third nanoparticle comprises a recombinant polynucleotide encoding a peptide or polypeptide antigen from a pathogen associated with a non-SARS-CoV-2 respiratory disease. In some embodiments, such a non-SARS-CoV-2 respiratory disease may be influenza (influenza) and / or respiratory syncytial virus.

[0162] In some embodiments, the first nanoparticle is present in the first pharmaceutical composition at a dose of about 100 ng to 500 micrograms.

[0163] In some embodiments, the first nanoparticles are present in the first pharmaceutical composition at a dose of about 1 microgram to 100 micrograms.

[0164] In some embodiments, the first nanoparticles are present in the first pharmaceutical composition at a dose of about 1 microgram to 30 micrograms, 5 micrograms to 40 micrograms, or 10 micrograms to 50 micrograms.

[0165] In some embodiments, the first nanoparticles are present in the first pharmaceutical composition at a dose of about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1,000 micrograms.

[0166] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition at a dose of about 100 ng to 500 micrograms.

[0167] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition at a dose of about 1 microgram to 100 micrograms.

[0168] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition at a dose of about 1 microgram to 30 micrograms, 5 micrograms to 40 micrograms, or 10 micrograms to 50 micrograms.

[0169] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition at a dose of about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1,000 micrograms.

[0170] Provided herein is a method for treating or preventing viral infection or treating a respiratory disease or condition associated with viral infection, comprising administering to a subject in need thereof: (i) a pharmaceutical composition comprising: (a) a polypeptide comprising at least two of the following: a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); or (b) a polynucleotide encoding a polypeptide comprising at least two of the following: a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a pharmaceutical composition comprising: (a) a polypeptide having an amino acid sequence of a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; or (b) a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; or a 2019 SARS-CoV comprising (ii)(a) or (ii)(b). 2. A spike protein pharmaceutical composition; wherein the dose of (ii)(a) or (ii)(b) received by the subject is lower than the dose of (ii)(a) or (ii)(b) administered to the subject alone.

[0171] Provided herein is a method for treating or preventing viral infection or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject in need thereof: (i) a pharmaceutical composition comprising: (a) a polypeptide comprising at least two of the following: a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); or (b) a polynucleotide encoding a polypeptide comprising at least two of the following: a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a pharmaceutical composition comprising: (a) a polypeptide having an amino acid sequence of a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; or (b) a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; or a 2019 SARS-CoV 2 spike protein pharmaceutical composition comprising (ii)(a) or (ii)(b).

[0172] Provided herein is a method for treating or preventing viral infection or treating a respiratory disease or condition associated with viral infection, comprising administering to a subject in need thereof: (i) a pharmaceutical composition comprising: (a) a polypeptide comprising at least two of the following: a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); or (b) a polynucleotide encoding a polypeptide comprising at least two of the following: a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a pharmaceutical composition comprising: (a) a polypeptide having an amino acid sequence of a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; (b) a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; or a 2019 SARS-CoV comprising (ii)(a) or (ii)(b). 2. A spike protein pharmaceutical composition; wherein the number of doses of (ii)(a) or (ii)(b) received by the subject is less than the number of doses of (ii)(a) or (ii)(b) administered to the subject alone.

[0173] In some embodiments, the subject receives a dose of (ii)(a) or (ii)(b) that is at least 1.1, 1, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100-fold lower than the dose of (ii)(a) or (ii)(b) administered to the subject alone.

[0174] In some embodiments, the subject receives 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 fewer doses of (ii)(a) or (ii)(b) than the subject would receive if (ii)(a) or (ii)(b) were administered alone.

[0175] In some embodiments, the pharmaceutical composition of (i) is co-formulated with the pharmaceutical composition of (ii).

[0176] In some embodiments, the pharmaceutical composition of (i) is formulated separately from the pharmaceutical composition of (ii).

[0177] In some embodiments, the pharmaceutical composition of (i) is administered separately from the pharmaceutical composition of (ii).

[0178] Provided herein is a method for treating or preventing viral infection or treating a respiratory disease or condition associated with viral infection, comprising administering to a subject in need thereof: (i) a pharmaceutical composition comprising: (a) a polypeptide comprising at least two of the following: a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); or (b) a polynucleotide encoding a polypeptide comprising at least two of the following: a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a pharmaceutical composition comprising: (a) a polypeptide having an amino acid sequence of a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; (b) a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; or a 2019 SARS-CoV comprising (ii)(a) or (ii)(b). 2. A spike protein pharmaceutical composition; wherein the dose of (i)(a) or (i)(b) received by the subject is lower than the dose of (i)(a) or (i)(b) administered to the subject alone.

[0179] Provided herein is a method for treating or preventing viral infection or treating a respiratory disease or condition associated with viral infection, comprising administering to a subject in need thereof: (i) a pharmaceutical composition comprising: (a) a polypeptide comprising at least two of the following: a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); or (b) a polynucleotide encoding a polypeptide comprising at least two of the following: a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a pharmaceutical composition comprising: (a) a polypeptide having an amino acid sequence of a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; (b) a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; or a 2019 SARS-CoV comprising (ii)(a) or (ii)(b). 2. A spike protein pharmaceutical composition; wherein the number of doses received by the subject of (i)(a) or (i)(b) is less than the number of doses of (i)(a) or (i)(b) administered to the subject alone.

[0180] In some embodiments, the subject receives a dose of (i)(a) or (i)(b) that is at least 1.1, 1, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100-fold lower than the dose of (i)(a) or (i)(b) administered to the subject alone.

[0181] In some embodiments, the subject receives 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 fewer doses of (i)(a) or (i)(b) than the number of doses of (i)(a) or (i)(b) administered to the subject alone.

[0182] In some embodiments, the pharmaceutical composition of (i) is co-formulated with the pharmaceutical composition of (ii).

[0183] In some embodiments, the pharmaceutical composition of (i) is formulated separately from the pharmaceutical composition of (ii).

[0184] In some embodiments, the pharmaceutical composition of (i) is administered separately from the pharmaceutical composition of (ii).

[0185] In some embodiments, the pharmaceutical composition is a coformulation.

[0186] In some embodiments, the first pharmaceutical composition is administered together with or on the same day as the second pharmaceutical composition.

[0187] In some embodiments, the first pharmaceutical composition and the second pharmaceutical composition are administered simultaneously.

[0188] In some embodiments, the first pharmaceutical composition is administered at a first location on the subject and the second pharmaceutical composition is administered at a second location on the subject that is different from the first location.

[0189] In some embodiments, the first location is at an appendage of the subject and the second location is at an opposite appendage of the subject,

[0190] In some embodiments, the first appendage is an arm and the second appendage is an arm.

[0191] In some embodiments, the first pharmaceutical composition and the second pharmaceutical composition are administered to the same site on the subject.

[0192] In some embodiments, the pharmaceutical composition is administered at a first time point and a second time point, wherein the second time point is at least about, at most about, or about 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, or 36 days after the first time point; and at least about, at most about, or about 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, or at least about, at most about, or about 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, or 36 months after the first time point.

[0193] In some embodiments, the pharmaceutical composition is administered at a third time point, wherein the third time point is at least about, at most about, or about 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, or 36 days after the second time point; or at least about, at most about, or about 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, or at least about, at most about, or about 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, or 36 months after the second time point.

[0194] In some embodiments, the third time point is at least about, at most about, or about 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 50 days after the first time point; or at least about, at most about, or about 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, or at least about, at most about, or about 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, or 36 months after the first time point.

[0195] In some embodiments, the first pharmaceutical composition is administered at a first time point and a second time point, wherein the second time point is at least about, at most about, or about 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, or 36 days after the first time point; and at least about, at most about, or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or at least about, at most about, or about 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, or 36 months after the first time point.

[0196] In some embodiments, the first pharmaceutical composition is administered at a third time point, wherein the third time point is at least about, at most about, or about 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, or 36 days after the second time point; and at least about, at most about, or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or at least about, at most about, or about 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, or 36 months after the second time point.

[0197] In some embodiments, the third time point is at least about, at most about, or about 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 50 days after the first time point; or at least about, at most about, or about 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, or at least about, at most about, or about 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, or 36 months after the first time point.

[0198] In some embodiments, the second pharmaceutical composition is administered at a first time point.

[0199] In some embodiments, the second pharmaceutical composition is administered at a second time point.

[0200] In some embodiments, the second pharmaceutical composition is administered at a third time point.

[0201] In some embodiments, the patient is at least about, at most about, or about 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, or 36 days after the first time point; at least about, at most about, or about 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, or at least about, at most about, or about 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, or 36 months after the first time point.

[0202] In some embodiments, the patient is at least about, at most about, or about 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, or 36 days after the second time point; or at least about, at most about, or about 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 or at least about, at most about, or about 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, or 36 months after the second time point.

[0203] Provided herein is a method for treating or preventing viral infection or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject in need thereof: (i) a pharmaceutical composition comprising: (a) a polypeptide comprising at least two of the following: a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); or (b) a polynucleotide encoding a polypeptide comprising at least two of the following: a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); wherein the pharmaceutical composition is administered at a first time point, a second time point, and a third time point, wherein the second time point is at least about 2 days after the first time point and the third time point is at least about 2 days after the second time point.

[0204] In some embodiments, the second time point is at least about 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, or 35 days after the first time point, and the second time point is at least about 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, or 35 weeks after the first time point, or at least about 1, 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, or 35 months after the first time point.

[0205] In some embodiments, the second time point is at most about 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, or 35 days after the first time point, and the second time point is at most about 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, or 35 weeks after the first time point, or up to about 1, 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, or 35 months after the first time point.

[0206] In some embodiments, the second time point is about 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, or 35 days after the first time point, and the second time point is about 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, or 35 days after the first time point. 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35 weeks, or about 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, or 35 months after the first time point.

[0207] In some embodiments, the third time point is at least about 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, or 35 days after the second time point. 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35 weeks after the second time point, or at least about 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, or 35 months after the second time point.

[0208] In some embodiments, the third time point is at most about 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, or 35 days after the second time point, and the third time point is at most about 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, or 35 weeks, or up to about 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, or 35 months after the second time point.

[0209] In some embodiments, the third time point is about 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, or 35 days after the second time point. 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35 weeks, or about 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, or 35 months after the second time point.

[0210] In some embodiments, the third time point is at least about 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, or 36 days after the first time point, and the third time point is at least about 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 or 35 weeks after the first time point, or at least about 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 or 35 months after the first time point.

[0211] In some embodiments, the third time point is at most about 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, or 36 days after the first time point, and the third time point is at most about 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, or 35 weeks after the first time point, or up to about 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, or 35 months after the first time point.

[0212] In some embodiments, the third time point is about 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, or 36 days after the first time point. 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35 weeks, or about 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, or 35 months after the first time point.

[0213] In some embodiments, the method further comprises administering to the subject: (ii)(a) a polypeptide having the amino acid sequence of a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; (b) a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; or a 2019 SARS-CoV 2 spike protein pharmaceutical composition comprising (ii)(a) or (ii)(b).

[0214] In some embodiments, the subject is immunodeficient.

[0215] In some embodiments, the subject has B cell immunodeficiency.

[0216] In some embodiments, the pharmaceutical composition is administered prophylactically.

[0217] Provided herein is a pharmaceutical composition comprising: (i) a recombinant polynucleotide encoding a polypeptide comprising at least two of the following: a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; wherein the ratio (e.g., mass ratio) of (i):(ii) is greater than 20:1 or less than 1:20.

[0218] In some embodiments, the ratio (e.g., mass ratio) of (i):(ii) is greater than 20:1, 30:1, 40:1, 50:1, 60:1, 70:1, 80:1, 90:1, or 100:1.

[0219] In some embodiments, the ratio (e.g., mass ratio) of (i):(ii) is less than 1:20, 1:30, 1:40, 1:50, 1:60, 1:70, 1:80, 1:90, or 1:100.

[0220] Provided herein is a composition comprising: (i) a first pharmaceutical composition comprising a first recombinant polynucleotide encoding a polypeptide comprising at least two of the following: a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a second pharmaceutical composition comprising a second recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; wherein the ratio (e.g., mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is 1:50 to 50:1.

[0221] In some embodiments, the ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:25 to 25:1.

[0222] In some embodiments, the ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:10 to 10:1.

[0223] In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:10, 1:9, 1:8, 1:7, 1:6, 1:5, 1:4, 1:3, 1:2, 1:1, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 1:9.5, 1:8.5, 1:7.5, 1:6.5, 1:5.5, 1:4.5, 1:3.5, 1:2.5, 1:1.5, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 1:9.5, 1:8.5, 1:7.5, 1:6.5, 1:5.5, 1:4.5, 1:3.5, 1:2.5, 1:1.5, 2:1, 3:1, 4:1, 5:1 In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:6. In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1: 3. In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1: 2.

[0224] In some embodiments, the recombinant polynucleotide in (i) is present at a dose of 0.1 μg to 100 μg, or 1 μg to 50 μg, or 1 μg to 30 μg, or 1 μg to 20 μg, or 3 μg to 20 μg, or 5 μg to 15 μg. In some embodiments, the recombinant polynucleotide in (i) is present at a dose of 0.05 μg to 10 μg, or 0.1 μg to 5 μg, or 0.3 μg to 5 μg. In some embodiments, the recombinant polynucleotide in (i) is present at a dose of 0.1 μg to 20 μg or 0.5 μg to 15 μg.

[0225] In some embodiments, the recombinant polynucleotide in (ii) is present at a dose of 0.1 microgram to 100 micrograms, or 1 microgram to 100 micrograms, or 1 microgram to 30 micrograms, or 1 microgram to 20 micrograms, or 3 micrograms to 30 micrograms.

[0226] In some embodiments, the recombinant polynucleotide in (ii) encompasses at least two recombinant polynucleotides, each encoding a SARS-CoV-2 S protein of a different strain or variant thereof. For example, in some embodiments, the recombinant polynucleotide in (ii) encompasses a recombinant polynucleotide encoding a SARS-CoV-2 protein of the Wuhan strain and a recombinant polynucleotide encoding a SARS-CoV-2 protein having one or more mutations characteristic of a SARS-CoV-2 variant (e.g., in some embodiments, an Omicron variant, such as Omicron BA.4 or BA.5).

[0227] In some embodiments, the recombinant polynucleotide in (i) is present at a dose of about 5 micrograms, and the recombinant polynucleotide in (ii) is present at a dose of about 30 micrograms. In some embodiments, the recombinant polynucleotide in (i) is present at a dose of about 10 micrograms, and the recombinant polynucleotide in (ii) is present at a dose of about 30 micrograms. In some embodiments, the recombinant polynucleotide in (i) is present at a dose of about 15 micrograms, and the recombinant polynucleotide in (ii) is present at a dose of about 30 micrograms.

[0228] Provided herein is a pharmaceutical composition comprising nanoparticles, wherein the nanoparticles comprise: (i) a first recombinant polynucleotide encoding a polypeptide comprising at least two of the following: a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a second recombinant polynucleotide encoding the 2019 SARS-CoV 2 spike protein or a variant or fragment thereof.

[0229] In some embodiments, the nanoparticles are present in the pharmaceutical composition at a dose of 100 ng to 500 micrograms.

[0230] In some embodiments, the nanoparticles are present in the pharmaceutical composition at a dose of 1 microgram to 100 micrograms.

[0231] In some embodiments, the nanoparticles are present in the pharmaceutical composition at a dose of 1 microgram to 30 micrograms, 5 micrograms to 40 micrograms, or 10 micrograms to 50 micrograms.

[0232] In some embodiments, the nanoparticles are present in the pharmaceutical composition at a dose of 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1,000 micrograms.

[0233] In some embodiments, the ratio (eg, mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:50 to 50:1.

[0234] In some embodiments, the ratio (eg, mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:25 to 25:1.

[0235] In some embodiments, the ratio (eg, mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:10 to 10:1.

[0236] In some embodiments, the ratio (e.g., mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:10, 1:9, 1:8, 1:7, 1:6, 1:5, 1:4, 1:3, 1:2, 1:1, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 1:9.5, 1:8.5, 1:7.5, 1:6.5, 1:5.5, 1:4.5, 1:3.5, 1:2.5, 1:1.5, 2.5:1, 3.5:1, 4.5:1, 5.5: In some embodiments, the ratio (e.g., mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:6. In some embodiments, the ratio (e.g., mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1: 3. In some embodiments, the ratio (e.g., mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1: 2.

[0237] In some embodiments, the first recombinant polynucleotide is present in the pharmaceutical composition at a dose of 0.1 microgram to 100 micrograms, or 1 microgram to 50 micrograms, or 1 microgram to 30 micrograms, or 1 microgram to 20 micrograms, or 3 micrograms to 20 micrograms, or 5 micrograms to 15 micrograms. In some embodiments, the first recombinant polynucleotide is present in the pharmaceutical composition at a dose of 0.05 micrograms to 10 micrograms, or 0.1 microgram to 5 micrograms, or 0.3 micrograms to 5 micrograms. In some embodiments, the first recombinant polynucleotide is present in the pharmaceutical composition at a dose of 0.1 microgram to 20 micrograms or 0.5 micrograms to 15 micrograms.

[0238] In some embodiments, the second recombinant polynucleotide is present in the pharmaceutical composition at a dose of 0.1 microgram to 100 micrograms, or 1 microgram to 100 micrograms, or 1 microgram to 30 micrograms, or 1 microgram to 20 micrograms, or 3 micrograms to 30 micrograms.

[0239] In some embodiments, the second recombinant polynucleotide encompasses at least two recombinant polynucleotides, each encoding a SARS-CoV-2 S protein of a different strain or variant thereof. For example, in some embodiments, the second recombinant polynucleotide encompasses a recombinant polynucleotide encoding a SARS-CoV-2 S protein of the Wuhan strain and a recombinant polynucleotide encoding a SARS-CoV-2 S protein having one or more mutations characteristic of a SARS-CoV-2 variant (e.g., in some embodiments, an Omicron variant, such as Omicron BA.1, BA.2, BA.4, or BA.5).

[0240] Provided herein is a composition comprising: (i) a first pharmaceutical composition comprising a first nanoparticle, wherein the first nanoparticle comprises a recombinant polynucleotide encoding a polypeptide comprising at least two of the following: a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a second pharmaceutical composition comprising a second nanoparticle, wherein the second nanoparticle comprises a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof.

[0241] In some embodiments, the ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:50 to 50:1.

[0242] In some embodiments, the ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:25 to 25:1.

[0243] In some embodiments, the ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:10 to 10:1.

[0244] In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:10, 1:9, 1:8, 1:7, 1:6, 1:5, 1:4, 1:3, 1:2, 1:1, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 1:9.5, 1:8.5, 1:7.5, 1:6.5, 1:5.5, 1:4.5, 1:3.5, 1:2.5, 1:1.5, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 1:9.5, 1:8.5, 1:7.5, 1:6.5, 1:5.5, 1:4.5, 1:3.5, 1:2.5, 1:1.5, 2:1, 3:1, 4:1, 5:1 In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:6. In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1: 3. In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1: 2.

[0245] In some embodiments, the recombinant polynucleotide in (i) is present at a dose of 0.1 μg to 100 μg, or 1 μg to 50 μg, or 1 μg to 30 μg, or 1 μg to 20 μg, or 3 μg to 20 μg, or 5 μg to 15 μg. In some embodiments, the recombinant polynucleotide in (i) is present at a dose of 0.05 μg to 10 μg, or 0.1 μg to 5 μg, or 0.3 μg to 5 μg. In some embodiments, the recombinant polynucleotide in (i) is present at a dose of 0.1 μg to 20 μg or 0.5 μg to 15 μg.

[0246] In some embodiments, the recombinant polynucleotide in (ii) is present at a dose of 0.1 microgram to 100 micrograms, or 1 microgram to 100 micrograms, or 1 microgram to 30 micrograms, or 1 microgram to 20 micrograms, or 3 micrograms to 30 micrograms.

[0247] In some embodiments, the recombinant polynucleotide in (ii) encompasses at least two recombinant polynucleotides, each encoding a SARS-CoV-2 S protein of a different strain or variant thereof. For example, in some embodiments, the recombinant polynucleotide in (ii) encompasses a recombinant polynucleotide encoding a SARS-CoV-2 protein of the Wuhan strain and a recombinant polynucleotide encoding a SARS-CoV-2 protein having one or more mutations characteristic of a SARS-CoV-2 variant (e.g., in some embodiments, an Omicron variant, such as Omicron BA.4 or BA.5).

[0248] In some embodiments, the first nanoparticle is present in the first pharmaceutical composition at a dose of about 100 ng to 500 micrograms.

[0249] In some embodiments, the first nanoparticles are present in the first pharmaceutical composition at a dose of about 1 microgram to 100 micrograms.

[0250] In some embodiments, the first nanoparticles are present in the first pharmaceutical composition at a dose of about 1 microgram to 30 micrograms, 5 micrograms to 40 micrograms, or 10 micrograms to 50 micrograms.

[0251] In some embodiments, the first nanoparticles are present in the first pharmaceutical composition at a dose of about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1,000 micrograms.

[0252] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition at a dose of about 100 ng to 500 micrograms.

[0253] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition at a dose of about 1 microgram to 100 micrograms.

[0254] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition at a dose of about 1 microgram to 30 micrograms, 5 micrograms to 40 micrograms, or 10 micrograms to 50 micrograms.

[0255] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition at a dose of about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1,000 micrograms.

[0256] In some embodiments, the recombinant polynucleotide of (i) is present in the first pharmaceutical composition at a dose of about 50 ng to 250 micrograms.

[0257] In some embodiments, the recombinant polynucleotide of (i) is present in the first pharmaceutical composition at a dose of about 0.5 to 50 micrograms.

[0258] In some embodiments, the recombinant polynucleotide of (i) is present in the first pharmaceutical composition at a dose of about 0.5 micrograms to 15 micrograms, 2.5 micrograms to 20 micrograms, or 5 micrograms to 25 micrograms.

[0259] In some embodiments, the recombinant polynucleotide of (i) is present in the first pharmaceutical composition at a dose of about 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, or 500 micrograms.

[0260] In some embodiments, the recombinant polynucleotide of (ii) is present in the second pharmaceutical composition at a dose of about 50 ng to 250 micrograms.

[0261] In some embodiments, the recombinant polynucleotide of (ii) is present in the second pharmaceutical composition at a dose of about 0.5 to 50 micrograms.

[0262] In some embodiments, the recombinant polynucleotide in (ii) is present in the second pharmaceutical composition at a dose of about 0.5 micrograms to 15 micrograms, 2.5 micrograms to 20 micrograms, or 5 micrograms to 25 micrograms.

[0263] In some embodiments, the recombinant polynucleotide of (ii) is present in the second pharmaceutical composition at a dose of about 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, or 500 micrograms.

[0264] In some embodiments, the nanoparticles are lipid nanoparticles.

[0265] Provided herein is a method for treating or preventing viral infection or treating a respiratory disease or condition associated with viral infection, comprising administering to a subject in need thereof a pharmaceutical composition comprising: (i) a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, (b) a sequence comprising an epitope sequence from membrane glycoprotein (M), and (c) a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); (ii) a polynucleotide encoding a polypeptide, wherein the polypeptide comprises at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, (b) a sequence comprising an epitope sequence from membrane glycoprotein (M), and (c) a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); (iii) a T cell receptor (TCR) or a T cell comprising a TCR, wherein the TCR binds to a corresponding HLA (iv) an antigen presenting cell comprising (i) or (ii); or (v) an antibody or a B cell comprising the antibody, wherein the antibody binds to the epitope sequence of the polypeptide.

[0266] In some embodiments, the subject is immunodeficient.

[0267] In some embodiments, the subject has B cell immunodeficiency.

[0268] In some embodiments, the subject has a reduced ability to mount an antibody response to an antigen compared to a subject that does not suffer from immunodeficiency.

[0269] In some embodiments, the subject has a reduced ability to mount an antibody response to vaccination compared to a non-immunodeficient subject.

[0270] In some embodiments, the subject has a reduced ability to generate an anti-Spike protein antibody response and / or an anti-RBD antibody response compared to a subject that does not have an immunodeficiency.

[0271] In some embodiments, the subject can mount a T cell response or has no reduced ability to mount a T cell response compared to a subject that does not have an immunodeficiency.

[0272] In some embodiments, the pharmaceutical composition has a protective effect against variants of 2019 SARS CoV-2.

[0273] In some embodiments, the variant of 2019 SARS CoV-2 is α, β, γ, δ, ε, ζ, η, θ, ι, κ, or λ.

[0274] In some embodiments, the subject generates a T cell response to an epitope of the polypeptide.

[0275] In some embodiments, the subject generates a T cell response to an epitope sequence from ORF1ab, an epitope sequence from the membrane glycoprotein (M), and / or an epitope sequence from the nucleocapsid phosphoprotein (N).

[0276] In some embodiments, the subject is an organ transplant recipient.

[0277] In some embodiments, the organ transplant recipient is a solid organ transplant recipient, a stem cell transplant recipient, or a bone marrow transplant recipient.

[0278] In some embodiments, the subject receives an organ transplant less than 1 year, less than 6 months, or less than 3 months after administration of the pharmaceutical composition.

[0279] In some embodiments, the subject is expected to receive an organ transplant less than 1 year, less than 6 months, or less than 3 months prior to administration of the pharmaceutical composition.

[0280] In some embodiments, the subject has cancer.

[0281] In some embodiments, the cancer is a B cell cancer.

[0282] In some embodiments, the B cell cancer is a B cell lymphoma or a B cell leukemia.

[0283] In some embodiments, the subject has an autoimmune disease or disorder.

[0284] In some embodiments, the autoimmune disease or condition is Addison's disease, anti-NMDA receptor encephalitis, antisynthetase syndrome, aplastic anemia, autoimmune anemia, autoimmune hemolytic anemia, autoimmune pancreatitis, Behçet's disease, bullous skin disorders, celiac sprue, chronic fatigue syndrome, chronic inflammatory demyelinating polyneuropathy, chronic lymphocytic leukemia, Crohn's disease, dermatomyositis, Devic's disease, erythroblastopenia, Evan's syndrome, focal segmental glomerulosclerosis, granulomatosis with polyangiitis, Graves' disease, Graves' ophthalmopathy, Guillain-Barré syndrome, Hashimoto's thyroiditis, idiopathic IgA nephropathy, IgA-mediated autoimmune diseases, IgG4-related diseases, inflammatory bowel disease, juvenile idiopathic arthritis, multiple sclerosis, myasthenia gravis, myeloma, non-Hodgkin's lymphoma, opsoclonus-myoclonus syndrome (OMS), pemphigoid, pemphigus, pemphigus vulgaris, pernicious anemia, polymyositis, psoriasis, pure red cell aplasia, reactive arthritis, rheumatoid arthritis, sarcoidosis, scleroderma, Sjögren's syndrome, systemic lupus erythematosus, thrombocytopenic purpura, thrombotic thrombocytopenic purpura, type 1 diabetes mellitus, ulcerative colitis, vasculitis, and vitiligo.

[0285] In some embodiments, the subject has congenital agammaglobulinemia or congenital IgA deficiency.

[0286] In some embodiments, the subject has HIV or AIDS. In some embodiments, the subject has age-related immunodeficiency, immunosenescence, multifactorial immunodeficiency, or is an elderly or senior citizen with age-related immunodeficiency.

[0287] In some embodiments, the subject is currently receiving an immunosuppressant or has received an immunosuppressant less than 1 year, less than 6 months, or less than 3 months prior to administration of the pharmaceutical composition.

[0288] In some embodiments, the immunosuppressant is abatacept, alilumab, acalabrutinib, adalimumab, corticosteroids, atelomod sodium, aldesleukin, alefacept, alemtuzumab, aleceptin, aspirin hydrochloride, flavopiridol, ambrisentan, aminocamptothecin, amimod, anakinra, andreximab, androlide, anirutumab, anti-thymocyte Ig, apatinib, apelis, asparaginase, atacicept, atezolizumab, avelumab, azacitidine, azathioprine, bafatinib, benecitinib, baricitinib, basiliximab, bekametinib, benetinib, belvuzumab, bevacizumab, bendamustine, betadine, rilotinib, or tadalafil. , bevacizumab, BIIB033, BIIB059, BIIB061, bimetinib, bimetinib, bleomycin, blinatumomab, bortezomib, vetinib-bentuximab, bryostatin 1, bucillamine, bupanib, busulfan, canakinumab, capecitabine, carboplatin, carfilzomib, carmustine, cediranib maleate, cemiplimab, salamod, certolizumab, certolizumab pegol, cetuximab, cedabenb, chlorambucil, cilengitide, cetuzumab, cisplatin, cladribine, clazakinumab, clemastine, clioquinol, corticosteroids, cyclophosphamide, cyclosporine, cytarabine, cytotoxic chemotherapy, daclizumab, dalfampridine, pegol-dapilimab, daptomycin Dasatinib, defatinib, defibrotide, denosumab, dexamethasone, diacerein, dimethyl fumarate, dinaciliib, deloximetate fumarate, doxorubicin, doxorubicin, durvalumab, duvelithid, dutuximab, eculizumab, efalizumab, etilimod alfa, a neuropeptide combination of metenfaline and tracoctide, elenuzumab, elotuzumab, connefenib, enfuvirtide, entinostat, entoptinib, enzastaurin, icandrostat, epirubicin, epratuzumab, eritoran tetrasodium, etanercept, etoposide, edrema, everolimus, ivotinib, filgotinib, fingolimod, fillast, fludarabine, fluorouracil, fentocillin, forodesine hydrochloride, fostamatinib, Galucetib, gataspir, ganitumomab, gemcitabine, gemtuzumab ozogamicin, gemtuzumab, galaxiba, galacia, glatiramer acetate, vetinib-gebatumumab, glecitinib, golimumab, guadecitabine, hydrocortisone, hydroxychloroquine sulfate, hydroxyurea, ibrutinib tiuxetan, ibrutinib, ibudilast, idarubicin, idebenone, idelalisib, ifosfamide, iguratimod, imatinib, imatinib, infliximab, inotuzumab, interferon alpha-2, interferon beta-1a, interferon beta-1b, interferon gamma-1, ipilimumab, ilofufen, isatuximab, ispins, itatinib, ixazomib, lapatinib, laquinimod, laromustine, ld-aminopterin, leflunomide,Lenalidomide, lenvatinib, letrozole, levamisole, levocabastine, lipoic acid, lirilumab, lonafarnib, ruximab, maraviroc, masitinib, mavelimab, melphalan, mercaptopurine, methotrexate, methoxsalen, methylprednisone, miracitumomab, mitoxantrone, mizoribine, motenozide, monalizumab, motuzumab, motuzumab diphosphate, pembrolimab, muromonab-CD3, mycophenolate mofetil, mycophenolic acid, namezumab, natalizumab, neviram Tork, nehulizumab, nerlipidin, neurovac, niraparib, nivolumab, obaclav mesylate, obinutuzumab, oblimersen sodium, ocrelizumab, ofatumumab, olotuzumab, opinumab, opreluzumab, osimertinib, oxaliplatin, oxaliplatin, oxcarbazepine, ozanimod, paclitaxel, paxillinib, palifermin, panobinostat, pazopanib, peftinib, pegfilgrastim, peginterferon beta-1a, penacept (peg stnf-ri), pembrolizumab, pemetrexed, phencomedine, pentostatin, perifosine, pedistat, pecidinib, picoplatin, pidilizumab, pivanec, pixantron, plenavasin, plevastatin acetate, vepotuzumab, pomalidomide, ponatinib, bonecitinib, prednisone / prednisolone, pyrrolamide, eculizumab-cwvz, recombinant IL-12, relalizumab Anti-, rhigf-1, rhigm22, reglucosidase, linacept, ritonavir, rituximab, ruxolitinib, salicylumab, secukinumab, selumetinib, simvastatin, sintilimab, cilizumab, sirolimus (rapamycin), sirolimus (rapamycin), sirolimus (rapamycin), sirolimus (rapamycin), selutinib, sonidegi, sorafenib, sotrastuzumab acetate, sunitinib, sunphenon Epigallocatechin gallate, taperumab, tacrolimus, taporstat mesylate, tatuzumab, tanspiramycin, tegafur / gimeracil / oteracil, temozolomide, temsirolimus, tenalicept, telameprolol, teriflunomide, thalidomide, thiabine, thiotepa, tipifarnib, tirabrutinib, tislelizumab, tivozanib, tocilizumab, tofacitinib, trelizumab, trexedin Milimumab, treoxazole, utuximab, upalicylate, upadacitinib, usrelumab, ustekinumab, varirizumab, varizumab, vedolizumab, veliparib, venetuximab, venetoclax, vinblastine, vincristine, vinorelbine bitartrate, visilizumab, vismodegib, velitusin, voriconazole, vorinostat, voxarubicin, ziv-aflibercept, or any combination thereof.

[0289] In some embodiments, the immunosuppressant is an A2aR antagonist, an Akt inhibitor, an anti-CD20, an anti-amyloidosis (AA) agent, an anti-CD37 protein therapeutic, an anti-CTLA4 mAb, an anti-CXCR4, an anti-huCD40 mAb, an anti-LAG3 mAb, an anti-PD-1 mAb, an anti-PD-L1 agent, an anti-PD-L1 agent, an anti-PD-L1 mAb, an anti-TGFb mAb, an anti-TIGIT mAb, an anti-TIM-3 mAb, an Aurora kinase inhibitor, a Bcl-2 inhibitor, a bifunctional fusion protein targeting TGFb and PD-L1, a bispecific anti-PD-1 and anti-LAG3 mAb, CD1d ligand, CD40 agonist, complement C5a inhibitor, CSF1R inhibitor, EZH2 inhibitor, FGFR3 inhibitor, FGFR4 inhibitor, FGFrR3 inhibitor, glucocorticoid-induced tumor necrosis factor receptor-related gene agonist, glutaminase inhibitor, anti-IL-12 human monoclonal antibody, ICOS agonist, IDO1 inhibitor, IL2 mutant protein, IL2 receptor agonist, MEK inhibitor, multi-targeted receptor tyrosine kinase inhibitor, neutrophil elastase inhibitor, Notch inhibitor, p38 MAPK inhibitor, PD-1 inhibitor, recombinant human Flt3L, ROCK inhibitor, selective sphingosine-1-phosphate receptor modulator, Src kinase inhibitor, TLR4 agonist, TLR9 agonist or any combination thereof.

[0290] In some embodiments, the subject is older than 55, 56, 57, 58, 59, 60, 65, 70, 75, or 80 years old.

[0291] In some embodiments, the polypeptide comprises (a) a sequence comprising an epitope sequence from ORF1ab, (b) a sequence comprising an epitope sequence from membrane glycoprotein (M), and (c) a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N).

[0292] In some embodiments, the sequence comprising the epitope sequence from ORF1ab is C-terminal to the sequence comprising the epitope sequence from the nucleocapsid phosphoprotein (N).

[0293] In some embodiments, the sequence comprising the epitope sequence from ORF1ab is N-terminal to the sequence comprising the epitope sequence from membrane glycoprotein (M).

[0294] In some embodiments, the sequence comprising an epitope sequence from the nucleocapsid phosphoprotein (N) is N-terminal to the sequence comprising an epitope sequence from the membrane glycoprotein (M).

[0295] In some embodiments, the polypeptide comprises (a) 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more epitope sequences from ORF1ab, (b) a sequence comprising an epitope sequence from a membrane glycoprotein (M), and (c) a sequence comprising an epitope sequence from a nucleocapsid phosphoprotein (N).

[0296] In some embodiments, the epitope sequence from ORF1ab is an epitope sequence from a nonstructural protein (NSP).

[0297] In some embodiments, the nonstructural protein (NSP) is selected from the group consisting of NSP1, NSP2, NSP3, NSP4, and combinations thereof.

[0298] In some embodiments, the polypeptide comprises a sequence comprising an epitope sequence from NSP1, a sequence comprising an epitope sequence from NSP2, a sequence comprising an epitope sequence from NSP3, and a sequence comprising an epitope sequence from NSP4.

[0299] In some embodiments, the epitope sequence from ORF1ab is selected from the group consisting of YLFDESGEFKL, YLFDESGEF, FGDDTVIEV, QLMCQPILL, TTDPSFLGRY, PTDNYITTY, PSFLGRY, AEAELAKNV, KTIQPRVEK, and any combination thereof.

[0300] In some embodiments, the epitope sequence from the nucleocapsid glycoprotein (N) is LLLDRLNQL.

[0301] In some embodiments, the epitope sequence from membrane phosphoprotein (M) is VATSRTLS Y.

[0302] In some embodiments, the polypeptide comprises an epitope sequence from the nucleocapsid glycoprotein (N), ie, LLLDRLNQL, and an epitope sequence from the membrane phosphoprotein (M), ie, VATSRTLSY.

[0303] In some embodiments, the polypeptide comprises (a) each of the following epitope sequences from ORF1ab: YLFDESGEFKL, YLFDESGEF, FGDDTVIEV, QLMCQPILL, TTDPSFLGRY, PTDNYITTY, PSFLGRY, AEAELAKNV, KTIQPRVEK; (b) an epitope sequence from nucleocapsid glycoprotein (N), i.e., LLLDRLNQL; and (c) an epitope sequence from membrane phosphoprotein (M), i.e., VATSRTLSY.

[0304] In some embodiments, the sequence comprising the epitope sequence from ORF1ab is selected from the group consisting of the following sequences or fragments thereof: MVTNNTFTLKVPHVGEIPVAYRKVLLKTIQPRVEKYLFDESGEFKLSEVGPEHSLAEYYIFFASFYY; MVTNNTFTLKVPHVGEIPVAYRKVLLKTIQPRVEKYLFDESGEFKLSEVGPEHSLAEY; APKEIIFLEGETLFGDDTVIEVAIILASFSAST; APKEIIFLEGETLFGDDTVIEV; HTTDPSFLGRYMSALFADDLNQLTGYHTDFSSEIIGYQLMCQPILLAEAELAKNVSLILGTVSWNL; TTDPSFLGRYMSALFADDLNQLTGYHTDFSSEIIGYQLMCQPILLAEAELAKNVSLILGTVSWNL; LLSAGIFGAITDVFYKENSYKVPTDNYITTY; and combinations thereof.

[0305] In some embodiments, the sequence comprising an epitope sequence from a membrane glycoprotein (M) is selected from the group consisting of the following sequences or fragments thereof: ADSNGTITVEELKKLLEQWNLVIGFLFLTWICLLQFAYANRNRFLYIIKLIFLWLLWPVTLACFVLAAVYRINWITGGIAIAMACLVGLMWLSYFIASFRLFARTRSMWSFNPETNILLNVPLHGTILTRPLLESELVIGAVILRGHLRIAGHHLGRCDIKDLPKEITVATSRTLSYYKLGASQRVAGDSG FAAYSRYRIGNYKLNTDHSSSSDNIALLVQ; FAYANRNRFLYIIKLIFLWLLWPVTLACFVLAAVYRINWITGGIAIAMACLVGLMWLSYFIASFRLF; LGRCDIKDLPKEITVATSR TLSYYKLGASQRVA; KLLEQWNLVIGF; NRNRFLYIIKLIFLWLLWPVTLACFVLAAVY; SELVIGAVILRGHLRIAGHHLGR; VATSRTLSYYKLGASQRV; GLMWLSYF; and combinations thereof.

[0306] In some embodiments, the sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N) is selected from the group consisting of the following sequences or fragments thereof: KDLSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGTTLPKGFYAEGSRGGSQASSRSSSRSRNSSRNSTPGSSRGTSPARMAGNGGDAALALLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDKKKKADETQALPQRQKKQQTVTLLPAADLDDFSKQLQQSMSSADSTQA;

[0307] RMAGNGGDAALALLLLDRLNQLESKMSGKGQQQ; YKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFP; and combinations thereof.

[0308] In some embodiments, the polypeptide comprises one or more linker sequences.

[0309] In some embodiments, the one or more linker sequences are selected from the group consisting of GGSGGGGSGG, GGSLGGGGSG.

[0310] In some embodiments, one or more linker sequences comprise a cleavage sequence.

[0311] In some embodiments, the one or more cleavage sequences are selected from the group consisting of FRAC, KRCF, KKRY, ARMA, RRSG, MRAC, KMCG, ARCA, KKQG, YRSY, SFMN, FKAA, KRNG, YNSF, KKNG, RRRG, KRYS, and ARYA.

[0312] In some embodiments, the polypeptide comprises a transmembrane domain sequence.

[0313] In some embodiments, the transmembrane domain sequence is C-terminal to a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N).

[0314] In some embodiments, the transmembrane domain sequence is EQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT.

[0315] In some embodiments, the polypeptide comprises a secretory signal sequence (SEC sequence).

[0316] In some embodiments, the SEC sequence is N-terminal to the sequence comprising the epitope sequence from ORF1ab, the sequence comprising the epitope sequence from membrane glycoprotein (M), and the sequence comprising the epitope sequence from nucleocapsid phosphoprotein (N).

[0317] In some embodiments, the SEC sequence is MFVFLVLLPLVSSQCVNLT.

[0318] In some embodiments, the composition comprises a polynucleotide encoding a polypeptide.

[0319] In some embodiments, the polynucleotide is mRNA.

[0320] In some embodiments, the polynucleotide comprises a codon-optimized sequence for expression in humans.

[0321] In some embodiments, the polynucleotide comprises a dEarI-hAg sequence.

[0322] In some embodiments, the dEarI-hAg sequence is ATTCTTCTGGTCCCCACAGACTCAGAGAGAACCC, optionally wherein each T is U.

[0323] In some embodiments, the polynucleotide comprises a Kozak sequence.

[0324] In some embodiments, the Kozak sequence is GCCACC.

[0325] In some embodiments, the polynucleotide comprises an F element sequence.

[0326] In some embodiments, the F element sequence is the 3UTR of the amino-terminal split enhancer (AES).

[0327] In some embodiments, the F element sequence is CTGGTACTGCATGCACGCAATGCTAGCTGCCCCTTTCCCGTCCTGGGTACCCCGAGTCTCCCCCGACCTCGGGTCCCAGGTATGCTCCCACCTCCACCTGCCCCACTCACCACCTCTGCTAGTTCCAGACACCTCC, optionally wherein each T is U.

[0328] In some embodiments, the polynucleotide comprises an I element sequence.

[0329] In some embodiments, the I element sequence is the 3'UTR of the mitochondrial-encoded 12S rRNA (mtRNR1).

[0330] In some embodiments, the I element sequence is CAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACACC, optionally wherein each T is U.

[0331] In some embodiments, the polynucleotide comprises a poly A sequence.

[0332] In some embodiments, the poly A sequence is AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGCATATGACTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA, optionally wherein each T is U.

[0333] In some embodiments, each of the epitope sequences from ORF1ab, membrane glycoprotein, and nucleocapsid phosphoprotein is from 2019 SARS-CoV-2.

[0334] In some embodiments, one or more epitopes, or each epitope, elicits a T cell response.

[0335] In some embodiments, one or more epitopes, or each epitope, has been observed by mass spectrometry to be presented by an HLA molecule.

[0336] In some embodiments, the composition comprises (i) a polypeptide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% sequence identity to a sequence selected from the group consisting of: RSC1p1full, RS C2p1full, RS C3p1full, RS C4p1full, RS C5p1, RS C5p2, RS C5p2full, RSC6p1, RS C6p2, RS C6p2full, RS C7p1, RS C7p2, RS C7p2full, RS C7p4, RS C7p4full, RSC8p1, RS C8p2, and RS C8p2full; and (ii) a polynucleotide encoding a polypeptide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% sequence identity to a sequence selected from the group consisting of: RSC1p1full, RS C2p1full, RS C3p1full, RS C4p1full, RS C5p1, RS C5p2, RS C5p2full, or (iii) a polynucleotide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% sequence identity to a sequence selected from the group consisting of SEQ ID NO: RS C1n1, RS C2n1, RS C3n1, RS C4n1, RS C5n1, RS C6n1, RS C7n1, RS C8n1, RS C5n2, RS C6n2, RS C7n2, RS C8n2, RS C5n2full, RS C6n2full, RS C7n2full, RS C8n2full, RS C7n4, RS C7n4full.

[0337] In some embodiments, the composition comprises (i) a polypeptide having at least 70%, 80%, 90% or 100% sequence identity to a sequence selected from the group consisting of RS C7p1, RS C7p2, RS C7p2full, RS C7p4 and RSC7p4full; or (iii) a polynucleotide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% sequence identity to a sequence selected from the group consisting of SEQ ID NO: RS C7n1, RS C7n2, RS C7n2full, RS C7n4, RS and C7n4full.

[0338] In some embodiments, the pharmaceutical composition comprises a pharmaceutically acceptable excipient, carrier, or diluent.

[0339] Provided herein is a method for treating or preventing a viral infection, or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject in need thereof a pharmaceutical composition comprising: (i) a polypeptide comprising an epitope sequence of Table 1A, Table 1B, Table 1C, Table 2Ai, Table 2Aii, Table 2B, and / or Table 16; (ii) a polynucleotide encoding a polypeptide comprising an epitope sequence of Table 1A, Table 1B, Table 1C, Table 2Ai, Table 2Aii, Table 2B, and / or Table 16; (iii) a T cell receptor (TCR) or a T cell comprising a TCR, wherein the TCR binds to the epitope sequence in complex with a corresponding HLA class I or class II molecule; (iv) an antigen presenting cell comprising (i) or (ii); or (v) an antibody or a B cell comprising the antibody, wherein the antibody binds to the epitope sequence.

[0340] In some embodiments, the subject is immunodeficient.

[0341] In some embodiments, the subject has B cell immunodeficiency.

[0342] In some embodiments, the epitope sequence comprises one or more or each of the following: YLFDESGEFKL, YLFDESGEF, FGDDTVIEV, LLLDRLNQL, QLMCQPILL, TTDPSFLGRY, PTDNYITTY, PSFLGRY, AEAELAKNV, VATSRTLSY, and KTIQPRVEK.

[0343] In some embodiments, the epitope sequence comprises one or more or each of the following: SAPPAQYEL, AVASKILGL, EYADVFHLY, DEFTPFDVV, VRIQPGQTF, SFRLFARTR, KFLPFQQF, VVQEGVLTA, RLDKVEAEV, FGADPIHSL, NYNYLYRLF, KYIKWPWYI, KWPWYIWLGF, LPFNDGVYF, QPTESIVRF, IPFAMQMAY, YLQPRTFLL, and RLQSLQTYV.

[0344] In some embodiments, the epitope sequence is from the orf1ab protein.

[0345] In some embodiments, the epitope sequence is from the orf1a protein.

[0346] In some embodiments, the epitope sequence is from a surface glycoprotein (S) or a shifted reading frame thereof.

[0347] In some embodiments, the epitope sequence is from the nucleocapsid phosphoprotein (N).

[0348] In some embodiments, the epitope sequence is from the ORF3a protein.

[0349] In some embodiments, the epitope sequence is from a membrane glycoprotein (M).

[0350] In some embodiments, the epitope sequence is from the ORF7a protein.

[0351] In some embodiments, the epitope sequence is from the ORF8 protein.

[0352] In some embodiments, the epitope sequence is from the envelope protein (E).

[0353] In some embodiments, the epitope sequence is from the ORF6 protein.

[0354] In some embodiments, the epitope sequence is from the ORF7b protein.

[0355] In some embodiments, the epitope sequence is from the ORF10 protein.

[0356] In some embodiments, the epitope sequence is from the ORF9b protein.

[0357] Provided herein is a method for treating or preventing viral infection, or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject in need thereof a pharmaceutical composition comprising: a polypeptide having an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% identical to the sequence of any one of the sequences depicted in Column 2 of Table 11, Column 2 of Table 12, or Column 3 of Table 15; or a recombinant polynucleotide encoding a polypeptide having an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% identical to the sequence of any one of the sequences depicted in Column 2 of Table 11, Column 2 of Table 12, or Column 3 of Table 15.

[0358] In some embodiments, the subject is immunodeficient.

[0359] In some embodiments, the subject has B cell immunodeficiency.

[0360] In some embodiments, the pharmaceutical composition comprises: a polypeptide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% sequence identity to a sequence selected from the group consisting of: RSC1p1full, RS C2p1full, RS C3p1full, RS C4p1full, RS C5p1, RS C5p2, RS C5p2full, RSC6p1, RS C6p2, RS C6p2full, RS C7p1, RS C7p2, RS C7p2full, RS C7p4, RS C7p4full, RSC8p1, RS C8p2, and RS C8p2full; or a polynucleotide encoding a polypeptide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% sequence identity to a sequence selected from the group consisting of: RSC1p1full, RS C2p1full, RS C3p1full, RS C4p1full, RS C5p1, RS C5p2, RS C5p2full, C2p1full, RS C3p1full, RS C4p1full, RS C5p1, RS C5p2, RS C5p2full, RSC6p1, RS C6p2, RS C6p2full, RS C7p1, RS C7p2, RS C7p2full, RS C7p4, RS C7p4full, RSC8p1, RS C8p2, and RS C8p2full.

[0361] In some embodiments, the pharmaceutical composition comprises a polynucleotide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% sequence identity to a sequence selected from the group consisting of SEQ ID NO: RS C1n1, RS C2n1, RS C3n1, RS C4n1, RS C5n1, RS C6n1, RS C7n1, RS C8n1, RSC5n2, RS C6n2, RS C7n2, RS C8n2, RS C5n2full, RS C6n2full, RS C7n2full, RS C8n2full, RS C7n4, and RS C7n4full.

[0362] In some embodiments, the polynucleotide is mRNA.

[0363] In some embodiments, the pharmaceutical composition further comprises one or more lipids.

[0364] In some embodiments, the one or more lipids comprise lipid nanoparticles (LNPs).

[0365] In some embodiments, the LNP encapsulates the recombinant polynucleotide construct.

[0366] In some embodiments, the polypeptide is synthetic.

[0367] In some embodiments, the polypeptide is recombinant.

[0368] In some embodiments, the polypeptide is 8-1000 amino acids in length.

[0369] In some embodiments, the epitope sequence binds or is predicted to bind to an HLA class I or class II molecule with a KD of 1000 nM or less.

[0370] In some embodiments, the epitope sequence binds or is predicted to bind to an HLA class I or class II molecule with a KD of 500 nM or less.

[0371] In some embodiments, the epitope sequence comprises the sequence of a viral protein expressed by a virus-infected cell of the subject.

[0372] In some embodiments, the virus is a coronavirus.

[0373] In some embodiments, the virus is 2019 SARS-CoV 2.

[0374] In some embodiments, at the time of administration, the HLA molecules expressed by the subject are unknown.

[0375] In some embodiments, the ability of a virus to avoid recognition by a subject's immune system is lower than the ability of a virus to avoid recognition by the immune system of a subject who has been administered a pharmaceutical composition containing epitopes from a single protein or from fewer proteins than in a pharmaceutical composition administered according to the methods described herein.

[0376] In some embodiments, the subject expresses an HLA molecule encoded by an HLA allele of any one of Table 1A, Table 1B, Table 1C, Table 2Ai, Table 2Aii, Table 2B, and Table 16, and the epitope sequence is an HLA allele-matched epitope sequence.

[0377] In some embodiments, the epitope sequence includes one or more or each of the following: SAPPAQYEL, AVASKILGL, EYADVFHLY, DEFTPFDVV, VRIQPGQTF, SFRLFARTR, KFLPFQQF, VVQEGVLTA, RLDKVEAEV, and FGADPIHSL.

[0378] In some embodiments, the method further comprises administering to the subject an additional therapy for 2019 SARS-CoV 2 viral infection.

[0379] In some embodiments, the method further comprises administering to the subject (a) a polypeptide having the amino acid sequence of a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; (b) a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; or a 2019 SARS-CoV 2 spike protein pharmaceutical composition comprising (a) or (b).

[0380] In some embodiments, the vaccine or therapeutic agent of (a) or (b) is administered to the subject once.

[0381] In some embodiments, the vaccine or therapeutic agent of (a) or (b) is administered to the subject more than once.

[0382] In some embodiments, the vaccine or therapeutic agent of (a) or (b) is administered at least twice, wherein the first administration dose is a primary immunization dose, and the second dose and subsequent doses are booster doses. In some embodiments, the vaccine or therapeutic agent of (a) or (b) is administered at least three times, wherein the first administration dose is a primary immunization dose, and the second dose, the third dose, and subsequent doses are booster doses.

[0383] In some embodiments, the priming dose and the boosting dose are administered at least 21 days apart.

[0384] In some embodiments, the interval between two booster doses is at least 30 days, at least 60 days, or at least 90 days.

[0385] In some embodiments, the vaccine or therapeutic agent is administered annually.

[0386] In some embodiments, the vaccine or therapeutic agent is administered twice per year.

[0387] In some embodiments, the vaccine or therapeutic agent is administered as a first high priming or loading dose and subsequent doses as lowered boosting or maintenance doses.

[0388] In some embodiments, the subject receives a SARS-CoV spike vaccine at a dose or frequency lower than the dose or frequency the subject receives the SARS-CoV spike vaccine alone.

[0389] Provided herein is a method for treating or preventing viral infection or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject in need thereof a pharmaceutical composition comprising: (i) a recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof.

[0390] In some embodiments, provided herein is a method for treating or preventing viral infection or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject in need thereof: (i) a first pharmaceutical composition comprising a first recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a second pharmaceutical composition comprising a second recombinant polynucleotide encoding the 2019 SARS-CoV 2 spike protein or a variant or fragment thereof.

[0391] In some embodiments, the ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is 20:1 to 1:20.

[0392] In some embodiments, the ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is 1:10 to 10:1.

[0393] In some embodiments, the ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:5 to 5:1.

[0394] In some embodiments, the ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:3 to 3:1.

[0395] In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:10, 1:9, 1:8, 1:7, 1:6, 1:5, 1:4, 1:3, 1:2, 1:1, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 1:9.5, 1:8.5, 1:7.5, 1:6.5, 1:5.5, 1:4.5, 1:3.5, 1:2.5, 1:1.5, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 1:9.5, 1:8.5, 1:7.5, 1:6.5, 1:5.5, 1:4.5, 1:3.5, 1:2.5, 1:1.5, 2:1, 3:1, 4:1, 5:1 .5:1, 6.5:1, 7.5:1, 8.5:1, 9.5:1, 2:9, 2:8, 2:7, 2:6, 2:5, 2:4, 2:3, 3:2, 4:2, 5:2, 6:2, 7:2, 8:2, 9:2, 3:8, 3:7, 3:5, 3:4, 4:3, 5:3, 7:3, 8:3, 4:9, 4:7, 4:5, 5:4, 7:4, 9:4, 5:9, 5:8, 5:7, 5:6, 6:5, 7:5, 8:5, 9:5, 6:7, 7:6, 7:8, 8:7, 8:9, or 9:8.

[0396] In some embodiments, the method of treating or preventing infection comprises administering the first pharmaceutical composition (i) and the second pharmaceutical composition (ii) to a subject who has previously been administered one or more doses of a SARS-CoV-2 vaccine (e.g., a SARS-CoV-2 vaccine comprising (a) a polypeptide comprising a SARS-CoV-2 spike protein, or a fragment or variant thereof, or (b) a recombinant polynucleotide comprising a sequence encoding a SARS-CoV-2 spike protein, or a fragment or variant thereof). In some embodiments, the method of treating or preventing infection comprises administering the first pharmaceutical composition (i) and the second pharmaceutical composition (ii) to a subject who has previously been administered two or more doses (e.g., three doses) of a SARS-CoV-2 vaccine.

[0397] In some embodiments, provided herein is a method for treating or preventing viral infection or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject in need thereof a pharmaceutical composition comprising: (i) a first recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a second recombinant polynucleotide encoding the 2019 SARS-CoV 2 spike protein or a variant or fragment thereof.

[0398] In some embodiments, the pharmaceutical composition comprises a nanoparticle, wherein the nanoparticle comprises the first recombinant polynucleotide and the second recombinant polynucleotide.

[0399] In some embodiments, the nanoparticles are present in the pharmaceutical composition at a dose of 100 ng to 500 micrograms.

[0400] In some embodiments, the nanoparticles are present in the pharmaceutical composition at a dose of 1 microgram to 100 micrograms.

[0401] In some embodiments, the nanoparticles are present in the pharmaceutical composition at a dose of 1 microgram to 30 micrograms, 5 micrograms to 40 micrograms, or 10 micrograms to 50 micrograms.

[0402] In some embodiments, the nanoparticles are present in the pharmaceutical composition at a dose of 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1,000 micrograms.

[0403] In some embodiments, the ratio (eg, mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:50 to 50:1.

[0404] In some embodiments, the ratio (eg, mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:25 to 25:1.

[0405] In some embodiments, the ratio (eg, mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:10 to 10:1.

[0406] In some embodiments, the ratio (e.g., mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:10, 1:9, 1:8, 1:7, 1:6, 1:5, 1:4, 1:3, 1:2, 1:1, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 1:9.5, 1:8.5, 1:7.5, 1:6.5, 1:5.5, 1:4.5, 1:3.5, 1:2.5, 1:1.5, 2.5:1, 3.5:1, 4.5:1, 5.5: 1, 6.5:1, 7.5:1, 8.5:1, 9.5:1, 2:9, 2:8, 2:7, 2:6, 2:5, 2:4, 2:3, 3:2, 4:2, 5:2, 6:2, 7:2, 8:2, 9:2, 3:8, 3:7, 3:5, 3:4, 4:3, 5:3, 7:3, 8:3, 4:9, 4:7, 4:5, 5:4, 7:4, 9:4, 5:9, 5:8, 5:7, 5:6, 6:5, 7:5, 8:5, 9:5, 6:7, 7:6, 7:8, 8:7, 8:9 or 9:8.

[0407] Provided herein is a method for treating or preventing viral infection or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject in need thereof: (i) a first pharmaceutical composition comprising a recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a second pharmaceutical composition comprising a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof.

[0408] In some embodiments, the ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:50 to 50:1.

[0409] In some embodiments, the ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:25 to 25:1.

[0410] In some embodiments, the ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:10 to 10:1.

[0411] In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:10, 1:9, 1:8, 1:7, 1:6, 1:5, 1:4, 1:3, 1:2, 1:1, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 1:9.5, 1:8.5, 1:7.5, 1:6.5, 1:5.5, 1:4.5, 1:3.5, 1:2.5, 1:1.5, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 1:9.5, 1:8.5, 1:7.5, 1:6.5, 1:5.5, 1:4.5, 1:3.5, 1:2.5, 1:1.5, 2:1, 3:1, 4:1, 5:1 .5:1, 6.5:1, 7.5:1, 8.5:1, 9.5:1, 2:9, 2:8, 2:7, 2:6, 2:5, 2:4, 2:3, 3:2, 4:2, 5:2, 6:2, 7:2, 8:2, 9:2, 3:8, 3:7, 3:5, 3:4, 4:3, 5:3, 7:3, 8:3, 4:9, 4:7, 4:5, 5:4, 7:4, 9:4, 5:9, 5:8, 5:7, 5:6, 6:5, 7:5, 8:5, 9:5, 6:7, 7:6, 7:8, 8:7, 8:9, or 9:8.

[0412] In some embodiments, the first pharmaceutical composition comprises a first nanoparticle, wherein the first nanoparticle comprises a recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and wherein the second pharmaceutical composition comprises a second nanoparticle, wherein the second nanoparticle comprises a recombinant polynucleotide encoding the 2019 SARS-CoV 2 spike protein or a variant or fragment thereof.

[0413] In some embodiments, the first nanoparticle is present in the first pharmaceutical composition at a dose of about 100 ng to 500 micrograms.

[0414] In some embodiments, the first nanoparticles are present in the first pharmaceutical composition at a dose of about 1 microgram to 100 micrograms.

[0415] In some embodiments, the first nanoparticles are present in the first pharmaceutical composition at a dose of about 1 microgram to 30 micrograms, 5 micrograms to 40 micrograms, or 10 micrograms to 50 micrograms.

[0416] In some embodiments, the first nanoparticles are present in the first pharmaceutical composition at a dose of about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1,000 micrograms.

[0417] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition at a dose of about 100 ng to 500 micrograms.

[0418] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition at a dose of about 1 microgram to 100 micrograms.

[0419] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition at a dose of about 1 microgram to 30 micrograms, 5 micrograms to 40 micrograms, or 10 micrograms to 50 micrograms.

[0420] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition at a dose of about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1,000 micrograms.

[0421] Provided herein is a method for treating or preventing viral infection or treating a respiratory disease or condition associated with viral infection, comprising administering to a subject in need thereof: (i) a pharmaceutical composition comprising: (a) a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); or (b) a polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a pharmaceutical composition comprising: (a) a polypeptide having an amino acid sequence of a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; (b) a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; or a 2019 SARS-CoV comprising (ii)(a) or (ii)(b). 2. Spike protein pharmaceutical composition.

[0422] wherein the subject receives a dose of (ii)(a) or (ii)(b) that is lower than the dose of (ii)(a) or (ii)(b) when administered to the subject alone.

[0423] Provided herein is a method for treating or preventing viral infection or treating a respiratory disease or condition associated with viral infection, comprising administering to a subject in need thereof: (i) a pharmaceutical composition comprising: (a) a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); or (b) a polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a pharmaceutical composition comprising: (a) a polypeptide having an amino acid sequence of a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; (b) a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; or a 2019 SARS-CoV comprising (ii)(a) or (ii)(b). 2. Spike protein pharmaceutical composition.

[0424] wherein the subject receives a number of doses of (ii)(a) or (ii)(b) that is less than the number of doses that would be administered to the subject if (ii)(a) or (ii)(b) were administered alone.

[0425] In some embodiments, the subject receives a dose of (ii)(a) or (ii)(b) that is at least 1.1, 1, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100-fold lower than the dose of (ii)(a) or (ii)(b) administered to the subject alone.

[0426] In some embodiments, the subject receives 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 fewer doses of (ii)(a) or (ii)(b) than the subject would receive if (ii)(a) or (ii)(b) were administered alone.

[0427] In some embodiments, the pharmaceutical composition of (i) is co-formulated with the pharmaceutical composition of (ii).

[0428] In some embodiments, the pharmaceutical composition of (i) is formulated separately from the pharmaceutical composition of (ii).

[0429] In some embodiments, the pharmaceutical composition of (i) is administered separately from the pharmaceutical composition of (ii).

[0430] Provided herein is a method for treating or preventing viral infection or treating a respiratory disease or condition associated with viral infection, comprising administering to a subject in need thereof: (i) a pharmaceutical composition comprising: (a) a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); or (b) a polynucleotide encoding a polypeptide comprising at least two of the following: a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a pharmaceutical composition comprising: (a) a polypeptide having an amino acid sequence of a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; (b) a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; or a 2019 SARS-CoV comprising (ii)(a) or (ii)(b). 2. A spike protein pharmaceutical composition; wherein the dose of (i)(a) or (i)(b) received by the subject is lower than the dose of (i)(a) or (i)(b) administered to the subject alone.

[0431] Provided herein is a method for treating or preventing viral infection or treating a respiratory disease or condition associated with viral infection, comprising administering to a subject in need thereof: (i) a pharmaceutical composition comprising: (a) a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); or (b) a polynucleotide encoding a polypeptide comprising at least two of the following: a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a pharmaceutical composition comprising: (a) a polypeptide having an amino acid sequence of a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; (b) a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; or a 2019 SARS-CoV comprising (ii)(a) or (ii)(b). 2. A spike protein pharmaceutical composition; wherein the number of doses received by the subject of (i)(a) or (i)(b) is less than the number of doses of (i)(a) or (i)(b) administered to the subject alone.

[0432] In some embodiments, the subject receives a dose of (i)(a) or (i)(b) that is at least 1.1, 1, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100-fold lower than the dose of (i)(a) or (i)(b) administered to the subject alone.

[0433] In some embodiments, the subject receives 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 fewer doses of (i)(a) or (i)(b) than the number of doses of (i)(a) or (i)(b) administered to the subject alone.

[0434] In some embodiments, the pharmaceutical composition of (i) is co-formulated with the pharmaceutical composition of (ii).

[0435] In some embodiments, the pharmaceutical composition of (i) is formulated separately from the pharmaceutical composition of (ii).

[0436] In some embodiments, the pharmaceutical composition of (i) is administered separately from the pharmaceutical composition of (ii).

[0437] In some embodiments, the pharmaceutical composition is a co-formulation.

[0438] In some embodiments, the first pharmaceutical composition is administered together with or on the same day as the second pharmaceutical composition.

[0439] In some embodiments, the first pharmaceutical composition and the second pharmaceutical composition are administered simultaneously.

[0440] In some embodiments, the first pharmaceutical composition is administered at a first location on the subject and the second pharmaceutical composition is administered at a second location on the subject that is different from the first location.

[0441] In some embodiments, the first location is at an appendage of the subject and the second location is at an opposite appendage of the subject,

[0442] In some embodiments, the first appendage is an arm and the second appendage is an arm.

[0443] In some embodiments, the first pharmaceutical composition and the second pharmaceutical composition are administered to the same site on the subject.

[0444] In some embodiments, the pharmaceutical composition is administered at a first time point and a second time point, wherein the second time point is at least about, at most about, or about 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, or 36 days after the first time point; and at least about, at most about, or about 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, or at least about, at most about, or about 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, or 36 months after the first time point.

[0445] In some embodiments, the pharmaceutical composition is administered at a third time point, wherein the third time point is at least about, at most about, or about 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, or 36 days after the second time point; or at least about, at most about, or about 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, or at least about, at most about, or about 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, or 36 months after the second time point.

[0446] In some embodiments, the third time point is at least about, at most about, or about 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 50 days after the first time point; or at least about, at most about, or about 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, or at least about, at most about, or about 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, or 36 months after the first time point.

[0447] In some embodiments, the first pharmaceutical composition is administered at a first time point and a second time point, wherein the second time point is at least about, at most about, or about 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, or 36 days after the first time point; and at least about, at most about, or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or at least about, at most about, or about 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, or 36 months after the first time point.

[0448] In some embodiments, the first pharmaceutical composition is administered at a third time point, wherein the third time point is at least about, at most about, or about 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, or 36 days after the second time point; and at least about, at most about, or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or at least about, at most about, or about 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, or 36 months after the second time point.

[0449] In some embodiments, the third time point is at least about, at most about, or about 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 50 days after the first time point; or at least about, at most about, or about 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, or at least about, at most about, or about 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, or 36 months after the first time point.

[0450] In some embodiments, the second pharmaceutical composition is administered at a first time point.

[0451] In some embodiments, the second pharmaceutical composition is administered at a second time point.

[0452] In some embodiments, the second pharmaceutical composition is administered at a third time point.

[0453] In some embodiments, the patient is at least about, at most about, or about 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, or 36 days after the first time point; at least about, at most about, or about 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, or at least about, at most about, or about 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, or 36 months after the first time point.

[0454] In some embodiments, the patient is at least about, at most about, or about 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, or 36 days after the second time point; or at least about, at most about, or about 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 or at least about, at most about, or about 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, or 36 months after the second time point.

[0455] Provided herein is a method for treating or preventing viral infection or treating respiratory diseases or conditions associated with viral infection, comprising administering to a subject in need thereof: (i) a pharmaceutical composition comprising: (a) a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); or (b) a polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); wherein the pharmaceutical composition is administered at a first time point and a second time point, wherein the second time point is at least about 2 days after the first time point.

[0456] In some embodiments, the pharmaceutical composition is administered at a third time point, wherein the third time point is at least about 2 days after the second time point.

[0457] In some embodiments, the second time point is at least about 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, or 35 days after the first time point, and the second time point is at least about 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, or 35 weeks after the first time point, or at least about 1, 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, or 35 months after the first time point.

[0458] In some embodiments, the second time point is at most about 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, or 35 days after the first time point, and the second time point is at most about 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, or 35 weeks after the first time point, or up to about 1, 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, or 35 months after the first time point.

[0459] In some embodiments, the second time point is about 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, or 35 days after the first time point, and the second time point is about 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, or 35 days after the first time point. 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35 weeks, or about 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, or 35 months after the first time point.

[0460] In some embodiments, the third time point is at least about 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, or 35 days after the second time point. 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35 weeks after the second time point, or at least about 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, or 35 months after the second time point.

[0461] In some embodiments, the third time point is at most about 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, or 35 days after the second time point, and the third time point is at most about 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, or 35 weeks, or up to about 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, or 35 months after the second time point.

[0462] In some embodiments, the third time point is about 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, or 35 days after the second time point. 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35 weeks, or about 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, or 35 months after the second time point.

[0463] In some embodiments, the third time point is at least about 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, or 36 days after the first time point, and the third time point is at least about 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 or 35 weeks after the first time point, or at least about 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 or 35 months after the first time point.

[0464] In some embodiments, the third time point is at most about 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, or 36 days after the first time point, and the third time point is at most about 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, or 35 weeks after the first time point, or up to about 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, or 35 months after the first time point.

[0465] In some embodiments, the third time point is about 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, or 36 days after the first time point. 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35 weeks, or about 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, or 35 months after the first time point.

[0466] In some embodiments, the method further comprises administering to the subject: (ii)(a) a polypeptide having the amino acid sequence of a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; (b) a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; or a 2019 SARS-CoV 2 spike protein pharmaceutical composition comprising (ii)(a) or (ii)(b).

[0467] In some embodiments, the subject is immunodeficient.

[0468] In some embodiments, the subject has B cell immunodeficiency.

[0469] In some embodiments, the pharmaceutical composition is administered prophylactically.

[0470] Provided herein is a pharmaceutical composition comprising: (i) a recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a recombinant polynucleotide encoding the 2019 SARS-CoV 2 spike protein or a variant or fragment thereof.

[0471] In some embodiments, the ratio (eg, mass ratio) of (i):(ii) is 20:1 to 1:20.

[0472] In some embodiments, the ratio (e.g., mass ratio) of (i):(ii) is less than 20:1, 30:1, 40:1, 50:1, 60:1, 70:1, 80:1, 90:1, or 100:1.

[0473] In some embodiments, the ratio (e.g., mass ratio) of (i):(ii) is greater than 1:20, 1:30, 1:40, 1:50, 1:60, 1:70, 1:80, 1:90, or 1:100.

[0474] Provided herein is a composition comprising: (i) a first pharmaceutical composition comprising a first recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a second pharmaceutical composition comprising a second recombinant polynucleotide encoding the 2019 SARS-CoV 2 spike protein or a variant or fragment thereof.

[0475] In some embodiments, the ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is 1:50 to 50:1.

[0476] In some embodiments, the ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:25 to 25:1.

[0477] In some embodiments, the ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:10 to 10:1.

[0478] In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:10, 1:9, 1:8, 1:7, 1:6, 1:5, 1:4, 1:3, 1:2, 1:1, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 1:9.5, 1:8.5, 1:7.5, 1:6.5, 1:5.5, 1:4.5, 1:3.5, 1:2.5, 1:1.5, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 1:9.5, 1:8.5, 1:7.5, 1:6.5, 1:5.5, 1:4.5, 1:3.5, 1:2.5, 1:1.5, 2:1, 3:1, 4:1, 5:1 .5:1, 6.5:1, 7.5:1, 8.5:1, 9.5:1, 2:9, 2:8, 2:7, 2:6, 2:5, 2:4, 2:3, 3:2, 4:2, 5:2, 6:2, 7:2, 8:2, 9:2, 3:8, 3:7, 3:5, 3:4, 4:3, 5:3, 7:3, 8:3, 4:9, 4:7, 4:5, 5:4, 7:4, 9:4, 5:9, 5:8, 5:7, 5:6, 6:5, 7:5, 8:5, 9:5, 6:7, 7:6, 7:8, 8:7, 8:9, or 9:8.

[0479] Provided herein is a pharmaceutical composition comprising: (i) a first recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a second recombinant polynucleotide encoding the 2019 SARS-CoV2 spike protein or a variant or fragment thereof.

[0480] In some embodiments, the pharmaceutical composition comprises a nanoparticle, wherein the nanoparticle comprises the first recombinant polynucleotide and the second recombinant polynucleotide.

[0481] In some embodiments, the nanoparticles are present in the pharmaceutical composition at a dose of 100 ng to 500 micrograms.

[0482] In some embodiments, the nanoparticles are present in the pharmaceutical composition at a dose of 1 microgram to 100 micrograms.

[0483] In some embodiments, the nanoparticles are present in the pharmaceutical composition at a dose of 1 microgram to 30 micrograms, 5 micrograms to 40 micrograms, or 10 micrograms to 50 micrograms.

[0484] In some embodiments, the nanoparticles are present in the pharmaceutical composition at a dose of 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1,000 micrograms.

[0485] In some embodiments, the ratio (eg, mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:50 to 50:1.

[0486] In some embodiments, the ratio (eg, mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:25 to 25:1.

[0487] In some embodiments, the ratio (eg, mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:10 to 10:1.

[0488] In some embodiments, the ratio (e.g., mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:10, 1:9, 1:8, 1:7, 1:6, 1:5, 1:4, 1:3, 1:2, 1:1, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 1:9.5, 1:8.5, 1:7.5, 1:6.5, 1:5.5, 1:4.5, 1:3.5, 1:2.5, 1:1.5, 2.5:1, 3.5:1, 4.5:1, 5.5: 1, 6.5:1, 7.5:1, 8.5:1, 9.5:1, 2:9, 2:8, 2:7, 2:6, 2:5, 2:4, 2:3, 3:2, 4:2, 5:2, 6:2, 7:2, 8:2, 9:2, 3:8, 3:7, 3:5, 3:4, 4:3, 5:3, 7:3, 8:3, 4:9, 4:7, 4:5, 5:4, 7:4, 9:4, 5:9, 5:8, 5:7, 5:6, 6:5, 7:5, 8:5, 9:5, 6:7, 7:6, 7:8, 8:7, 8:9 or 9:8.

[0489] Provided herein is a composition comprising: (i) a first pharmaceutical composition comprising a recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a second pharmaceutical composition comprising a recombinant polynucleotide encoding the 2019 SARS-CoV 2 spike protein or a variant or fragment thereof.

[0490] In some embodiments, the first pharmaceutical composition comprises a first nanoparticle, wherein the first nanoparticle comprises a recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and wherein the second pharmaceutical composition comprises a second nanoparticle, wherein the second nanoparticle comprises a recombinant polynucleotide encoding the 2019 SARS-CoV 2 spike protein or a variant or fragment thereof.

[0491] In some embodiments, the ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:50 to 50:1.

[0492] In some embodiments, the ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:25 to 25:1.

[0493] In some embodiments, the ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:10 to 10:1.

[0494] In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:10, 1:9, 1:8, 1:7, 1:6, 1:5, 1:4, 1:3, 1:2, 1:1, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 1:9.5, 1:8.5, 1:7.5, 1:6.5, 1:5.5, 1:4.5, 1:3.5, 1:2.5, 1:1.5, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 1:9.5, 1:8.5, 1:7.5, 1:6.5, 1:5.5, 1:4.5, 1:3.5, 1:2.5, 1:1.5, 2:1, 3:1, 4:1, 5:1 .5:1, 6.5:1, 7.5:1, 8.5:1, 9.5:1, 2:9, 2:8, 2:7, 2:6, 2:5, 2:4, 2:3, 3:2, 4:2, 5:2, 6:2, 7:2, 8:2, 9:2, 3:8, 3:7, 3:5, 3:4, 4:3, 5:3, 7:3, 8:3, 4:9, 4:7, 4:5, 5:4, 7:4, 9:4, 5:9, 5:8, 5:7, 5:6, 6:5, 7:5, 8:5, 9:5, 6:7, 7:6, 7:8, 8:7, 8:9, or 9:8.

[0495] In some embodiments, the first nanoparticle is present in the first pharmaceutical composition at a dose of about 100 ng to 500 micrograms.

[0496] In some embodiments, the first nanoparticles are present in the first pharmaceutical composition at a dose of about 1 microgram to 100 micrograms.

[0497] In some embodiments, the first nanoparticles are present in the first pharmaceutical composition at a dose of about 1 microgram to 30 micrograms, 5 micrograms to 40 micrograms, or 10 micrograms to 50 micrograms.

[0498] In some embodiments, the first nanoparticles are present in the first pharmaceutical composition at a dose of about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1,000 micrograms.

[0499] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition at a dose of about 100 ng to 500 micrograms.

[0500] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition at a dose of about 1 microgram to 100 micrograms.

[0501] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition at a dose of about 1 microgram to 30 micrograms, 5 micrograms to 40 micrograms, or 10 micrograms to 50 micrograms.

[0502] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition at a dose of about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1,000 micrograms.

[0503] In some embodiments, the recombinant polynucleotide of (i) is present in the first pharmaceutical composition at a dose of about 50 ng to 250 micrograms.

[0504] In some embodiments, the recombinant polynucleotide of (i) is present in the first pharmaceutical composition at a dose of about 0.5 to 50 micrograms.

[0505] In some embodiments, the recombinant polynucleotide of (i) is present in the first pharmaceutical composition at a dose of about 0.5 micrograms to 15 micrograms, 2.5 micrograms to 20 micrograms, or 5 micrograms to 25 micrograms.

[0506] In some embodiments, the recombinant polynucleotide of (i) is present in the first pharmaceutical composition at a dose of about 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, or 500 micrograms.

[0507] In some embodiments, the recombinant polynucleotide of (ii) is present in the second pharmaceutical composition at a dose of about 50 ng to 250 micrograms.

[0508] In some embodiments, the recombinant polynucleotide of (ii) is present in the second pharmaceutical composition at a dose of about 0.5 to 50 micrograms.

[0509] In some embodiments, the recombinant polynucleotide in (ii) is present in the second pharmaceutical composition at a dose of about 0.5 micrograms to 15 micrograms, 2.5 micrograms to 20 micrograms, or 5 micrograms to 25 micrograms.

[0510] In some embodiments, the recombinant polynucleotide of (ii) is present in the second pharmaceutical composition at a dose of about 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, or 500 micrograms.

[0511] In some embodiments, the nanoparticles are lipid nanoparticles.

[0512] Provided herein is a composition comprising: (i) a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, (b) a sequence comprising an epitope sequence from membrane glycoprotein (M), and (c) a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); (ii) a polynucleotide encoding a polypeptide, wherein the polypeptide comprises at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, (b) a sequence comprising an epitope sequence from membrane glycoprotein (M), and (c) a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); (iii) a T cell receptor (TCR) or a T cell comprising a TCR, wherein the TCR binds to the epitope sequence of the polypeptide in complex with a corresponding HLA class I or class II molecule; (iv) an antigen presenting cell comprising (i) or (ii); or (v) an antibody or a B cell comprising an antibody, wherein the antibody binds to the epitope sequence of the polypeptide; and a pharmaceutically acceptable excipient.

[0513] In some embodiments, the polypeptide comprises (a) a sequence comprising an epitope sequence from ORF1ab, (b) a sequence comprising an epitope sequence from a membrane glycoprotein (M), and (c) a sequence comprising an epitope sequence from a nucleocapsid phosphoprotein (N). In some embodiments, the sequence comprising the epitope sequence from ORF1ab is at the C-terminus of the sequence comprising the epitope sequence from the nucleocapsid phosphoprotein (N). In some embodiments, the sequence comprising the epitope sequence from ORF1ab is at the N-terminus of the sequence comprising the epitope sequence from the membrane glycoprotein (M). In some embodiments, the sequence comprising the epitope sequence from the nucleocapsid phosphoprotein (N) is at the N-terminus of the sequence comprising the epitope sequence from the membrane glycoprotein (M).

[0514] In some embodiments, the polypeptide comprises at least two of: (a) a sequence comprising an epitope sequence from ORF1ab, (b) a sequence comprising an epitope sequence from membrane glycoprotein (M), and (c) a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N).

[0515] In some embodiments, the polypeptide comprises (a) 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more epitope sequences from ORF1ab, (b) a sequence comprising an epitope sequence from a membrane glycoprotein (M), and (c) a sequence comprising an epitope sequence from a nucleocapsid phosphoprotein (N).

[0516] In some embodiments, the epitope sequence from ORF1ab is an epitope sequence from a nonstructural protein. In some embodiments, the nonstructural protein is selected from the group consisting of NSP1, NSP2, NSP3, NSP4, and combinations thereof. In some embodiments, the polypeptide comprises a sequence comprising an epitope sequence from NSP1, a sequence comprising an epitope sequence from NSP2, a sequence comprising an epitope sequence from NSP3, and a sequence comprising an epitope sequence from NSP4.

[0517] In some embodiments, the epitope sequence from ORF1ab is selected from the group consisting of YLFDESGEFKL, YLFDESGEF, FGDDTVIEV, QLMCQPILL, TTDPSFLGRY, PTDNYITTY, PSFLGRY, AEAELAKNV, KTIQPRVEK, and any combination thereof.

[0518] In some embodiments, the epitope sequence from the nucleocapsid glycoprotein (N) is LLLDRLNQL. In some embodiments, the epitope sequence from the membrane phosphoprotein (M) is VATSRTLSY. In some embodiments, the polypeptide comprises an epitope sequence from the nucleocapsid glycoprotein (N), namely LLLDRLNQL, and an epitope sequence from the membrane phosphoprotein (M), namely VATSRTLSY.

[0519] In some embodiments, the polypeptide comprises (a) each of the following epitope sequences from ORF1ab: YLFDESGEFKL, YLFDESGEF, FGDDTVIEV, QLMCQPILL, TTDPSFLGRY, PTDNYITTY, PSFLGRY, AEAELAKNV, KTIQPRVEK; (b) an epitope sequence from nucleocapsid glycoprotein (N), i.e., LLLDRLNQL; and (c) an epitope sequence from membrane phosphoprotein (M), i.e., VATSRTLSY.

[0520] In some embodiments, the sequence comprising the epitope sequence from ORF1ab is selected from the group consisting of the following sequences or fragments thereof: MVTNNTFTLKVPHVGEIPVAYRKVLLKTIQPRVEKYLFDESGEFKLSEVGPEHSLAEYYIFFASFYY; MVTNNTFTLKVPHVGEIPVAYRKVLLKTIQPRVEKYLFDESGEFKLSEVGPEHSLAEY; APKEIIFLEGETLFGDDTVIEVAIILASFSAST; APKEIIFLEGETLFGDDTVIEV; HTTDPSFLGRYMSALFADDLNQLTGYHTDFSSEIIGYQLMCQPILLAEAELAKNVSLILGTVSWNL; TTDPSFLGRYMSALFADDLNQLTGYHTDFSSEIIGYQLMCQPILLAEAELAKNVSLILGTVSWNL; LLSAGIFGAITDVFYKENSYKVPTDNYITTY; and combinations thereof.

[0521] In some embodiments, the sequence comprising an epitope sequence from a membrane glycoprotein (M) is selected from the group consisting of the following sequences or fragments thereof: ADSNGTITVEELKKLLEQWNLVIGFLFLTWICLLQFAYANRNRFLYIIKLIFLWLLWPVTLACFVLAAVYRINWITGGIAIAMACLVGLMWLSYFIASFRLFARTRSMWSFNPETNILLNVPLHGTILTRPLLESELVIGAVILRGHLRIAGHHLGRCDIKDLPKEITVATSRTLSYYKLGASQRVAGDSG FAAYSRYRIGNYKLNTDHSSSSDNIALLVQ; FAYANRNRFLYIIKLIFLWLLWPVTLACFVLAAVYRINWITGGIAIAMACLVGLMWLSYFIASFRLF; LGRCDIKDLPKEITVATSR TLSYYKLGASQRVA; KLLEQWNLVIGF; NRNRFLYIIKLIFLWLLWPVTLACFVLAAVY; SELVIGAVILRGHLRIAGHHLGR; VATSRTLSYYKLGASQRV; GLMWLSYF; and combinations thereof.

[0522] In some embodiments, the sequence comprising an epitope sequence from the nucleocapsid phosphoprotein (N) is selected from the group consisting of the following sequences or fragments thereof: KDLSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGTTLPKGFYAEGSRGGSQASSRSSSRSRNSSRNSTPGSSRGTSPARMAGNGGDAALALLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDKKKK ADETQALPQRQKKQQTVTLLPAAADLDDFSKQLQQSMSSADSTQA;RMAGNGGDAALALLLLDRLNQLESKMSGKGQQQ;YKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFP;SPARMAGNGGDAA LALLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDK and combinations thereof.

[0523] In some embodiments, the polypeptide comprises one or more linker sequences. In some embodiments, the one or more linker sequences are selected from the group consisting of GGSGGGGSGG, GGSLGGGGSG. In some embodiments, the one or more linker sequences comprise a cleavage sequence. In some embodiments, the one or more cleavage sequences are selected from the group consisting of FRAC, KRCF, KKRY, ARMA, RRSG, MRAC, KMCG, ARCA, KKQG, YRSY, SFMN, FKAA, KRNG, YNSF, KKNG, RRRG, KRYS, and ARYA.

[0524] In some embodiments, the polypeptide comprises a transmembrane domain sequence. In some embodiments, the transmembrane sequence is at the C-terminus of a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N). In some embodiments, the transmembrane sequence is EQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT.

[0525] In some embodiments, the polypeptide comprises a SEC sequence. In some embodiments, the SEC sequence is at the N-terminus of a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N). In some embodiments, the SEC sequence is MFVFLVLLPLVSSQCVNLT.

[0526] In some embodiments, the composition comprises a polynucleotide encoding a polypeptide. In some embodiments, the polynucleotide is an mRNA. In some embodiments, the polynucleotide comprises a codon-optimized sequence for expression in humans.

[0527] In some embodiments, the polynucleotide comprises a dEarI-hAg sequence. In some embodiments, the dEarI-hAg sequence is ATTCTTCTGGTCCCCACAGACTCAGAGAGAACCC, optionally wherein each T is U.

[0528] In some embodiments, the polynucleotide comprises a Kozak sequence. In some embodiments, the Kozak sequence is GCCACC.

[0529] In some embodiments, the polynucleotide comprises an F element sequence. In some embodiments, the F element sequence is the 3UTR of an amino-terminal split enhancer (AES). In some embodiments, the F element sequence is CTGGTACTGCATGCACGCAATGCTAGCTGCCCCTTTCCCGTCCTGGGTACCCCGAGTCTCCCCCGACCTCGGGTCCCAGGTATGCTCCCACCTCCACCTGCCCCACTCACCACCTCTGCTAGTTCCAGACACCTCC, optionally wherein each T is U.

[0530] In some embodiments, the polynucleotide comprises an I element sequence. In some embodiments, the I element sequence is the 3'UTR of mitochondrial-encoded 12S rRNA (mtRNR1). In some embodiments, the I element sequence is CAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACACC, optionally wherein each T is U.

[0531] In some embodiments, the polynucleotide comprises a poly A sequence. In some embodiments, the poly A sequence is AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGCATATGACTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA, optionally wherein each T is U.

[0532] In some embodiments, each of the epitope sequences from ORF1ab, membrane glycoprotein, and nucleocapsid phosphoprotein is from 2019 SARS-CoV-2.

[0533] In some embodiments, one or more epitopes, or each epitope, elicits a T cell response.

[0534] In some embodiments, one or more epitopes, or each epitope, has been observed by mass spectrometry to be presented by an HLA molecule.

[0535] In some embodiments, the composition comprises (i) a polypeptide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% sequence identity to a sequence selected from the group consisting of: RSC1p1full, RS C2p1full, RS C3p1full, RS C4p1full, RS C5p1, RS C5p2, RS C5p2full, RSC6p1, RS C6p2, RS C6p2full, RS C7p1, RS C7p2, RS C7p2full, RS C7p4, RS C7p4full, RSC8p1, RS C8p2, and RS C8p2full; and (ii) a polynucleotide encoding a polypeptide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% sequence identity to a sequence selected from the group consisting of: RSC1p1full, RS C2p1full, RS C3p1full, RS C4p1full, RS C5p1, RS C5p2, RS C5p2full, or (iii) a polynucleotide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% sequence identity to a sequence selected from the group consisting of SEQ ID NO: RS C1n1, RS C2n1, RS C3n1, RS C4n1, RS C5n1, RS C6n1, RS C7n1, RS C8n1, RS C5n2, RS C6n2, RS C7n2, RS C8n2, RS C5n2full, RS C6n2full, RS C7n2full, RS C8n2full, RS C7n4, RS C7n4full.

[0536] Also provided herein is a pharmaceutical composition comprising any one of the compositions described herein.

[0537] Also provided herein is a pharmaceutical composition comprising: (i) a polypeptide comprising an epitope sequence of Table 1A, Table 1B, Table 1C, Table 2Ai, Table 2Aii, Table 2B and / or Table 16; (ii) a polynucleotide encoding the polypeptide; (iii) a T cell receptor (TCR) or a T cell comprising a TCR, wherein the TCR binds to the epitope sequence in complex with a corresponding HLA class I or class II molecule; (iv) an antigen presenting cell comprising (i) or (ii); or (v) an antibody or a B cell comprising the antibody, wherein the antibody binds to the epitope sequence; and a pharmaceutically acceptable excipient.

[0538] In some embodiments, the epitope sequence comprises one or more or each of the following: YLFDESGEFKL, YLFDESGEF, FGDDTVIEV, LLLDRLNQL, QLMCQPILL, TTDPSFLGRY, PTDNYITTY, PSFLGRY, AEAELAKNV, VATSRTLSY, and KTIQPRVEK. In some embodiments, the epitope sequence comprises one or more or each of the following: SAPPAQYEL, AVASKILGL, EYADVFHLY, DEFTPFDVV, VRIQPGQTF, SFRLFARTR, KFLPFQQF, VVQEGVLTA, RLDKVEAEV, FGADPIHSL, NYNYLYRLF, KYIKWPWYI, KWPWYIWLGF, LPFNDGVYF, QPTESIVRF, IPFAMQMAY, YLQPRTFLL, and RLQSLQTYV.

[0539] In some embodiments, the epitope sequence is from the orf1ab protein. In some embodiments, the epitope sequence is from the orf1a protein. In some embodiments, the epitope sequence is from the surface glycoprotein (S) or its shifted reading frame. In some embodiments, the epitope sequence is from the nucleocapsid phosphoprotein (N). In some embodiments, the epitope sequence is from the ORF3a protein. In some embodiments, the epitope sequence is from the membrane glycoprotein (M). In some embodiments, the epitope sequence is from the ORF7a protein. In some embodiments, the epitope sequence is from the ORF8 protein. In some embodiments, the epitope sequence is from the envelope protein (E). In some embodiments, the epitope sequence is from the ORF6 protein. In some embodiments, the epitope sequence is from the ORF7b protein. In some embodiments, the epitope sequence is from the ORF10 protein. In some embodiments, the epitope sequence is from the ORF9b protein.

[0540] Also provided herein is a pharmaceutical composition comprising: a polypeptide having an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% identical to the sequence of any one of the sequences depicted in Column 2 of Table 11, Column 2 of Table 12 or Column 3 of Table 15; or a recombinant polynucleotide encoding a polypeptide having an amino acid sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% identical to the sequence of any one of the sequences depicted in Column 2 of Table 11, Column 2 of Table 12 or Column 3 of Table 15.

[0541] In some embodiments, the pharmaceutical composition comprises: a polypeptide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% sequence identity to a sequence selected from the group consisting of: RSC1p1full, RS C2p1full, RS C3p1full, RS C4p1full, RS C5p1, RS C5p2, RS C5p2full, RSC6p1, RS C6p2, RS C6p2full, RS C7p1, RS C7p2, RS C7p2full, RS C7p4, RS C7p4full, RSC8p1, RS C8p2, and RS C8p2full; or a polynucleotide encoding a polypeptide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% sequence identity to a sequence selected from the group consisting of: RSC1p1full, RS C2p1full, RS C3p1full, RS C4p1full, RS C5p1, RS C5p2, RS C5p2full, C2p1full, RS C3p1full, RS C4p1full, RS C5p1, RS C5p2, RS C5p2full, RSC6p1, RS C6p2, RS C6p2full, RS C7p1, RS C7p2, RS C7p2full, RS C7p4, RS C7p4full, RSC8p1, RS C8p2, and RS C8p2full. In some embodiments, the pharmaceutical composition comprises a polynucleotide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% sequence identity to a sequence selected from the group consisting of SEQ ID NO: RS C1n1, RS C2n1, RS C3n1, RS C4n1, RS C5n1, RS C6n1, RSC7n1, RS C8n1, RS C5n2, RS C6n2, RS C7n2, RS C8n2, RS C5n2full, RS C6n2full, RSC7n2full, RS C8n2full, RS C7n4, and RS C7n4full.

[0542] In some embodiments, the polynucleotide is mRNA.

[0543] In some embodiments, the pharmaceutical composition further comprises one or more lipid components. In some embodiments, one or more lipids comprise lipid nanoparticles (LNPs). In some embodiments, LNP encapsulates recombinant polynucleotide constructs.

[0544] In some embodiments, the polypeptide is synthetic. In some embodiments, the polypeptide is recombinant.

[0545] In some embodiments, the polypeptide is 8-1000 amino acids in length.

[0546] In some embodiments, the epitope sequence is expressed with a K of 1000 nM or less. D Binds or is predicted to bind to HLA class I or class II molecules. In some embodiments, the epitope sequence has a K of 500 nM or less D Binds or is predicted to bind to an HLA class I or class II molecule.

[0547] In some embodiments, the epitope sequence comprises the sequence of a viral protein expressed by a virus-infected cell of the subject.

[0548] Also provided herein is a method for treating or preventing viral infection or treating respiratory diseases or disorders associated with viral infection, comprising administering the pharmaceutical composition described herein to a subject in need thereof.

[0549] In some embodiments, the virus is a coronavirus. In some embodiments, the virus is 2019SARS-CoV2. In some embodiments, at the time of administration, the HLA molecules expressed by the subject are unknown. In some embodiments, the ability of the virus to avoid escaping recognition by the immune system of a subject to which a pharmaceutical composition (containing an epitope from a single protein or an epitope from a protein less than that in the pharmaceutical composition described herein) has been administered is compared to the ability of the virus to avoid escaping recognition by the immune system of the subject is lower. In some embodiments, the subject expresses an HLA molecule encoded by any one of the HLA alleles of Table 1A, Table 1B, Table 1C, Table 2Ai or Table 2Aii, Table 2B or Table 16, and the epitope sequence is an epitope sequence that matches the HLA allele.

[0550] In some embodiments, the epitope sequence includes one or more or each of the following: SAPPAQYEL, AVASKILGL, EYADVFHLY, DEFTPFDVV, VRIQPGQTF, SFRLFARTR, KFLPFQQF, VVQEGVLTA, RLDKVEAEV, and FGADPIHSL.

[0551] Also provided herein is a method of treating or preventing 2019 SARS-CoV 2 infection in a subject in need thereof, comprising administering to the subject a pharmaceutical composition described herein.

[0552] In some embodiments, a pharmaceutical composition is administered in addition to one or more therapeutic agents for 2019 SARS-CoV 2 viral infection in a subject. In some embodiments, the pharmaceutical composition is administered in combination with: (a) a polypeptide having the amino acid sequence of a 2019 SARS-CoV 2 spike protein, or a variant or fragment thereof; (b) a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein, or a variant or fragment thereof; or a 2019 SARS-CoV 2 spike protein pharmaceutical composition comprising (a) or (b). In some embodiments, the 2019 SARS-CoV 2 spike protein, or a variant or fragment thereof, is a SARS-CoV-2 spike protein, or a fragment thereof.

[0553] In some embodiments, the pharmaceutical composition is administered 1-10 weeks after the first administration of the 2019 SARS-CoV 2 spike protein pharmaceutical composition. In some embodiments, the pharmaceutical composition is administered 1-6 weeks, 1-6 months, or 1-2 years after the first administration of the 2019 SARS-CoV 2 spike protein pharmaceutical composition. In some embodiments, the pharmaceutical composition is administered on the same day as or concurrently with the administration of the 2019 SARS-CoV 2 spike protein pharmaceutical composition. In some embodiments, the pharmaceutical composition is co-formulated with: a polypeptide having the amino acid sequence of the 2019 SARS-CoV 2 spike protein, or a variant or fragment thereof; or a recombinant polynucleotide encoding the 2019 SARS-CoV 2 spike protein, or a variant or fragment thereof. In some embodiments, the pharmaceutical composition is administered prior to administration of the 2019 SARS-CoV 2 spike protein pharmaceutical composition, such as 2-10 weeks prior to administration of the 2019 SARS-CoV 2 spike protein pharmaceutical composition. In some embodiments, the pharmaceutical composition is administered prophylactically. In some embodiments, the pharmaceutical composition is administered once every 1, 2, 3, 4, 5, 6, or more weeks; or once every 1-7, 7-14, 14-21, 21-28, or 28-35 days; or once every 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, or 35 days.

[0554] Also provided herein is the use of the composition described herein for preparing a therapeutic agent for treating or preventing respiratory viral infection caused by the 2019 SARS CoV-2 virus.

[0555] Also provided herein are compositions described herein or pharmaceutical compositions described herein for use as medicaments.

[0556] Also provided herein is a composition described herein or a pharmaceutical composition described herein for treating or preventing respiratory viral infection caused by the 2019 SARS CoV-2 virus.

[0557] Provided herein are antigenic peptides comprising an epitope sequence from Table 1A, Table 1B, Table 1C, Table 2Ai, Table 2Aii, or Table 2B. Also provided herein are polynucleotides encoding antigenic peptides and antigenic peptides comprising an epitope sequence from Table 1A, Table 1B, Table 1C, Table 2Ai, Table 2Aii, or Table 2B. The antigenic peptides and / or polynucleotides can be recombinant. The antigenic peptides and / or polynucleotides can be isolated or purified. The antigenic peptides can be synthesized or expressed from polynucleotides.

[0558] Also provided herein is an antibody or a B cell comprising an antibody that binds to an antigenic peptide comprising an epitope sequence from Table 1A, Table 1B, Table 1C, Table 2Ai, Table 2Aii, or Table 2B.

[0559] Also provided herein is a T cell receptor (TCR) or a T cell comprising a TCR that binds to an epitope sequence from Table 1A or Table 1B and compounded with a corresponding MHC class I molecule according to Table 1A or Table 1B. For example, a TCR can bind to an epitope sequence compounded with a corresponding MHC class I molecule from column 2 (Group 1) of Table 1A and column 3 (Group 1) in the same row of Table 1A. For example, a TCR can bind to an epitope sequence compounded with a corresponding MHC class I molecule from column 4 (Group 2) of Table 1A and column 5 (Group 2) in the same row of Table 1A. For example, a TCR can bind to an epitope sequence compounded with a corresponding MHC class I molecule from column 6 (Group 3) of Table 1A and column 7 (Group 3) in the same row of Table 1A. For example, the TCR may bind to an epitope sequence from column 2 (Group 1) of Table 1B in complex with the corresponding MHC class I molecule from column 3 (Group 1) in the same row of Table 1B. For example, the TCR may bind to an epitope sequence from column 4 (Group 2) of Table 1B in complex with the corresponding MHC class I molecule from column 5 (Group 2) in the same row of Table 1B.

[0560] Also provided herein is a T cell receptor (TCR) or a T cell comprising a TCR, the TCR being combined with an epitope sequence from Table 2Ai or Table 2Aii and compounded with the corresponding MHC class II molecules according to Table 2Ai or Table 2Aii. For example, the TCR can be combined with an epitope sequence compounded with the corresponding MHC class II molecules from the 2nd column (Group 1) of Table 2Ai and the 3rd column (Group 1) in the same row of Table 2Ai. For example, the TCR can be combined with an epitope sequence compounded with the corresponding MHC class II molecules from the 4th column (Group 2) of Table 2Ai and the 5th column (Group 2) in the same row of Table 2Ai. Similarly, the TCR can be combined with an epitope sequence compounded with the corresponding MHC class II molecules from the left column of Table 2Aii and the right column of Table 2Aii.

[0561] Provided herein is a method for treating or preventing a viral infection in a subject in need thereof, comprising administering to the subject an antigenic peptide comprising an epitope sequence from Table 1A, Table 1B, Table 1C, Table 2Ai, Table 2Aii, or Table 2B. Also provided herein is a method for treating or preventing a viral infection in a subject in need thereof, comprising administering to the subject a polynucleotide encoding an antigenic peptide comprising an epitope sequence from Table 1A, Table 1B, Table 1C, Table 2Ai, Table 2Aii, or Table 2B and an antigenic peptide.

[0562] Also provided herein is a method of treating or preventing a viral infection in a subject in need thereof, comprising administering to the subject an antibody or a B cell comprising an antibody that binds to an antigenic peptide comprising an epitope sequence from Table 1A, Table 1B, Table 1C, Table 2Ai, Table 2Aii, or Table 2B.

[0563] Also provided herein is a method of treating or preventing a viral infection in a subject in need thereof, comprising administering to the subject a T cell receptor (TCR) or a T cell comprising a TCR that binds an epitope sequence from Table 1A or Table 1B and complexed with a corresponding MHC class I molecule according to Table 1A or Table 1B.

[0564] For example, the method may comprise administering to a subject a TCR or a T cell comprising a TCR that binds to an epitope sequence from column 2 (Group 1) of Table 1A and complexed with a corresponding MHC class I molecule from column 3 (Group 1) in the same row of Table 1A. For example, the method may comprise administering to a subject a TCR or a T cell comprising a TCR that binds to an epitope sequence from column 2 (Group 1) of Table 1A and complexed with a corresponding MHC class I molecule from column 3 (Group 1) in the same row of Table 1A, the subject expressing the corresponding MHC class I molecule from column 3 (Group 1). For example, the method may comprise administering to a subject a TCR or a T cell comprising a TCR that binds to an epitope sequence from column 4 (Group 2) of Table 1A and complexed with a corresponding MHC class I molecule from column 5 (Group 2) in the same row of Table 1A. For example, the method may comprise administering to a subject a TCR or a T cell comprising a TCR that binds to an epitope sequence from column 4 (Group 2) of Table 1A and complexed with a corresponding MHC class I molecule from column 5 (Group 2) in the same row of Table 1A, the subject expressing the corresponding MHC class I molecule from column 5 (Group 2). For example, the method may comprise administering to a subject a TCR or a T cell comprising a TCR that binds to an epitope sequence from column 6 (Group 3) of Table 1A and complexed with a corresponding MHC class I molecule from column 7 (Group 3) in the same row of Table 1A. For example, the method may comprise administering to a subject a TCR or a T cell comprising a TCR that binds to an epitope sequence from column 6 (Group 3) of Table 1A and complexed with a corresponding MHC class I molecule from column 7 (Group 3) in the same row of Table 1A, the subject expressing the corresponding MHC class I molecule from column 7 (Group 3).

[0565] For example, the method may comprise administering to a subject a TCR or a T cell comprising a TCR that binds to an epitope sequence from column 2 (Group 1) of Table 1B and complexed with a corresponding MHC class I molecule from column 3 (Group 1) in the same row of Table 1B. For example, the method may comprise administering to a subject a TCR or a T cell comprising a TCR that binds to an epitope sequence from column 2 (Group 1) of Table 1B and complexed with a corresponding MHC class I molecule from column 3 (Group 1) in the same row of Table 1B, the subject expressing the corresponding MHC class I molecule from column 3 (Group 1). For example, the method may comprise administering to a subject a TCR or a T cell comprising a TCR that binds to an epitope sequence from column 4 (Group 2) of Table 1B and complexed with a corresponding MHC class I molecule from column 5 (Group 2) in the same row of Table 1B. For example, the method can comprise administering to a subject a TCR or a T cell comprising a TCR that binds to an epitope sequence from column 4 (Group 2) of Table 1B and complexed with a corresponding MHC class I molecule from column 5 (Group 2) in the same row of Table 1B, wherein the subject expresses the corresponding MHC class I molecule from column 5 (Group 2).

[0566] For example, the method may comprise administering to a subject a TCR or a T cell comprising a TCR that binds to an epitope sequence from column 2 (Group 1) of Table 2Ai and complexed with a corresponding MHC class II molecule from column 3 (Group 1) in the same row of Table 2Ai. For example, the method may comprise administering to a subject a TCR or a T cell comprising a TCR that binds to an epitope sequence from column 2 (Group 1) of Table 2Ai and complexed with a corresponding MHC class II molecule from column 3 (Group 1) in the same row of Table 2Ai, the subject expressing the corresponding MHC class II molecule from column 3 (Group 1). For example, the method may comprise administering to a subject a TCR or a T cell comprising a TCR that binds to an epitope sequence from column 4 (Group 2) of Table 2Ai and complexed with a corresponding MHC class II molecule from column 5 (Group 2) in the same row of Table 2Ai. For example, the method may comprise administering to a subject a TCR or a T cell comprising a TCR that binds to an epitope sequence from column 4 (Group 2) of Table 2Ai and complexed with a corresponding MHC class II molecule from column 5 (Group 2) in the same row of Table 2Ai, wherein the subject expresses the corresponding MHC class II molecule from column 5 (Group 2). For example, the method may comprise administering to a subject a TCR or a T cell comprising a TCR that binds to an epitope sequence from the left column of Table 2Aii and complexed with a corresponding MHC class II molecule from the right column in the same row of Table 2Aii.

[0567] In one embodiment, the antigenic peptide is a viral antigen. In another embodiment, the antigenic peptide is an unmutated overexpressed antigen. In some embodiments, the viral antigen is derived from publicly available information about viral genetic information. In some embodiments, the viral antigen is derived from analysis of the viral genome to predict suitable epitopes for T cell activation. In some embodiments, the viral antigen is derived from analysis of viral genome sequences in an MHC-peptide presentation prediction algorithm implemented in a computer processor. In some embodiments, the viral antigen is derived from analysis of viral sequences in an MHC-peptide presentation prediction algorithm implemented in a computer processor that has been trained by machine learning software, the algorithm predicting the likelihood of an epitope being bound and presented by an MHC class I or MHC class II antigen. In some embodiments, the MHC-peptide presentation predictor is neonmc2.

[0568] In some embodiments, the MHC-peptide presentation prediction algorithm or MHC-peptide presentation predictor is NetMHCpan or NetMHCIIpan, and in addition, further analysis is performed in the MHC-peptide presentation predictor NetMHCpan or NetMHCIIpan for comparison. In some embodiments, a skilled artisan can use a hidden Markov model approach to perform MHC-peptide presentation prediction. In some embodiments, the peptide prediction model MARIA can be utilized. In some embodiments, the MHC-peptide presentation prediction algorithm or MHC-peptide presentation predictor used is not NetMHCpan or NetMHCIIpan. In some embodiments, viral sequences are analyzed in an MHC-peptide presentation prediction algorithm implemented in a computer processor, wherein the MHC-peptide presentation predictor is neonmhc1 or neonmhc2, which refer to class I and class II binding predictions, respectively. In some embodiments, the MHC-peptide presentation predictor model is RECON, which provides high-quality MHC-peptide presentation predictions based on expression, processing, and binding capacity.

[0569] In one aspect, the present invention provides a method for treating a viral disease caused by a coronavirus in a subject, comprising administering to the subject a composition comprising one or more viral peptide antigens, wherein the viral peptide antigens are predicted to bind to the subject's MHC class I or MHC class II peptides and are predicted to be presented by antigen-presenting cells to the subject's T cells, thereby triggering an antiviral response in the subject. In some embodiments, the viral antigens are derived from an analysis of viral genomic sequences in an MHC-peptide presentation prediction algorithm implemented in a computer processor. In some embodiments, the viral antigens are derived from an analysis of viral sequences in an MHC-peptide presentation prediction algorithm that has been trained by machine learning software and implemented in a computer processor, the algorithm predicting the likelihood of an epitope being bound and presented by an MHC class I or MHC class II antigen. In some embodiments, the MHC-peptide presentation predictor is neonmc2. In some embodiments, the method further comprises analyzing a nucleic acid sequence derived from a viral genome in an MHC-peptide presentation prediction model, the MHC-peptide presentation prediction model comprising an algorithm implemented in a computer processor that has been trained by machine learning software, wherein the MHC-peptide presentation prediction model predicts the likelihood that an epitope encoded by the viral genome will be bound and presented by an MHC class I or MHC class II antigen. In some embodiments, the method further comprises analyzing a biological sample from the subject to identify MHC class I and MHC class II repertoires, wherein the analysis comprises analysis by genome or whole exome sequencing or by analyzing proteins encoded by HLA genes. In some embodiments, the method further comprises matching epitopes predicted by the MHC-peptide presentation prediction model to have high affinity for MHC class I or MHC class II peptides encoded by the subject's HLA genes, and selecting one or more peptides that are predicted to bind to MHC peptides encoded by the subject's HLA genes with an affinity ranked by the MHC-peptide presentation prediction model. In some embodiments, the selected one or more peptides have been predicted to bind to MHC peptides encoded by the subject's HLA genes with an affinity of at least 1000 nM. In some embodiments, the selected one or more peptides have been predicted to bind to MHC class I peptides encoded by the subject's HLA genes with an affinity of at least 500 nM. In some embodiments, the selected one or more peptides have been predicted to bind to MHC class II peptides encoded by the subject's HLA genes with an affinity of at least 1000 nM.

[0570] In some embodiments, the MHC-peptide presentation prediction model is programmed to provide a ranking order of the likelihood of a particular epitope or antigenic peptide binding to an HLA allele that presents the peptide to the T cell receptor in descending order. In some embodiments, the epitope sequence with the highest likelihood of binding and presented by the HLA is selected for the preparation of a therapeutic agent. In some embodiments, the choice of HLA may be limited to the HLA expressed in the subject. In some embodiments, the selection of HLA may be based on the prevalence of the allele in the population (e.g., a higher prevalence). In some embodiments, an epitope may be selected for the preparation of a therapeutic agent based on the higher likelihood that the peptide (epitope) binds to and is presented by an HLA allele (e.g., a target HLA allele). In some embodiments, the % ranking value can be determined by evaluating the percentile of the query peptide score for a particular allele compared to a set of fixed reference peptides (different sets of reference peptides are used for class I and class II). In some embodiments, the top 10% epitopes with the highest likelihood of binding to the HLA allele can be selected. In some embodiments, epitopes in the top 2% with the highest likelihood of binding to an HLA allele may be selected. In some embodiments, epitopes in the top 5% with the highest likelihood of binding to an HLA allele may be selected. In some embodiments, epitopes in the top 8% with the highest likelihood of binding to an HLA allele may be selected. In some embodiments, epitopes in the top 1% with the highest likelihood of binding to an HLA allele may be selected. In some embodiments, epitopes in the top 0.5% with the highest likelihood of binding to an HLA allele may be selected. In some embodiments, epitopes in the top 0.1% with the highest likelihood of binding to an HLA allele may be selected. In some embodiments, epitopes in the top 0.01% with the highest likelihood of binding to an HLA allele may be selected. In some embodiments, the choice of cutoff value may depend on the availability and number of epitopes predicted to have a high likelihood of binding to an HLA allele, as determined by a predictive model.

[0571] In some embodiments, the subject may be infected by a virus. In some embodiments, the subject may be at risk of being infected by a virus. In some embodiments, the virus is a coronavirus. In some embodiments, the coronavirus is selected from SARS virus, MERS coronavirus or 2019SARS CoV-2 virus. In some embodiments, one or more viral peptide antigens include peptides comprising at least 8 consecutive amino acids of a sequence in Table 1A, Table 1B, Table 1C, Table 2Ai, Table 2Aii, Table 2B, Table 9, Table 10, Table 11, Table 12, Table 14A, Table 14B, Table 15 or Table 16. In some embodiments, one or more viral peptide antigens include peptides comprising at least 7 consecutive amino acids of a sequence in Table 1A, Table 1B, Table 1C, Table 2Ai, Table 2Aii, Table 2B, Table 9, Table 10, Table 11, Table 12, Table 14A, Table 14B, Table 15 or Table 16. In some embodiments, the one or more viral peptide antigens include a peptide comprising at least 6 consecutive amino acids of a sequence in Table 1A, Table 1B, Table 1C, Table 2Ai, Table 2Aii, Table 2B, Table 9, Table 10, Table 11, Table 12, Table 14A, Table 14B, Table 15, or Table 16.

[0572] In one embodiment, the length of the antigenic peptide is between about 5 to about 50 amino acids. In another embodiment, the length of the antigenic peptide is between about 15 to about 35 amino acids. In another embodiment, the length of the antigenic peptide is about 15 amino acids or shorter. In another embodiment, the length of the antigenic peptide is between about 8 and about 11 amino acids. In another embodiment, the length of the antigenic peptide is 9 or 10 amino acids. In one embodiment, the antigenic peptide is in conjunction with major histocompatibility complex (MHC) class I. In another embodiment, the antigenic peptide is in conjunction with MHC class I with a binding affinity less than about 500nM.

[0573] In one embodiment, the length of the antigenic peptide is about 30 amino acids or shorter. In another embodiment, the length of the antigenic peptide is between about 6 and about 25 amino acids. In another embodiment, the length of the antigenic peptide is between about 15 and about 24 amino acids. In another embodiment, the length of the antigenic peptide is between about 9 and about 15 amino acids. In one embodiment, the antigenic peptide is in conjunction with MHC II class. In another embodiment, the antigenic peptide is in conjunction with MHC II class with a binding affinity less than about 1000nM.

[0574] In one embodiment, the antigenic peptide further comprises flanking amino acids. In another embodiment, the flanking amino acids are not natural flanking amino acids. In one embodiment, the antigenic peptide is connected to at least a second antigenic peptide. In another embodiment, the peptide is connected using a polyglycine or polyserine linker. In another embodiment, the second antigenic peptide binds to MHC class I or class II with a binding affinity less than about 1000nM. In another embodiment, the second antigenic peptide binds to MHC class I or class II with a binding affinity less than about 500nM. In another embodiment, both epitopes are combined with human leukocyte antigen (HLA)-A, HLA-B, HLA-C, HLA-DP, HLA-DQ or HLA-DR. In another embodiment, the antigenic peptide binds to class I HLA and the second antigenic peptide binds to class II HLA. In another embodiment, the antigenic peptide binds to class II HLA and the second antigenic peptide binds to class I HLA.

[0575] In one embodiment, the antigenic peptide further comprises modifications that increase half-life in vivo, cell targeting, antigen uptake, antigen processing, MHC affinity, MHC stability, or antigen presentation. In another embodiment, modification is conjugation to a carrier protein, conjugation to a part, conjugation to an antibody, PEGylation, polysialylation HESylation, recombinant PEG mimics, Fc fusions, albumin fusions, nanoparticle attachment, nanoparticle encapsulation, cholesterol fusions, iron fusions, acylations, amidations, glycosylation, side chain oxidation, phosphorylation, biotinylation, addition of surfactants, addition of amino acid mimics, or addition of non-natural amino acids, such as synthetic amino acids or f-moc amino acids, D-amino acids, N-methyl amino acids. In one embodiment, the targeted cell is an antigen presenting cell. In another embodiment, the antigen presenting cell is a dendritic cell. In another embodiment, dendritic cells are targeted using a DEC205, XCR1, CD197, CD80, CD86, CD123, CD209, CD273, CD283, CD289, CD184, CD85h, CD85j, CD85k, CD85d, CD85g, CD85a, CD141, CD11c, CD83, TSLP receptor, or CD1a marker. In another embodiment, dendritic cells are targeted using a CD141, DEC205, or XCR1 marker.

[0576] In one embodiment, there is provided herein a kind of in vivo delivery system, it includes antigen peptide as described herein.In another embodiment, delivery system includes cell penetrating peptide, nanoparticle encapsulation, virus-like particle or liposome.In another embodiment, cell penetrating peptide is TAT ​​peptide, herpes simplex virus VP22, transporter (transportan) or Antp.

[0577] In one embodiment, the present invention provides a cell comprising an antigenic peptide as described herein. In another embodiment, the cell is an antigen presenting cell. In another embodiment, the cell is a dendritic cell.

[0578] In one embodiment, a composition is provided herein comprising an antigenic peptide as described herein. In another embodiment, the composition comprises 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, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29 or at least 30 antigenic peptides comprising an epitope of Table 1A. In another embodiment, the composition comprises 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, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, or at least 30 antigenic peptides comprising an epitope of Table IB. In another embodiment, the composition comprises 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, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, or at least 30 antigenic peptides comprising an epitope of Table 2B. In another embodiment, the composition comprises between 2 and 20 antigenic peptides. In another embodiment, the composition further comprises at least 1, 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, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, or at least 30 additional antigenic peptides. In another embodiment, the composition comprises between about 4 and about 20 additional antigenic peptides. In another embodiment, the additional antigenic peptides are specific for a coronavirus.

[0579] In one embodiment, a polynucleotide is provided herein that encodes an antigenic peptide as described herein. In another embodiment, the polynucleotide is RNA, optionally self-amplifying RNA. In some embodiments, the polynucleotide is DNA. In another embodiment, RNA is modified to increase stability, increase cell targeting, increase translation efficiency, adjuvantity, cytosolic accessibility and / or reduce cytotoxicity. In another embodiment, modification is conjugation with a carrier protein, conjugation with a ligand, conjugation with an antibody, codon optimization, increased GC content, incorporation of modified nucleosides, incorporation of 5'-caps or cap analogs, and / or incorporation of poly-A sequences, such as unmasked poly-A sequences or destroyed poly-A sequences, wherein two continuous A sequence segments are connected by a joint.

[0580] In one embodiment, provided herein is a cell comprising a polynucleotide described herein.

[0581] In one embodiment, the present invention provides a vector comprising a polynucleotide as described herein. In another embodiment, the polynucleotide is operably linked to a promoter. In another embodiment, the vector is a self-amplifying RNA replicon, plasmid, phage, transposon, cosmid, virus or virion. In another embodiment, the vector is an adeno-associated virus, herpes virus, lentivirus or a pseudotype thereof.

[0582] In one embodiment, the present invention provides an in vivo delivery system comprising a polynucleotide as described herein. In another embodiment, the delivery system comprises a spherical nucleic acid, a virus, a virus-like particle, a plasmid, a bacterial plasmid or a nanoparticle.

[0583] In one embodiment, the present invention provides a cell comprising a vector or delivery system as described herein. In another embodiment, the cell is an antigen presenting cell. In another embodiment, the cell is a dendritic cell. In another embodiment, the cell is an immature dendritic cell.

[0584] In some embodiments, a composition is provided herein, comprising at least one polynucleotide as described herein. In some embodiments, a composition is provided herein, comprising one or more antigenic peptides as described herein and one or more 2019SARS CoV-2 vaccines (e.g., mRNA-based vaccines, DNA-based vaccines, AAV-based vaccines, protein-based vaccines). In some embodiments, a composition is provided herein, comprising a combination of one or more polynucleotides encoding at least one antigenic peptide as described herein and one or more 2019SARS CoV-2 vaccines (e.g., mRNA-based vaccines, DNA-based vaccines, AAV-based vaccines, protein-based vaccines). In some embodiments, a single polynucleotide is provided herein, encoding more than one antigenic peptide as described herein. In some embodiments, a single polynucleotide is provided herein, encoding (i) at least one antigenic peptide as described herein and (ii) 2019SARS CoV-2 protein (e.g., S protein) and / or its immunogenic fragment (e.g., receptor binding domain (RBD) of S protein). In another embodiment, the composition comprises 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, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, or at least 30 polynucleotides. In another embodiment, the composition comprises between about 2 and about 20 polynucleotides. In another embodiment, the composition further comprises at least 1, 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, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29 or at least 30 additional antigenic polynucleotides encoding additional antigenic peptides. In another embodiment, the composition comprises between about 4 and about 20 additional antigenic polynucleotides. In another embodiment, the polynucleotide is connected to the additional antigenic polynucleotide. In another embodiment, the polynucleotide is connected using a nucleic acid encoding a polyglycine or polyserine linker.

[0585] In one embodiment, the present invention provides a T cell receptor (TCR) that is capable of binding to at least one antigenic peptide described herein. In another embodiment, the TCR is capable of binding to the antigenic peptide in the context of MHC class I or class II.

[0586] In one embodiment, a chimeric antigen receptor is provided herein, comprising: (i) a T cell activation molecule; (ii) a transmembrane region; and (iii) an antigen recognition portion capable of binding to an antigenic peptide as described herein. In another embodiment, CD3-ζ is a T cell activation molecule. In another embodiment, the chimeric antigen receptor further comprises at least one costimulatory signaling domain. In another embodiment, the signaling domain is CD28, 4-1BB, ICOS, OX40, ITAM or FcεRI-γ. In another embodiment, the antigen recognition portion is capable of binding to an antigenic peptide in the context of MHC class I or class II. In another embodiment, the chimeric antigen receptor comprises CD3-ζ, CD28, CTLA-4, ICOS, BTLA, KIR, LAG3, CD137, OX40, CD27, CD4OL, Tim-3, A2aR or PD-1 transmembrane region.

[0587] In one embodiment, the present invention provides a T cell comprising a T cell receptor or a chimeric antigen receptor as described herein. In one embodiment, the T cell is a helper T cell or a cytotoxic T cell.

[0588] In one embodiment, a nucleic acid is provided herein comprising a promoter operably linked to a polynucleotide encoding a T cell receptor as described herein. In another embodiment, the TCR is capable of binding to at least one antigenic peptide in the presence of a major histocompatibility complex (MHC) class I or class II. In one embodiment, the nucleic acid comprises a promoter operably linked to a polynucleotide encoding a chimeric antigen receptor as described herein. In another embodiment, the antigen recognition portion is capable of binding to at least one antigenic peptide in the presence of a major histocompatibility complex (MHC) class I or class II.

[0589] In one embodiment, provided herein is an antibody that is capable of binding to a peptide comprising an epitope of Table 1A, Table 1B, Table 1C, Table 2Ai, Table 2Aii, Table 2B, Table 9, Table 10, Table 11, Table 12, Table 14A, Table 14B, Table 15, or Table 16. In one embodiment, provided herein is an antibody that is capable of binding to a peptide comprising an epitope of Table 1B. In one embodiment, provided herein is an antibody that is capable of binding to a peptide comprising an epitope of Table 2Ai or Table 2Aii.

[0590] In one embodiment, the present invention provides a modified cell that is transfected or transduced with a nucleic acid as described herein. In one embodiment, the modified cell is a T cell, a tumor infiltrating lymphocyte, a NK-T cell, a TCR expressing cell, a CD4+T cell, a CD8+T cell, or a NK cell.

[0591] In one embodiment, provided herein is a composition comprising a T cell receptor or a chimeric antigen receptor as described herein. In another embodiment, the composition comprises a patient's autologous T cells containing a T cell receptor or a chimeric antigen receptor as described herein. In another embodiment, the composition further comprises an immune checkpoint inhibitor. In another embodiment, the composition further comprises at least two immune checkpoint inhibitors. In another embodiment, each of the immune checkpoint inhibitors inhibits a checkpoint protein selected from the group consisting of: CTLA-4, PDL1, PDL2, PD1, B7-H3, B7-H4, BTLA, HVEM, TIM3, GAL9, LAG3, VISTA, KIR, 2B4, CD160, CGEN-15049, CLIK1, CHK2, A2aR and B-7 family ligands or a combination thereof. In another embodiment, each of the immune checkpoint inhibitors interacts with a ligand of a checkpoint protein selected from the group consisting of CTLA-4, PDL1, PDL2, PD1, B7-H3, B7-H4, BTLA, HVEM, TIM3, GAL9, LAG3, VISTA, KIR, 2B4, CD160, CGEN-15049, CHK1, CHK2, A2aR, and B-7 family ligands, or a combination thereof.

[0592] In one embodiment, the composition further comprises an immunomodulator or adjuvant. In another embodiment, the immunomodulator is a co-stimulatory ligand, a TNF ligand, an Ig superfamily ligand, CD28, CD80, CD86, ICOS, CD4OL, OX40, CD27, GITR, CD30, DR3, CD69 or 4-1BB. In another embodiment, the immunomodulator is at least one infected cell extract. In another embodiment, the infected cells are autologous for the subject in need of the composition. In another embodiment, the infected cells have undergone lysis or have been exposed to UV radiation. In another embodiment, the composition further comprises an adjuvant. In another embodiment, the adjuvant is selected from the group consisting of: Poly(I:C), Poly-ICLC, STING agonists, 1018ISS, aluminum salts, Amplivax, AS15, BCG, CP-870,893, CpG7909, CyaA, dSLIM, GM-CSF, IC30, IC31, Imiquimod, ImuFact IMP321, IS Patch, ISS, ISCOMATRIX, JuvImmune, LipoVac, MF59, monophosphoryl lipid A, Montanide IMS1312VG, Montanide ISA 206VG, ​​Montanide ISA 50V2, Montanide ISA 51VG, OK-432, OM-174, OM-197-MP-EC, ISA-TLR2 agonists, ONTAK, In one embodiment, the adjuvant induces humoral responses when administered to a subject. In another embodiment, the adjuvant induces type 1 helper T cells when administered to a subject.

[0593] In one embodiment, provided herein is a method of inhibiting viral infection by administering a vaccine composition to a subject at risk of viral infection, the vaccine composition comprising one or more peptides comprising at least 8 consecutive amino acids from an epitope defined in Table 1A, Table 1B, Table 1C, Table 2Ai, Table 2Aii or Table 2B, the method comprising contacting a cell with the peptide, polynucleotide, delivery system, vector, composition, antibody or cell of the present disclosure.

[0594] In one embodiment, provided herein is a method for treating a viral infection, in particular a coronavirus infection, such as a 2019 SARS CoV-2 infection, by enhancing or prolonging an antiviral response in a subject in need thereof, the method comprising administering to the subject a peptide, polynucleotide, vector, composition, antibody or cell described herein.

[0595] In one embodiment, the subject is a human. In another embodiment, the subject suffers from a viral infection. In one embodiment, the subject is infected with a respiratory virus, such as an acute respiratory virus, for example a SARS-like virus or MERS or a MERS-like virus, or more specifically, a coronavirus of the 2019SARS CoV-2 strain. In some embodiments, the subject is infected with the 2019SARS CoV-2 coronavirus. In some embodiments, the subject has been detectably infected with the 2019SARS CoV-2 coronavirus. In some embodiments, the subject is asymptomatic. In some embodiments, the subject is symptomatic. In some embodiments, the subject is not detected to have been infected with the 2019SARS CoV-2 virus or a related virus, but the subject is in close proximity to an infected person, is in an infected area, or is otherwise at risk of infection.

[0596] In one embodiment of the method, a peptide is administered. In another embodiment, the administration is systemic. In another embodiment of the method, a polynucleotide is administered, optionally with RNA. In one embodiment, the polynucleotide is administered parenterally. In one embodiment, the polynucleotide is administered intravenously. In another embodiment, the polynucleotide is administered intradermally, intramuscularly, or subcutaneously. In one embodiment, the polynucleotide is administered intramuscularly. In one embodiment of the method, a cell is administered. In another embodiment, the cell is a T cell or a dendritic cell. In another embodiment, the peptide or polynucleotide comprises an antigen presenting cell targeting moiety.

[0597] In one embodiment, the peptide, polynucleotide, vector, composition or cell is administered prior to another therapy, such as another antiviral therapy, administered concurrently. In another embodiment, the peptide, polynucleotide, vector, composition or cell is administered before or after another antiviral therapy. In another embodiment, another antiviral therapy is administered continuously throughout the antigenic peptide, polynucleotide, vector, composition or cell therapy.

[0598] In one embodiment of the method, an additional agent is administered. In another embodiment, the agent is a chemotherapeutic agent, an immunomodulatory drug, an immunometabolism regulating drug, a targeted therapy, radiation, an anti-angiogenic agent, or an agent that reduces immunosuppression. In another embodiment, the administration of the pharmaceutical composition described herein triggers or promotes a CD4+ T cell immune response. In another embodiment, the administration of the pharmaceutical composition described herein triggers or promotes a CD4+ T cell immune response and a CD8+ T cell immune response.

[0599] In another embodiment, the patient receives a chemotherapeutic agent, an immunomodulatory drug, an immunometabolism regulating drug, a targeted therapy, or radiation before and / or during the period of receiving the antigenic peptide or nucleic acid vaccine. In another embodiment, autologous T cells are obtained from a patient who has received at least one round of antigen-containing T cell therapy. In another embodiment, the method further comprises adoptive T cell therapy. In another embodiment, the adoptive T cell therapy comprises autologous T cells. In another embodiment, the autologous T cells target viral antigens. In another embodiment, the adoptive T cell therapy further comprises allogeneic T cells. In another embodiment, the allogeneic T cells target viral antigens.

[0600] In one embodiment, provided herein is a method for evaluating therapeutic efficacy, comprising: (i) measuring the number or concentration of target cells in a first sample obtained from a subject before administering the modified cells; (ii) measuring the number or concentration of target cells in a second sample obtained from the subject after administering the modified cells; and (iii) determining an increase or decrease in the number or concentration of target cells in the second sample compared to the number or concentration of target cells in the first sample. In another embodiment, the efficacy of the treatment is determined by monitoring: clinical outcomes; an increase, enhancement, or prolongation of T cell antiviral activity; an increase in the number of antiviral T cells or activated T cells compared to the number before treatment; B cell activity; CD4 T cell activity; or a combination thereof. In another embodiment, the efficacy of the treatment is determined by monitoring biomarkers. In another embodiment, the effect of the treatment is predicted by the presence of T cells or by the presence of a gene signature indicative of T cell inflammation, or a combination thereof.

[0601] Provided herein is a pharmaceutical composition comprising: one or more polypeptides having an amino acid sequence of any one of the sequences depicted in Table 11 and Column 2 of Table 12; or one or more recombinant polynucleotide constructs each encoding a polypeptide having an amino acid sequence of any one of the sequences depicted in Table 11 and Column 2 of Table 12.

[0602] In some embodiments, the one or more polypeptides comprise at least two, three, four, five, six, seven, or eight different polypeptides having an amino acid sequence of any of the sequences depicted in column 2 of Tables 11 and 12; or wherein the one or more recombinant polynucleotide constructs comprise at least two, three, four, five, six, seven, or eight different recombinant polynucleotide constructs, each encoding a different polypeptide having an amino acid sequence of any of the sequences depicted in column 2 of Tables 11 and 12. In some embodiments, the pharmaceutical composition comprises at least eight recombinant polynucleotide strings. In some embodiments, the one or more recombinant polynucleotide strings encoding multiple coronavirus peptide antigens comprise a sequence selected from the group consisting of SEQ IDs RS C1n, RS C2n, RS C3n, RSC4n, RSC5n, RS C6n, RS C7n, and RS C8n, or a sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% sequence identity to any of the foregoing sequences. In some embodiments, the recombinant polynucleotide construct comprises mRNA. In some embodiments, the recombinant polynucleotide construct is mRNA. In some embodiments, the pharmaceutical composition also includes one or more lipid components. In some embodiments, one or more lipids include lipid nanoparticles (LNP). In some embodiments, LNP encapsulates the recombinant polynucleotide construct. In some embodiments, the pharmaceutical composition is administered to a subject in need.

[0603] Provided herein is a method for treating COVID-19 in a subject in need thereof, comprising administering to the subject a pharmaceutical composition described above. In some embodiments, the pharmaceutical composition is administered in addition to one or more therapeutic agents for COVID-19. In some embodiments, the pharmaceutical composition is administered in combination with one or more polypeptides having the amino acid sequence of a 2019 SARS CoV-2 spike protein or a fragment thereof; or one or more recombinant polynucleotide constructs encoding a 2019 SARS CoV-2 spike protein or a fragment thereof. In some embodiments, the 2019 SARS-CoV-2 spike protein or a fragment thereof is a SARS-CoV-2 spike protein or a fragment thereof. In some embodiments, the pharmaceutical composition is administered 2-10 weeks after the first administration of a 2019 SARS CoV-2 spike protein or a fragment thereof. In some embodiments, the pharmaceutical composition is administered 1-6 months after the first administration of a 2019 SARS-CoV-2 spike protein or a fragment thereof. In some embodiments, the pharmaceutical composition is administered concurrently with administration of a 2019 SARS CoV-2 spike protein or a fragment thereof. In some embodiments, the pharmaceutical composition is administered 2-10 weeks before administration of a 2019 SARS CoV-2 spike protein or a fragment thereof. In some embodiments, the pharmaceutical composition is administered 2-10 weeks after the first administration of a vaccine comprising a SARS-CoV-2 spike protein or a polynucleotide encoding thereof. In some embodiments, the pharmaceutical composition is administered 1-6 months after the first administration of a SARS-CoV-2 spike protein or a polynucleotide encoding thereof. In some embodiments, the pharmaceutical composition is administered concurrently with the administration of a SARS-CoV-2 spike protein or a polynucleotide encoding thereof. In some embodiments, the pharmaceutical composition is administered prophylactically. In some embodiments, the pharmaceutical composition is administered once every 1, 2, 3, 4, 5, 6, or more weeks.

[0604] Provided herein is the use of any one of the compositions described herein for the preparation of a therapeutic agent for treating or preventing respiratory viral infection caused by the 2019 SARSCoV-2 virus.

[0605] Where aspects or embodiments of the present disclosure are described in terms of Markush groups or other alternative groups, the present disclosure encompasses not only the entire group listed as a whole, but also each member of the individual group and all possible subgroups of the main group, as well as the main group lacking one or more group members. The present disclosure also contemplates the explicit exclusion of one or more of any group members in embodiments of the present disclosure. BRIEF DESCRIPTION OF THE DRAWINGS

[0606] Figure 1A Depicted is an exemplary flow diagram of a method for identifying peptides most associated with generating CD8+ T cell responses against the viral epitopes described herein.

[0607] Figure 1B Shown is a graphical representation of the SARS-CoV 2 genome.

[0608] Figure 2 Depict an exemplary diagram of the results obtained using a T cell epitope prediction algorithm applied to class I peptide-MHC allele pairs in a validation dataset, and comparing the calculated percentage rankings of these pairs with reported MHC binding assay results. Peptide-MHC allele pairs with binary "positive" results in the MHC binding assay had significantly lower percentage rankings than pairs with "negative" results. In more refined positive results, stronger assay results (low < medium < high) were associated with significantly lower percentage rankings.

[0609] Figure 3 Depicts experimental validation of the HLA-A02:01 predicted epitope from 2019SARS CoV-2 in human T cell induction assays. 23 peptides predicted to be high binders of HLA-A02:01 were synthesized (see Table 4 of Example 8) and assayed in T cell induction using PBMCs from three human donors. If at least one donor produces a T cell response to the peptide by pMHC polymer technology, the epitope is considered to be immunogenic. Representative flow cytometry images of pMHC staining using the peptides from Table 4 of Example 8 are shown. Multimer positive colonies are circled, with the frequency of multimer positive CD8+ T cells being shown in the upper right corner of each figure.

[0610] Figure 4A Exemplary graphs depicting cumulative U.S. population coverage of HLA alleles for a given peptide predicted to be an MHC class I epitope (left panel) and cumulative U.S. population coverage of HLA alleles for a 25-mer peptide predicted to be an MHC class II epitope (right panel).

[0611] Figure 4B Depicts a small number of predicted multi-allelic binding epitopes from individual 2019SARS-CoV-2 proteins (or 2019-CoV-2 proteins) that can achieve broad population coverage. The upper figure shows the cumulative HLA-I coverage of the US, EUR, and API populations relative to the number of included preferential HLA-I epitopes for the M, N, and S proteins. Table 6 shows the peptide sequences corresponding to the upper figure. The lower figure shows the cumulative HLA-II coverage of each population relative to the number of included preferential HLA-II 25-mers for the M, N, and S proteins. Table 7 shows the peptide sequences corresponding to the lower figure.

[0612] Figure 5Depicts the results of an analysis of publicly available proteomic datasets showing relative 2019 SARS CoV-2 protein expression levels that can be used to prioritize potential vaccine targets. Three datasets examining the proteomic response to 2019 SARS CoV-2 infection (alternatively referred to as 2019 SARS CoV-2 infection) were reanalyzed, and protein abundance was estimated by spectral counts normalized to protein length. None of the annotated ORFs not shown in the figure were detected in these proteomic studies. In all three studies, the nucleocapsid protein was the most abundant protein during 2019 SARS CoV-2 infection.

[0613] Figure 6A Depicted is a graphical representation of the string constructs described as Group 1, also described in Tables 9 and 11.

[0614] Figure 6B Provided Figure 6A Detailed and expanded views of the constructs in .

[0615] Figure 7A Depicted is a graphical representation of the string constructs described as Group 2, also described in Tables 10 and 12.

[0616] Figure 7B Provided Figure 7A Detailed and expanded views of the constructs in .

[0617] Figure 8Ai-Figure 8Aii Figure 3: Characterization of T cells induced by the BNT mRNA vaccine at the individual epitope level. Included data show epitope-reactive T cells for the indicated epitopes in three different participants. The vaccine contains mRNA encoding the SARS-CoV-2 spike protein of 2019 SARS COV-2, encapsulated in lipid nanoparticles.

[0618] Figure 8B Shown are multimer-positive CD8+ cells analyzed by flow cytometry for the cell surface markers CCR7, CD45RA, CD3, PD-1, CD38, HLA-DR, CD28, and CD27.

[0619] Figure 8C An mRNA vaccine comprising spike proteins S1 and S2 is shown, wherein the designated epitope region that can bind to a specific MHC molecule is indicated by a solid shape along the length, and the corresponding HLA alleles to which the mRNA vaccine binds are indicated below.

[0620] Figure 8DThe time course of T cell responses following vaccination of patients with different doses of the spike protein mRNA vaccine (10, 20, and 30 μg as shown) is shown. The upper graph shows the CD4+ T cell response, which is indicated by IFN-g expression using an ELISPOT assay. The lower graph shows the CD8+ T cell response, which is indicated by IFN-g expression using an ELISPOT assay. CEF and CEFT are control CMV, EBV, and influenza pools.

[0621] Figure 8E Shown are the time courses of CD4+ T cell and CD8+ T cell responses in an elderly population administered spike protein mRNA vaccines (30 μg each).

[0622] Figure 9 The design of a vaccine string containing the ORF-1ab epitope is shown, in which the epitopes are specifically ranked using MS-based HLA-I lysis predictor information. This design uses a minimal number of linker sequences.

[0623] Figure 10A The experimental design used to validate the immunogenicity of the string vaccine composition in an animal model is shown.

[0624] Figure 10B Shown is a representative experimental setup of an animal model study to determine the immunogenicity of four CorVac 2.0 trains when administered in vivo. 5 groups (16 animals / 8-10 removed on d14 / 8-10 on d28).

[0625] Figure 11A Schematic diagram of different dosing schedules for the spike vaccine (BNT162b2) and CorVac 2.0.

[0626] Figure 11B Depicts a schematic diagram of the animal studies used to determine the immune responses elicited by different formulation ratios and doses of CorVac2.0 and BNT162b2 in HLA-A02 transgenic mice.

[0627] Figure 11C Schematic diagram depicting the animal studies used to determine the immune responses elicited by different formulations and doses of CorVac 2.0 and BNT162b2 in transgenic mice expressing human ACE2.

[0628] Figure 12A Sequence variants and mutants of the spike protein in various SARS CoV-2 isolates are shown, along with corresponding maps of vaccine epitope sequences.

[0629] Figure 12B is a graph showing spike mutation frequency over time.

[0630] Figure 13A Sequence variants and mutants of the nucleocapsid protein in various SARS CoV-2 isolates are shown, along with corresponding maps of vaccine epitope sequences.

[0631] Figure 13B is a graph showing the frequency of nucleocapsid mutations over time.

[0632] Figure 14 Sequence variants and mutants of the membrane protein in various SARS CoV-2 isolates are shown, along with corresponding maps of vaccine epitope sequences.

[0633] Figure 15 Sequence variants and mutants of the NSP1 protein in various SARS CoV-2 isolates are shown, along with corresponding maps of vaccine epitope sequences.

[0634] Figure 16 Sequence variants and mutants of the NSP2 protein in various SARS CoV-2 isolates are shown, along with corresponding maps of vaccine epitope sequences.

[0635] Figure 17 Sequence variants and mutants of the NSP3 protein in various SARS CoV-2 isolates are shown, along with corresponding maps of vaccine epitope sequences.

[0636] Figure 18 Sequence variants and mutants of the NSP4 protein in various SARS CoV-2 isolates are shown, along with the corresponding maps of vaccine epitope sequences.

[0637] Figure 19A CorVac 2.0-string design for maximal CD8 and CD4 T cell responses is shown.

[0638] Figure 19B RS-C7 was shown to be enriched in known ORF1ab T-cell epitopes and to avoid most variants of interest / variants of interest (VOC / VOI) mutations.

[0639] Figure 19C RS-C7 was shown to be enriched in known nucleocapsid and membrane T-cell epitopes and to avoid most variants of interest / variants of interest (VOC / VOI) mutations.

[0640] Figure 20 Shown is an outlined exemplary experimental setup to test peptide presentation of polynucleotide strings complexed with MHC proteins.

[0641] Figure 21Depicted are representative data showing exemplary target epitope presentation verified by mass spectrometry; endogenous in the experimental setting when the epitope is expressed on A375 cells expressing endogenous HLA; synthetic in the experimental setting when the epitope is expressed in cells expressing exogenous HLA.

[0642] Figure 22 Shown is a graphical representation of the list of epitopes identified by the above method using mass spectrometry.The identified epitopes span the viral genome, encompassing epitopes of the nucleocapsid protein, the ORF1ab domain, and the membrane protein.

[0643] Figure 23 Shown is a representation of a map of all identified CorVac 2.0 epitopes in the viral nucleocapsid, ORF1ab and membrane regions.

[0644] Figure 24 Representative data demonstrating that Corvac 2.0 elicits T cell responses from the nucleocapsid region in BALB / C mice after a single injection on day 0. Immunoreactive T cells were determined by elispot assay (number of spots / 1×10^6 cells). Statistical significance was determined by two-way ANOVA with Sidak's multiple comparison test.

[0645] Figure 25 Representative data demonstrating that Corvac 2.0 elicits T cell responses from membrane regions in BALB / C mice after a single injection on day 0 are shown. Immunoreactive T cells were determined by elispot assay (number of spots / 1×10^6 cells). Statistical significance was determined by two-way ANOVA with Sidak's multiple comparison test.

[0646] Figure 26 A graphical representation showing a summary of the performance of the different strings tested to date is shown. The number of stars is proportional to the statistical significance of the immunogenicity of each string compared to the vehicle control.

[0647] Figure 27 Representative data demonstrating that Corvac 2.0 tandems elicit T cell responses to epitopes from the nucleocapsid region following a single injection on day 0 in HLA-A2tg mice (mice expressing humanized HLA-A02:01) are shown. T cell immunoreactivity was determined by ELISpot assay (number of spots / 1×10^6 cells). Statistical significance was determined by two-way ANOVA with Sidak's multiple comparison test. Data are from mice on day 28 after injection of the tandem composition.

[0648] Figure 28Representative data demonstrating that Corvac 2.0 tandems elicit T cell responses to epitopes from the membrane region following a single injection on day 0 in HLA-A2tg mice (mice expressing humanized HLA-A02:01) are shown. T cell immunoreactivity was determined by ELISpot assay (number of spots / 1×10^6 cells). Statistical significance was determined by two-way ANOVA with Sidak's multiple comparison test. Data are from mice on day 28 after injection of the tandem composition.

[0649] Figure 29 Representative data are shown demonstrating that Corvac 2.0 tandems elicit T cell responses to epitopes from the ORF1ab region following a single injection on day 0 in HLA-A2tg mice (mice expressing humanized HLA-A02:01). T cell immunoreactivity was determined by ELISpot assay (number of spots / 1×10^6 cells). Statistical significance was determined by two-way ANOVA with Sidak's multiple comparison test. Data are from mice on day 28 after injection of the tandem composition.

[0650] Figure 30 A graphical representation of the statistical significance of the immunogenicity of the different strings tested in the HLA-A02 transgenic mouse model compared to vehicle control is summarized and the results are depicted in Figure 27 、 Figure 28 and Figure 29 This representation shows that RS-C7 had the largest T cell response in the pool in the HLA-A02 transgenic mouse model.

[0651] Figure 31 Shown is a graphical representation of the RS-C7 string design showing the string regions that elicited an immune response as determined by ELISpot assay and the epitopes presented by HLA as a validated process and using mass spectrometry.

[0652] Figure 32A Shown is a graphical representation of the string design, wherein the encoded nucleocapsid sequence contains, inter alia, a tiled, overlapping 15-mer epitope sequence with an 11 amino acid overlap.

[0653] Figure 32B Shown is a graphical representation of the string design, where the encoded membrane sequence contains, inter alia, a tiled 15-mer sequence with an 11 amino acid overlap.

[0654] Figure 32C A graphical representation of the string design is shown, wherein the encoded ORF 1ab sequence contains, inter alia, a tiled 15-mer sequence with an 11 amino acid overlap.

[0655] Figure 32D Shown from Figure 10BThe results of the experimental design shown in , which showed that CorVac2.0 string did not generate T cell responses caused by the ORF1ab region in the BALB / C mouse model. Figure 29 The results shown in (left panel, pool 11) and (right panel, pool 12) indicate that CorVac 2.0 indeed generates T cell responses in the HLA-A02 transgenic mouse model driven by the ORF1ab region. Statistical significance was determined by one-way ANOVA with Sidak's multiple comparison test.

[0656] Figure 32E Figure 3 is a graphical representation of the summary of the performance of the different strings tested in the BALB / C mouse model and demonstrates that RS-C7 has the most T cell responses in the pool in the BALB / C mouse model. The RS-C7 string generated the most T cell responses in the pool in the BALB / C mouse model.

[0657] Figure 33 Graphical representation showing that the CorVac 2.0 string C7 epitope does or does not overlap with regions that have few mutations of the variant of interest.

[0658] Figure 34A Describes and uses Figure 11A Data related to B cell responses to S1-binding antibodies in mouse sera assessed by ELISA at the indicated time points and serum dilutions for the indicated dosing schedules.

[0659] Figure 34B Describes and uses Figure 11A Data related to B cell responses to NP-conjugated antibodies in mouse sera assessed by ELISA at the indicated time points and serum dilutions according to the indicated dosing schedule.

[0660] Figure 35 Show how to use according to Figure 11A ELISA results of serum IgG concentrations on days 14, 21, and 35 after treatment (injection) with saline control (NaCl), BNT162b2, C7 strings, or the combination as indicated by the dosing schedule of . The results indicate that including CorVac 2.0 in the co-formulation environment does not affect spike-specific Ab production.

[0661] Figure 36 Show how to use according to Figure 11AResults of pseudovirus neutralization tests (pVNTs) using viral particles pseudotyped with the VSV envelope containing the SARS-CoV-2 spike protein were performed on days 14, 21, and 35 after treatment (injection) with saline control (NaCl), BNT162b2, C7 cluster, or the combination, as indicated by the dosing schedule. The results showed that CorVac 2.0 did not adversely affect the formation of neutralizing antibodies against SARS-CoV-2 viral proteins (Wuhan strain).

[0662] Figure 37A Show the basis for use Figure 11A Lymph node phenotyping results on day 35 of the dosing schedule of the 1:1 co-formulation. The B cell population is represented by the % CD19+ cells in the CD45+ cell population. The percentage of activated B cells is determined by % IgD-CD3-CD4-CD8- cells; the percentage of converted B cells is determined by % activated B cells / B220+IgM-CD19+CD138- cells; and % GC B cells are determined by % activated B cells / B220+IgM-CD19+CD138- cells of the total CD45+ cells in the population. The results show that including CorVac2.0 in the 1:1 co-formulation does not affect the B cell response driven by BNT162b2 and slightly enhances the response.

[0663] Figure 37B Show the basis for use Figure 11A Lymph node phenotyping results were obtained on day 35 following the dosing schedule of the previous trial. The results showed that the inclusion of CorVac 2.0 maintained the frequency of Tfh cells in the lymph nodes.

[0664] Figure 38 Describes the activation of splenocytes that have been activated using Figure 11A The dosing schedule was followed by stimulation with peptides present in BNT162b2 on day 35, and flow cytometry was used to assess the presence of the activation marker CD69 on a large number of T cell populations (left panel) or CD4 T cells (middle panel) or CD8 T cells (right panel). The results showed that when restimulated with spike peptides (Spike 1 pool), T cell activation increased in the vaccine group with BNT162b2 (Group 2) and was not suppressed in the groups with both CorVac2.0 and BNT162b2 (Groups 4-7).

[0665] Figure 39 Describes the activation of splenocytes that have been activated using Figure 11AThe dosing schedule was followed by stimulation with peptides present in BNT162b2 on day 35, and the presence of the activation marker IFN-γ on a large number of T cell populations (left panel) or CD8 T cells (middle panel) or CD4 T cells (right panel) was assessed by flow cytometry. The results showed that when restimulated with spike peptides (Spike 1 pool), T cell activation increased in the vaccine group with BNT162b2 (Group 2) and was not suppressed in the CD3 T cell population and CD8 T cell population in the groups with both CorVac 2.0 and BNT162b2 (Groups 4-7), but was not significantly increased in any group in the CD4 T cell population.

[0666] Figure 40 Describes the activation of splenocytes that have been activated using Figure 11A The dosing schedule was followed by stimulation with peptides present in BNT162b2 on day 35, and the presence of the activation marker CD69 on a large population of T cells (left panel) or CD4 T cells (middle panel) or CD8 T cells (right panel) was assessed by flow cytometry. The results showed that when restimulated with spike peptides (Spike 2 pool), T cell activation was most significantly increased in the groups given BNT162b2 co-formulated in the same LNP (Groups 5-7).

[0667] Figure 41A Describes the activation of splenocytes that have been activated using Figure 11A The dosing schedule was followed by stimulation on day 35 with peptides present in the nucleocapsid sequence of CorVac 2.0, and flow cytometry was used to assess the presence of the activation marker CD69 on either CD4 T cells (center) or CD8 T cells (right). The results showed that upon restimulation with the nucleocapsid peptides, T cell activation increased in both the CD3 T cell and CD8 T cell populations in the vaccine groups with CorVac 2.0 (Group 3) and separately formulated and co-formulated BNT162b2 and CorVac 2.0 (Groups 4 and 5), and modestly increased in the CD4 T cell population.

[0668] Figure 41B Describes the activation of splenocytes that have been activated using Figure 11AThe dosing schedule was followed by stimulation on day 35 with peptides present in the nucleocapsid sequence of the CorVac 2.0 string, and the presence of the functional marker IFN-γ was assessed by flow cytometry on a large number of T cell populations (left panel) or CD8 T cells (middle panel) or CD4 T cells (right panel). The results showed that when restimulated with the nucleocapsid peptide, IFN-γ production in T cells increased in both CD3 T cell populations and CD4 T cell populations in the vaccine groups with CorVac 2.0 (Group 3) and the same ratio of BNT162b2 and CorVac 2.0 string (Group 5), and modestly increased in the CD8 T cell population.

[0669] Figure 42 Depicted is an ELISpot assay using Figure 11A Results of spike (N-terminal and C-terminal) antigen-specific T cell responses obtained on samples taken on day 35 of the 1:1 dosing schedule. The results showed that the addition of CorVac 2.0 did not inhibit the Ag-specific spike T cell response and that this response was slightly enhanced by 1:1 co-formulation.

[0670] Figure 43 Depicted is an ELISpot assay using Figure 11A Results of nucleocapsid, membrane, and Orf1ab antigen-specific T cell responses were obtained on samples taken on day 35 of the 35-dose schedule for the same CorVac 2.0 regimen. The results showed that the CorVac 2.0 cascade response was stronger in the CorVac 2.0-only group but remained when the CorVac 2.0 cascade was combined with BNT162b2.

[0671] Figure 44 Describes the use of Figure 11A The effects of BNT162b2 and CorVac 2.0 alone or in combination on anti-Spike T cell responses were assessed by ELISPOT on days 14 and 35 following the dosing schedule described herein. The kinetic studies described herein demonstrate that Spike T cell responses increased after the boost in all groups.

[0672] Figure 45 Describes the use of Figure 11A The effects of booster doses on the immune response to CorVac 2.0 were investigated on days 14 and 35 of the same dosing schedule. The kinetic studies described herein demonstrate that the CorVac 2.0 response does not increase after the booster.

[0673] Figure 46 Depicts the use of flow cytometry to determine the expression of cytokines following restimulation with cognate peptide groups (spike N-terminus, spike C-terminus, nucleocapsid, and membrane as described). Figure 11AThe polyfunctionality of CD4 and CD8 T cell responses elicited by BNT162b2 and CorVac 2.0 was determined by the expression of IFNγ+IL-2+TNFα+.

[0674] Figure 47 Shows a summary of the usage Figure 11A Graphical representation of the effect of the different formulations indicated on the left column on the spike N-terminal antigen-specific responses of CD4 / CD8 cells. The number of stars is proportional to the statistical significance and strength of the response compared to vehicle control.

[0675] Figure 48 Shows a summary of the usage Figure 11A Graphical representation of the effect of the different formulations indicated on the left column on the spike C-terminal antigen-specific responses of CD4 / CD8 cells. The number of stars is proportional to the statistical significance and strength of the response compared to vehicle control.

[0676] Figure 49 Shows a summary of the usage Figure 11A Graphical representation of the effect of the different formulations indicated on the left column on the nucleocapsid antigen-specific responses of CD4 / CD8 cells. The number of stars is proportional to the statistical significance and strength of the response compared to vehicle control.

[0677] Figure 50 Shows a summary of the usage Figure 11A Graphical representation of the effect of the different formulations on membrane antigen-specific responses of CD4 / CD8 cells at the indicated dosing schedules on the left column. The number of stars is proportional to the statistical significance and magnitude of the response compared to vehicle control.

[0678] Figure 51 Schematic diagram depicting the animal studies used to determine the immune responses elicited by different formulations and doses of CorVac 2.0 and BNT162b2 in transgenic mice expressing human ACE2.

[0679] Figure 52 Shown from Figure 51 Data from an animal study described in , which showed that boosting with a 0.3 μg dose of separately formulated CorVac2.0 enhanced anti-spike IgG production (quantified at day 56). CorVac2.0 alone slightly boosted anti-spike IgG production, a 3:1 separately formulated boost of anti-spike IgG production, and including multiple doses of separately formulated CorVac2.0 did not adversely affect anti-spike IgG responses.

[0680] Figure 53 Shown from Figure 51Data from an animal study described in , which showed that boosting with a 0.3 μg dose of separately formulated CorVac2.0 enhanced anti-spike IgG production (as measured by optical density (OD) at day 56). CorVac2.0 alone slightly boosted anti-spike IgG production, a 3:1 separately formulated boost of anti-spike IgG production, and including multiple doses of separately formulated CorVac2.0 did not adversely affect anti-spike IgG responses.

[0681] Figure 54 Shown from Figure 51 Data from an animal study depicted in Figure 2, which demonstrates anti-spike IgG kinetics over time. A third boost increased anti-spike IgG in all CorVac 2.0 variants.

[0682] Figure 55 Shown from Figure 51 Data from an animal study depicted in , which shows anti-Spike IgG levels in serum on the indicated days using the indicated serum dilutions.

[0683] Figure 56 Shown from Figure 51 Pseudovirus neutralization test (pVNT) data from the animal study depicted in Figure 2 demonstrate that including CorVac 2.0 did not adversely affect neutralization titers at the indicated days following treatment with the indicated dosing regimen. The pVNT was performed using viral particles pseudotyped with a VSV envelope containing the SARS-CoV-2 spike protein at the indicated dilutions.

[0684] Figure 57 Shown using Figure 51 Tetramer staining data obtained from PBLs from the animal studies depicted in , which show the percentage of CD8+ T cells specific for the indicated membrane and indicated spike epitopes or epitope combinations, indicate that the addition of CorVac2.0 does not affect the anti-spike response.

[0685] Figure 58 Shown using Figure 51 Tetramer staining data obtained from PBLs from the animal studies depicted in , which show the percentage of CD8+ T cells specific for the indicated spike epitopes, indicate that the addition of CorVac2.0 does not affect the anti-spike response.

[0686] Figure 59 Shown from Figure 51The spot formation assay from the animal study depicted in Figure 5, which shows the number of spots formed per 1×10^6 cells on day 56 after treatment with the indicated regimen, shows that the addition of CorVac2.0 as a single formulation in the third booster slightly improved the anti-spike T cell response. CorVac2.0 alone slightly enhanced the anti-spike T cell response, 3:1 and 9:1 separate formulations slightly enhanced the anti-spike T cell response, and including multiple doses of separately formulated CorVac2.0 did not adversely affect the anti-spike T cell response.

[0687] Figure 60 Shown from Figure 51 The spot formation assay from the animal study depicted in Figure 5, which shows the number of spots formed per 1×10^6 cells on day 56 after treatment with the indicated regimen, demonstrates that a weak anti-nucleocapsid response was observed with one booster dose, and that multiple doses of separately formulated BNT162b2+CorVac2.0 resulted in an increased response. A weak response to nucleocapsid was observed in K18-hACE2 mice that received a single CorVac2.0 boost. An increase in the anti-nucleocapsid response was also observed with increasing numbers of CorVac2.0 doses.

[0688] Figure 61 Shown from Figure 51 The spot formation assay from the animal study depicted in Figure 5, which shows the number of spots formed per 1×10^6 cells on day 56 after treatment with the indicated regimen, demonstrates that the strongest anti-membrane response was observed with the separately formulated group as a booster; multiple doses of separately formulated BNT162b2 plus CorVac2.0 resulted in an increased response. The strongest anti-membrane response was observed with the separately formulated condition. An increase in the anti-membrane response was observed with increasing numbers of CorVac2.0 doses.

[0689] Figure 62 Shown from Figure 51 Data from an animal study described in , in which harvested inguinal lymph nodes (draining lymph nodes (dLN)) were dissected and viable cell counts were determined after treatment with the indicated regimens. Three samples with 0% viability (G5, G7, G9) were removed. The data demonstrated that the group containing the combination of CorVac2.0 boost and BNT162b2 exhibited an increase in viable LN cell counts.

[0690] Figure 63 Shown from Figure 51 Data from an animal study depicted in , in which harvested lymph nodes were dissected and cell counts of the indicated cell populations were determined as percentages of CD45.2 cells after treatment with the indicated regimens. The data demonstrated a trend toward increased germinal center (GC) cells and CD27+ memory B cells in the groups treated with separately formulated CorVac2.0 + BNT162.

[0691] Figure 64A Shown from Figure 51 Data from an animal study depicted in , in which harvested lymph nodes were dissected and cell counts of the indicated cell populations were determined as a percentage of CD45.2 cells after treatment with the indicated regimens. The data demonstrate that class-switched B cells were slightly higher in the group treated with separately formulated CorVac2.0 + BNT162.

[0692] Figure 64B Shown from Figure 51 Data from an animal study depicted in , in which harvested lymph nodes were dissected and total cell counts of the indicated cell populations were determined after treatment with the indicated regimens. The data demonstrate that class-switched B cells were slightly higher in the group treated with separately formulated CorVac2.0 + BNT162.

[0693] Figure 65 The results obtained from the harvested lymph node samples are shown. Figure 51 Tetramer-specific staining data for animal studies depicted in Figure 2 shows the percentage of CD8+ T cells specific for spike or membrane epitopes. Also depicted is a graph showing the percentage of central memory T cells, effector memory T cells, naive T cells, and effector T cells as a percentage of spike-positive CD8 T cells. Slightly less differentiated cells were observed in the CorVac2.0-treated group.

[0694] Figure 66 Schematic diagram depicting the animal studies used to determine the immune responses elicited by different formulation ratios and doses of CorVac 2.0 and BNT162b2 in HLA-A02 transgenic mice.

[0695] Figure 67A Shown from Figure 66 The spot formation assay of the animal study depicted in , which shows the number of spots formed per 1×10^6 cells on day 14 after treatment with the indicated regimens, indicates that CorVac2.0 induces the strongest immune response at the highest dose.

[0696] Figure 67B Shown from Figure 66 The spot formation assay from the animal study depicted in Figure 3, which shows the number of spots formed per 1×10^6 cells at day 35 after treatment with the indicated regimens, demonstrates that the spike T cell response was enhanced by the inclusion of CorVac 2.0. The 1 μg dose produced the strongest response.

[0697] Figure 67C Shown from Figure 66Spot formation assay from an animal study depicted in Figure 2, showing the number of spots formed per 1×10^6 cells over time. Improved T cell responses were observed in all regions after boosting.

[0698] Figure 67D Shown from Figure 66 Figure 2. Co-culture spot formation assay from the animal study depicted in Figure 2, showing the number of spots formed per 1×10^6 cells at day 35 after treatment with the indicated regimens. Spike responses were observed in both CD4 T cells and CD8 T cells. Spike CD8 T cells exhibited greater cytokine secretion and degranulation than CD4 T cells.

[0699] Figure 67E Shown from Figure 66 Figure 2. Co-culture spot formation assay from the animal study depicted in Figure 2, showing the number of spots formed per 1×10^6 cells at day 35 after treatment with the indicated regimens. Membrane responses were observed in both CD4 T cells and CD8 T cells and were greatest at the highest dose. IL2 secretion was observed in both CD4 T cells and CD8 T cells.

[0700] Figure 67F Shown from Figure 66 Figure 5. Spot formation assay from an animal study depicted in Figure 5. Spot formation assay from an animal study depicted in Figure 5. Showing the number of spots formed per 1×10^6 cells on day 56 after treatment with the indicated regimen. CorVac2.0 did not adversely affect the spike response. CorVac2.0 alone boosted the spike response. Boosting with CorVac2.0 alone increased the spike response. No statistically significant changes in the spike response were observed with the inclusion of CorVac2.0. The strongest membrane response was observed in the highest dose group. The strongest N response was observed with the highest dose of CorVac2.0 alone. The strongest Orf1ab response was observed with CorVac2.0 alone and the 3:1 dose formulated separately.

[0701] Figure 67G Shown from Figure 66 Figure 5. Co-culture spot formation assay of the animal study depicted in Figure 5, which shows the number of spots formed per 1×10^6 cells on day 56 after treatment with the indicated regimens. Spike responses were observed in both CD4 T cells and CD8 T cells and some spike responses were boosted by the inclusion of CorVac 2.0.

[0702] Figure 67H Shown from Figure 66 Figure 5. Co-culture spot formation assay from the animal study depicted in Figure 5. The number of spots formed per 1×10^6 cells on day 56 after treatment with the indicated regimens is shown. Polyfunctional spike CD4 T cells and CD8 T cells were slightly enhanced at the higher dose of CorVac 2.0.

[0703] Figure 67I Shown from Figure 66 Co-culture spot formation assay from the animal study depicted in Figure 5, showing the number of spots formed per 1×10^6 cells on day 56 after treatment with the indicated regimens. A stronger membrane response was observed in CD8 T cells.

[0704] Figure 67J Shown from Figure 66 Figure 5. Co-culture spot formation assay from the animal study depicted in Figure 5, showing the number of spots formed per 1×10⁶ cells on day 56 after treatment with the indicated regimens. Multifunctional membranes were observed for both CD4 T cells and CD8 T cells.

[0705] Figure 68A Shown from Figure 66 Phenotypic analysis data for the animal study depicted in , in which harvested lymph nodes were dissected and cell counts of the indicated cell populations were determined as a percentage of CD45.2 cells on day 14 after treatment with the indicated regimens. Memory B cells: CD3-IgD-IgM-CD27+; Activated B cells: IgD-CD3-CD4-CD8-; Switched B cells: IgD-CD3-CD4-CD8-B220+IgM-CD19+CD138-. GC B cells: IgD-CD3-CD4-CD8-B220+IgM-CD19+CD138-CD95+CD38-.

[0706] Figure 68B Shown from Figure 66 Phenotypic analysis data from the animal study depicted in Figure 2, in which harvested lymph nodes were dissected and cell counts of the indicated cell populations were determined as the percentage of CD45.2 cells at day 35 after treatment with the indicated regimens. Memory B cells: CD3-IgD-IgM-CD27+; activated B cells: IgD-CD3-CD4-CD8-; switched B cells: IgD-CD3-CD4-CD8-B220+IgM-CD19+CD138-. GC B cells: IgD-CD3-CD4-CD8-B220+IgM-CD19+CD138-CD95+CD38-. Addition of CorVac2.0 to BNT162b2 slightly enhanced class-switched B cells and GC B cells. CorVac2.0 resulted in a slight increase in Tfh cells.

[0707] Figure 68C Shown from Figure 66Phenotypic analysis data from an animal study described in , in which harvested lymph nodes were dissected and cell counts of the indicated cell populations were determined as the percentage of CD45.2 cells on day 56 after treatment with the indicated regimens. Memory B cells: CD3-IgD-IgM-CD27+; Activated B cells: IgD-CD3-CD4-CD8-; Switched B cells: IgD-CD3-CD4-CD8-B220+IgM-CD19+CD138-. GC B cells: IgD-CD3-CD4-CD8-B220+IgM-CD19+CD138-CD95+CD38-. Boosting with CorVac2.0 alone enhanced B cell responses compared to no boost. The combination of CorVac2.0 and BNT162b2 did not significantly affect B cell responses.

[0708] Figure 69 An exemplary clinical study design to evaluate the safety of the CorVac 2.0 vaccine in healthy human subjects is shown.

[0709] Figure 70 An exemplary clinical study design to evaluate the safety of the CorVac 2.0 vaccine in immunocompromised human subjects is shown.

[0710] Figure 71 An exemplary clinical study design to evaluate the safety of the CorVac 2.0 vaccine in immunocompromised human subjects is shown.

[0711] Figure 72 Sequence variants and mutants of the spike protein in various SARS CoV-2 isolates are shown as indicated on the right. The data suggest that the spike protein is putatively highly mutated due to selection pressure.

[0712] Figure 73 The sequence variants and mutants of the nucleocapsid (N) and membrane (M) proteins in various SARS CoV-2 isolates, as indicated on the right, are shown, along with the corresponding maps of the vaccine epitope sequences encoded by CorVac 2.0. The data demonstrate that the CorVac 2.0 vaccine sequence is rarely affected by variant mutations in N and M.

[0713] Figure 74 Shown are sequence variants and mutants of ORF 1ab in various SARS CoV-2 isolates, as indicated on the right, and the corresponding maps of vaccine epitope sequences encoded by CorVac 2.0. The data demonstrate that the CorVac 2.0 vaccine sequence is rarely affected by variant mutations in ORF1ab.

[0714] Figure 75AShown is a map representation of an exemplary CorVac2.0 RS-C7 string, depicting the linker, SEC domain, transmembrane (TM) domain, and viral epitopes contained in the string, including the nucleocapsid epitope, ORF1ab epitope, and membrane epitope.

[0715] Figure 75B Shown is a map representation of an exemplary CorVac2.0 RS-C7 string depicting the observed viral epitopes contained in the string as revealed by mass spectrometry (MS), including the nucleocapsid epitope, the ORF1ab epitope, and the membrane epitope.

[0716] Figure 76 Shown is a representation of the MS-based HLA-I cleavage predictor used to optimize the ranking of candidate ORF1ab sequences, adding as few linkers as possible while retaining efficient epitope cleavage (top) and 18 ORF1ab epitopes optimized for the GSS linker background.

[0717] Figure 77A -C shows a map representation of an exemplary CorVac2.0 RS-C7 string. The antigens selected for CorVac 2.0 are rarely mutated: RS-C7 is affected by only three mutations among all WHO-designated variants, leaving the vast majority of epitopes unchanged. Figure 77B As shown in Figure ​-C, even in the highly mutated Omicron variant, only a single mutation affects the CorVac 2.0 string (as opposed to ~39 amino acid changes in the spike protein).

[0718] Figures 78A-78B Shown are the kinetics of antibody concentrations against the spike protein.

[0719] Figure 79 Depicts an exemplary structure of the RS C7 and illustrates certain factors that were considered when designing a CorVac 2.0 string. Figure 79 As used herein, "count" refers to the number of pMHC allele pairs that overlap with a specified residue of a protein sequence. The count can be determined by reference to a database of epitopes (e.g., a database of epitopes observed and / or predicted in experimental studies). Figure 79 As used herein, "entropy" refers to Shannon entropy and is a measure of the level of conservation (where lower entropy indicates greater conservation).

[0720] Figure 80A Depicted are epitopes present in exemplary CorVac 2.0 strings (e.g., RS C7 strings) as observed by mass spectrometry, as processed and presented by the MHC complex.

[0721] Figure 80BData for one exemplary epitope (epitope 23 of Table 19) observed by mass spectrometry are depicted.

[0722] Figure 81 Depicted is the study design for testing the immunogenicity of various BNT162b2+CorVac2.0 serial dosing regimens in K18-hACE2 mice.

[0723] Figures 82A-82B Shown in Figure 81 Anti-Spike protein, IgG concentrations measured over time in serum samples collected during the experiment depicted in Figure 1. IgG concentrations were measured by ELISA. Error bars represent standard error of the mean.

[0724] Figures 83A-83B Shown in Figure 81 Neutralization titers were measured in serum samples collected during the experiment depicted in Figure 1. Neutralization titers were measured using a pseudovirus neutralization assay using pseudoviruses containing the SARS-CoV-2 S protein from the Wuhan strain.

[0725] Figure 84 Depicted is the experimental protocol used to measure the efficacy of CorVac2.0 administered alone or in combination with RNA encoding the SARS-CoV-2 S protein in Syrian hamsters.

[0726] Figure 85 Shown from Figure 84 Specifically, Figure 85 Shown are changes in hamster body weight after challenge with SARS-CoV-2 (Wuhan strain).

[0727] Figure 86 An exemplary protocol for clonotyping spike-specific B and T cells is shown.

[0728] Figure 87 Summary of T cell clonotypes observed in animals administered: (i) two doses of RNA encoding the SARS-CoV-2 S protein (BNT162b2) or (ii) two doses of RNA encoding the SARS-CoV-2 S protein and one dose of CorVac2.0 (string C7). Circles correspond to samples with identical clonotypes, with clonotypes in the same "clonotype cluster" (i.e., clonotypes with similar sequences) represented by lines connecting the dots. As shown in the figure, administration of the CorVac2.0 construct increased the trend toward higher clonal expansion without adversely affecting clonality.

[0729] Figure 88An exemplary clinical study design for evaluating the safety of the CorVac 2.0 vaccine in healthy human subjects is shown. "Spike Vac" refers to RNA encoding the SARS-CoV-2 S protein and containing one or more mutations that stabilize the prefusion conformation (e.g., one or more mutations disclosed herein or known in the art); in the exemplary clinical study design, a bivalent vaccine is administered comprising RNA encoding a SARS-CoV-2 S polypeptide of the Wuhan strain and a SARS-CoV-2 S polypeptide containing one or more mutations unique to the BA.4 / 5 Omicron variant (e.g., one or more mutations disclosed herein). a If acceptable tolerability is demonstrated and stopping / pause rules are not met, further dosing may continue to the subject or a new cohort may be opened. b An exemplary SpikeVac bivalent is BNT162b2 bivalent (Wuhan+OMI BA.4 / BA.5). Abbreviations: d = day; h = hour; FIH = first in humans; IRC = internal review committee; N = number of subjects; OMI = Omicore; WT = wild type. Trial population: Healthy volunteers aged 18-55 years who had previously received at least three doses of any authorized COVID19 RNA vaccine (the last COVID19 RNA vaccine dose must have been administered at least 4 months before the first follow-up). Subjects infected with SARS-CoV-2 60 days or more before randomization were not excluded from the trial. DETAILED DESCRIPTION

[0730] Novel therapeutic agents and vaccines based on viral epitopes are described herein. Thus, the disclosure described herein provides peptides, polynucleotides encoding the peptides, and peptide binding agents that can be used, for example, to stimulate an immune response to a viral antigen to produce an immunogenic composition or vaccine for treating or preventing a viral infection.

[0731] definition

[0732] To facilitate understanding of this disclosure, a number of terms and phrases are defined below.

[0733] "Viral antigen" refers to an antigen encoded by a virus. Such antigens include but are not limited to antigens of coronaviruses such as COVID19.

[0734] Throughout this disclosure, "binding data" results may be expressed in terms of "IC50." The IC50 is the concentration of the peptide tested in the binding assay at which 50% inhibition of the binding of the labeled reference peptide is observed. Given the conditions under which the assay is run (i.e., limiting HLA protein and labeled reference peptide concentrations), these values ​​are close to the K DValues. Assays for determining binding are well known in the art and are described in detail in, for example, PCT publications WO 94 / 20127 and WO 94 / 03205, and other publications such as 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 of a reference standard peptide. For example, it can be expressed based on its IC 50 , relative to the IC of the reference standard peptide 50 Binding can also be determined using other assay systems, including those using living 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 et al., J. Immunol. 147:189 (1991); These include, for example, 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 et al., 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-throughput soluble phase assays (Hammer et al., J. Exp. Med. 180:2353 (1994)), and measurements of class I MHC stabilization or assembly (e.g., Ljunggren et al., Nature 2003). 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)).

[0735] When used to discuss epitopes, the term "derived" is a synonym for "prepared." A derived epitope can be derived from a natural source, or it can be synthesized according to standard protocols in the art. Synthetic epitopes can contain artificial amino acid residues, "amino acid mimetics," such as naturally occurring L amino acid residues or non-naturally occurring amino acid residues such as the D isomer of cyclohexylalanine. A derived or prepared epitope can be an analog of a natural epitope.

[0736] "Diluents" include sterile liquids such as water and oils, including those of petroleum, animal, vegetable, or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil, and the like. Water is also a diluent for pharmaceutical compositions. Saline solutions and aqueous dextrose and glycerol solutions can also be used as diluents, for example, in injectable solutions.

[0737] "Epitope" is the collective characteristics and charge of molecules such as primary, secondary and tertiary peptide structures, which together form a site recognized by, for example, an immunoglobulin, a T cell receptor, an HLA molecule or a chimeric antigen receptor. Alternatively, an epitope can be a group of amino acid residues involved in the recognition of a specific immunoglobulin, or in the case of a T cell, those residues necessary for recognition by a T cell receptor protein, a chimeric antigen receptor and / or a major histocompatibility complex (MHC) receptor. An epitope can be prepared by isolation from a natural source, or it can be synthesized according to standard protocols in the art. Synthetic epitopes can include artificial amino acid residues, "amino acid mimetics," such as naturally occurring L amino acid residues or non-naturally occurring amino acid residues such as the D isomer of cyclohexylalanine. Throughout this disclosure, an epitope may be referred to as a peptide or peptide epitope in some cases.

[0738] It is understood that proteins or peptides comprising the epitopes or analogs described herein and additional amino acids are still within the scope of the present disclosure.In certain embodiments, the peptide comprises an antigenic fragment.

[0739] In certain embodiments, there is limitation in the length of peptide of the present disclosure.When the protein or peptide comprising epi-position as herein described comprise the region (that is, a series of continuous amino acid residues) with 100% homogeneity of native sequence, there is embodiment with limited length.In order to avoid, for example, reading the definition of epi-position on whole natural molecule, there is limitation in the length of any region with 100% homogeneity of native peptide sequence.Therefore, for the peptide comprising epi-position as herein described and the region with 100% homogeneity of native peptide sequence, the region with 100% homogeneity of native sequence generally has following length: less than or equal to 600 amino acid residues, less than or equal to 500 amino acid residues, less than or equal to 400 amino acid residues, less than or equal to 250 amino acid residues, less than or equal to 100 amino acid residues, less than or equal to 85 amino acid residues, less than or equal to 75 amino acid residues, less than or equal to 65 amino acid residues and less than or equal to 50 amino acid residues. In certain embodiments, an “epitope” as described herein consists of a peptide having a region that is 100% identical to a native peptide sequence, said region having at least 51 amino acid residues, in any increment down to 5 amino acid residues; for example, 50, 49, 48, 47, 46, 45, 44, 43, 42, 41, 40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, or 5 amino acid residues.

[0740] "Human leukocyte antigens" or "HLA" are human class I or class II major histocompatibility complex (MITC) proteins (see, eg, Stites et al., IMMUNOLOGY, 8th ed., Lange Publishing, Los Altos, Calif. (1994)).

[0741] As used herein, "HLA supertype or HLA family" describes a collection of HLA molecules grouped based on shared peptide-binding specificities. HLA class I molecules that share a similar binding affinity for peptides bearing certain amino acid motifs are grouped into such HLA supertypes. The terms HLA superfamily, HLA supertype family, HLA family, and HLA xx-like molecule (where "xx" indicates a specific HLA type) are synonymous.

[0742] The term "identical" or percent "identity" in the context of two or more peptide sequences or antigenic fragments refers to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues that are the same, when compared and aligned for maximum correspondence over a comparison window, as measured using a sequence comparison algorithm or by manual alignment and visual inspection.

[0743] An "immunogenic" peptide or "immunogenic" epitope or "peptide epitope" is a peptide that contains an allele-specific motif such that the peptide will bind to an HLA molecule and induce a cell-mediated or humoral response, such as a cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL) and / or B lymphocyte response. Thus, the immunogenic peptides described herein are capable of binding to an appropriate HLA molecule and subsequently inducing a CTL (cytotoxic) response or an HTL (and humoral) response to the peptide.

[0744] As used herein, "chimeric antigen receptor" or "CAR" refers to an antigen binding protein, including an immunoglobulin antigen binding domain (e.g., immunoglobulin variable domain) and a T cell receptor (TCR) constant domain in the antigen binding protein. As used herein, the "constant domain" of a TCR polypeptide includes a near-membrane TCR constant domain and may also include a TCR transmembrane domain and / or a TCR cytoplasmic tail. For example, in some embodiments, CAR is a dimer comprising a first polypeptide comprising an immunoglobulin heavy chain variable domain connected to a TCR-β constant domain and a second polypeptide comprising an immunoglobulin light chain variable domain (e.g., 1c or 2\. variable domain) connected to a TCR α constant domain. In some embodiments, CAR is a dimer comprising a first polypeptide comprising an immunoglobulin heavy chain variable domain connected to a TCR α constant domain and a second polypeptide comprising an immunoglobulin light chain variable domain connected to a TCR β constant domain.

[0745] The phrases "isolated" or "biologically pure" refer to a substance that is substantially or essentially free of components that normally accompany it in its native state. Thus, the peptides described herein are free of some or all of the substances that normally associate with the peptide in its native environment. An "isolated" epitope is an epitope that does not include the entire sequence of the antigen from which the epitope is derived. Typically, an "isolated" epitope does not have additional amino acid residues attached to it that produce a sequence that is 100% identical over the entire length of the native sequence. A native sequence can be a sequence from which the epitope is derived, such as a viral antigen. Thus, the term "isolated" refers to a substance that is removed from its original environment (e.g., the natural environment if it is naturally occurring). For example, a naturally occurring polynucleotide or peptide present in a living organism is not isolated, but the same polynucleotide or peptide separated from some or all of the coexisting substances in the natural system is isolated. Such a polynucleotide can be part of a vector, and / or such a polynucleotide or peptide can be part of a composition and still be "isolated" because such a vector or composition is not part of its natural environment. RNA molecules include in vivo or in vitro RNA transcripts of the DNA molecules described herein, and also include such molecules produced synthetically.

[0746] The "major histocompatibility complex" or "MHC" is a cluster of genes that plays a role in the control of cellular interactions responsible for physiological immune responses. In humans, the MHC complex is also known as the human leukocyte antigen (HLA) complex. For a detailed description of the MHC and HLA complexes, see Paul, FUNDAMENTAL IMMUNOLOGY, 3.sup.RD ED., Raven Press, New York (1993).

[0747] A "native" or "wild-type" sequence is a sequence found in nature. Such a sequence may inherently comprise longer sequences.

[0748] "T-cell epitope" is understood to mean a peptide sequence which can be bound by an MHC molecule of class I or class II in the form of a peptide-presenting MHC molecule or MHC complex and which is subsequently recognized and bound in this form by cytotoxic T lymphocytes or T helper cells, respectively.

[0749] "Receptor" is understood to mean a biological molecule or group of molecules that is capable of binding to a ligand. Receptors can be used to transmit information in cells, cell formations, or organisms. A receptor comprises at least one receptor unit, for example, wherein each receptor unit can be composed of a protein molecule. The receptor has a structure that is complementary to that of the ligand and can complex with the ligand to form a binding partner. This information is transmitted, in particular, by a conformational change in the receptor after complexing with the ligand on the cell surface. In some embodiments, a receptor is understood to mean, in particular, a protein of MHC class I and class II that is capable of forming a receptor / ligand complex with the ligand, in particular a peptide or peptide fragment of suitable length.

[0750] "Ligand" is understood to mean a molecule having a structure complementary to that of a receptor and capable of forming a complex with this receptor. In some embodiments, a ligand is understood to mean a peptide or peptide fragment having a suitable length and a suitable binding motif in its amino acid sequence, such that the peptide or peptide fragment is able to form a complex with a protein of MHC class I or MHC class II.

[0751] In some embodiments, "receptor / ligand complex" is also understood to refer to a "receptor / peptide complex" or "receptor / peptide fragment complex" comprising a class I or class II peptide-presenting or peptide fragment-presenting MHC molecule.

[0752] "Proteins or molecules of the major histocompatibility complex (MHC)," "MHC molecules," "MHC proteins," or "HLA proteins" are understood to mean proteins that are capable of binding peptides generated by proteolytic cleavage of protein antigens and presenting potential lymphocyte epitopes (e.g., T-cell epitopes and B-cell epitopes), transporting said epitopes to the cell surface, and presenting them to specific cells (particularly cytotoxic T lymphocytes, T helper cells, or B cells). The major histocompatibility complex in the genome comprises genetic regions whose gene products expressed on the cell surface are crucial for binding and presenting endogenous and / or foreign antigens and, therefore, for regulating immune processes. The major histocompatibility complex is classified into two gene sets encoding different proteins, namely, MHC class I molecules and MHC class II molecules. The cell biology and expression patterns of the two MHC classes are adapted to these different roles.

[0753] The terms "peptide" and "peptide epitope" are used interchangeably with "oligopeptide" in this specification to refer to a series of residues interconnected, typically by peptide bonds between the α-amino and carboxyl groups of adjacent amino acid residues.

[0754] "Synthetic peptide" refers to a peptide obtained from a non-natural source, e.g., an artificial peptide. Such peptides can be produced using methods such as chemical synthesis or recombinant DNA technology. "Synthetic peptide" includes "fusion proteins."

[0755] A "PanDR binding" peptide, a "PanDR binding epitope" is a member of a family of molecules that binds to more than one HLA class II DR molecule.

[0756] "Pharmaceutically acceptable" refers to compositions or components of compositions that are generally non-toxic, inert, and / or physiologically compatible.

[0757] "Pharmaceutical excipients" or "excipients" include substances such as adjuvants, carriers, pH regulators and buffers, tonicity regulators, wetting agents, preservatives, and the like. A "pharmaceutical excipient" is a pharmaceutically acceptable excipient. The term "motif" refers to a pattern of residues in an amino acid sequence of a defined length, such as a peptide of less than about 15 amino acid residues in length or less than about 13 amino acid residues in length, for example, about 8 to about 13 amino acid residues (e.g., 8, 9, 10, 11, 12, or 13) for a class I HLA motif and about 6 to about 25 amino acid residues (e.g., 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25) for a class II HLA motif, which is recognized by a specific HLA molecule. The motif is generally different for each HLA protein encoded by a given human HLA allele. These motifs differ in their pattern of primary and secondary anchor residues.In some embodiments, the MHC class I motif recognizes peptides that are 9, 10, or 11 amino acid residues in length.

[0758] A "supermotif" is a peptide binding specificity shared by HLA molecules encoded by two or more HLA alleles. In some embodiments, a peptide carrying a supermotif as described herein is recognized by two or more HLA antigens with high or intermediate affinity (as defined herein).

[0759] As used herein, the term "naturally occurring" refers to the fact that an object can be found in nature. For example, a peptide or nucleic acid that is present in an organism (including a virus) and that can be derived from a source in nature and has not been intentionally modified by man in a laboratory is naturally occurring.

[0760] According to the present disclosure, the term "vaccine" refers to a pharmaceutical preparation (pharmaceutical composition) or product that induces an immune response (e.g., a cellular or humoral immune response) upon administration that recognizes and attacks pathogens or diseased cells (such as cells infected with a virus). Vaccines can be used to prevent or treat disease.

[0761] A "protective immune response" or "therapeutic immune response" refers to a CTL and / or HTL response to an antigen derived from a pathogenic antigen (e.g., a viral antigen) that in some way prevents or at least partially suppresses disease symptoms, side effects, or progression. The immune response may also include an antibody response that has been promoted by stimulating helper T cells.

[0762] "Antigen processing" or "processing" refers to the degradation of a polypeptide or antigen into processing products that are fragments of the polypeptide or antigen (e.g., degradation of a polypeptide into peptides), and the association (e.g., by binding) of one or more of these fragments with MHC molecules for presentation by a cell (e.g., an antigen-presenting cell) to a specific T cell.

[0763] "Antigen presenting cells" (APCs) are cells that present peptide fragments of protein antigens associated with MHC molecules on their cell surface. Some APCs can activate antigen-specific T cells. Professional antigen presenting cells are very efficient in internalizing antigens by phagocytosis or by receptor-mediated endocytosis, and then display antigen fragments bound to class II MHC molecules on their membranes. T cells recognize and interact with the antigen class II MHC molecule complexes on the antigen presenting cell membrane. Subsequently, the antigen presenting cells produce additional costimulatory signals, leading to T cell activation. The expression of costimulatory molecules is a defining characteristic of professional antigen presenting cells.

[0764] The major types of professional antigen-presenting cells are dendritic cells, which have the broadest repertoire of antigen presentation and are probably the most important antigen-presenting cells, macrophages, B cells, and certain activated epithelial cells.

[0765] Dendritic cells (DCs) are a population of white blood cells that present antigens captured in peripheral tissues to T cells via the MHC class II and class I antigen presentation pathways. It is well known that DCs are potent inducers of immune responses, and the activation of these cells is a key step in the induction of antiviral immunity.

[0766] Dendritic cells are conveniently classified as "immature" and "mature" cells, which serves as a simple way to distinguish between two well-characterized phenotypes. However, this nomenclature should not be interpreted as excluding all possible intermediate differentiation stages.

[0767] Immature dendritic cells are characterized as antigen presenting cells with high antigen uptake and processing capacity, which are associated with high expression of Fey receptors and mannose receptors. The typical feature of the mature phenotype is that the expression of these markers is low, but the expression of cell surface molecules (such as class I and class II MHC), adhesion molecules (such as CD54 and CD11) and costimulatory molecules (such as CD40, CD80, CD86 and 4-1BB) responsible for T cell activation is high.

[0768] The term "residue" refers to an amino acid residue or amino acid mimetic residue incorporated into a peptide or protein via an amide bond or an amide bond mimetic, or a nucleic acid (DNA or RNA) encoding an amino acid or amino acid mimetic.

[0769] The nomenclature used to describe peptides or proteins follows a convention in which the amino group is located to the left of each amino acid residue (the amino terminus or N-terminus) and the carboxyl group is located to the right (the carboxyl terminus or C-terminus). When referring to amino acid residue positions in a peptide epitope, the positions are numbered in an amino to carboxyl direction, with position one being the residue at the amino terminus of the epitope or a peptide or protein of which it may be a part.

[0770] In the formula representing the selected specific embodiments of the present disclosure, unless otherwise indicated, the amino terminal group and the carboxyl terminal group (although not specifically shown) are in a form that will be presented at physiological pH values. In the amino acid structural formula, each residue is generally represented by a standard three-letter or single-letter name. The L-type of the amino acid residue is represented by the capital initials of the uppercase single letter or three-letter symbol, and the D-type of the amino acid residue with the D-type is represented by a lowercase single letter or lowercase three-letter symbol. However, when using three-letter symbols or full names instead of capital letters, it can refer to L amino acid residues. Glycine does not have an asymmetric carbon atom and is abbreviat...

Claims

1. A method for treating or preventing viral infection or treating respiratory diseases or disorders associated with viral infection, comprising administering a pharmaceutical composition to a subject suffering from B cell immunodeficiency, the pharmaceutical composition comprising: (i) a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, (b) a sequence comprising an epitope sequence from a membrane glycoprotein (M), and (c) a sequence comprising an epitope sequence from a nucleocapsid phosphoprotein (N); (ii) a polynucleotide encoding a polypeptide, wherein the polypeptide comprises at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, (b) a sequence comprising an epitope sequence from a membrane glycoprotein (M), and (c) a sequence comprising an epitope sequence from a nucleocapsid phosphoprotein (N); (iii) a T cell receptor (TCR) or a T cell comprising said TCR, wherein said TCR binds to an epitope sequence of said polypeptide in complex with a corresponding HLA class I or class II molecule; (iv) an antigen presenting cell comprising (i) or (ii); or (v) an antibody or a B cell comprising the antibody, wherein the antibody binds to an epitope sequence of the polypeptide.

2. The method of claim 1, wherein the subject has a reduced ability to produce an antibody response to an antigen compared to a subject without B cell immunodeficiency, or wherein the subject has a reduced ability to produce an anti-spike protein antibody response and / or an anti-RBD antibody response compared to a subject without B cell immunodeficiency.

3. The method of claim 1, wherein the subject is capable of generating a T cell response or has no reduced ability to generate a T cell response compared to a subject that does not suffer from B cell immunodeficiency.

4. The method of claim 1, wherein the pharmaceutical composition has a protective effect against variants of 2019 SARS CoV-2.

5. The method of claim 1, wherein the subject generates a T cell response to an epitope of the polypeptide.

6. The method of claim 1, wherein the subject is an organ transplant recipient, or suffers from cancer or autoimmune disease or HIV or AIDS or suffers from age-related immune decline, or immunosenescence, or multifactorial immunodeficiency, or age-related immunodeficiency.

7. The method of claim 1, wherein the composition comprises the polynucleotide encoding the polypeptide.

8. The method of claim 7, wherein the polynucleotide is mRNA.

9. The method of claim 1, wherein the composition comprises (i) a polypeptide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% sequence identity to a sequence selected from the group consisting of RS C1p1full, RS C2p1full, RS C3p1full, RS C4p1full, RS C5p1, RS C5p2, RS C5p2full, RS C6p1, RS C6p2, RS C6p2full, RS C7p1, RS C7p2, RS C7p2full, RS C7p4, RSC7p4full, RS C8p1, RS C8p2, and RS C8p2full; and (ii) a polynucleotide encoding a polypeptide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% sequence identity to a sequence selected from the group consisting of RS RS C4n1, RS C5n1, RS C6n1, RS C7n1, RS C8n1, RS C5n2, RS C6n2, RS C7n1, RS C7p2, RS C7p2full, RS C7p4, RS C7p4full, RS C8p1, RS C8p2, and RS C8p2full; or (iii) a polynucleotide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% sequence identity to a sequence selected from the group consisting of SEQ ID NO: RS C1n1, RS C2n1, RS C3n1, RS C4n1, RS C5n1, RS C6n1, RS C7n1, RS C8n1, RS C5n2, RS C6n2, RS C7n2, RS C8n2, RS C5n2full, RS C6n2full, RS C7n2full, RSC8n2full, RS C7n4 and RS C7n4full.

10. The method of claim 1, wherein the composition comprises (i) a polypeptide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% sequence identity to a sequence selected from the group consisting of RS C7p1, RS C7p2, RS C7p2full, RS C7p4 and RS C7p4full; or (iii) a polynucleotide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% sequence identity to a sequence selected from the group consisting of SEQ ID NO: RS C7n1, RS C7n2, RS C7n2full, RS C7n4 and RSC7n4full.

11. A method for treating or preventing viral infection or treating respiratory diseases or disorders associated with viral infection, comprising administering a pharmaceutical composition to a subject suffering from B cell immunodeficiency, the pharmaceutical composition comprising: (i) a polypeptide comprising an epitope sequence of Table 1A, Table 1B, Table 1C, Table 2Ai, Table 2Aii, Table 2B and / or Table 16; (ii) a polynucleotide encoding a polypeptide comprising an epitope sequence of Table 1A, Table 1B, Table 1C, Table 2Ai, Table 2Aii, Table 2B and / or Table 16; (iii) a T cell receptor (TCR) or a T cell comprising said TCR, wherein said TCR binds to said epitope sequence in complex with a corresponding HLA class I or class II molecule; (iv) an antigen presenting cell comprising (i) or (ii); or (v) an antibody or a B cell comprising the antibody, wherein the antibody binds to the epitope sequence.

12. A method for treating or preventing viral infection or treating respiratory diseases or disorders associated with viral infection, comprising administering a pharmaceutical composition to a subject with B cell immunodeficiency, the pharmaceutical composition comprising: a polypeptide having an amino acid sequence that has at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% sequence identity to any of the sequences depicted in Column 2 of Table 11, Column 2 of Table 12, or Column 3 of Table 15; or a recombinant polynucleotide encoding a polypeptide having an amino acid sequence that has at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% sequence identity to any of the sequences depicted in Column 2 of Table 11, Column 2 of Table 12, or Column 3 of Table 15.

13. The method of claim 12, wherein the pharmaceutical composition comprises: a polypeptide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% sequence identity to a sequence selected from the group consisting of RS C1p1full, RS C2p1full, RS C3p1full, RS C4p1full, RS C5p1, RS C5p2, RS C5p2full, RS C6p1, RS C6p2, RS C6p2full, RS C7p1, RS C7p2, RS C7p2full, RS C7p4, RSC7p4full, RS C8p1, RS C8p2, and RS C8p2full; or a polynucleotide encoding a polypeptide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% sequence identity to a sequence selected from the group consisting of RS C1p1full, RS C2p1full, RS C3p1full, RS C4p1full, RS C5p1, RS C5p2, RSC5p2full, RS C6p1, RS C6p2, RS C6p2full, RS C7p1, RS C7p2, RS C7p2full, RS C7p4, RSC7p4full, RS C8p1, RS C8p2, and RS C8p2full.

14. The method of claim 12, wherein the pharmaceutical composition comprises a polynucleotide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% sequence identity to a sequence selected from the group consisting of SEQ ID NO: RS C1n1, RS C2n1, RS C3n1, RS C4n1, RS C5n1, RS C6n1, RS C7n1, RS C8n1, RS C5n2, RS C6n2, RS C7n2, RS C8n2, RS C5n2full, RS C6n2full, RS C7n2full, RS C8n2full, RS C7n4, RS C7pn4full.

15. The method of any one of claims 1, 11 or 12, wherein the polynucleotide is mRNA.

16. The method of any one of claims 1, 11 or 12, wherein the pharmaceutical composition further comprises one or more lipid components.

17. The method of claim 16, wherein the one or more lipids comprise lipid nanoparticles (LNPs).

18. The method of claim 17, wherein the LNP encapsulates a recombinant polynucleotide construct.

19. A method for treating or preventing viral infection or treating respiratory diseases or disorders associated with viral infection, comprising administering to a subject in need thereof a pharmaceutical composition comprising: (i) a recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from a membrane glycoprotein (M), and a sequence comprising an epitope sequence from a nucleocapsid phosphoprotein (N); and (ii) a recombinant polynucleotide encoding the 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; The ratio (eg, mass ratio) of (i):(ii) is greater than 20:1 or less than 1:

20.

20. A method for treating or preventing viral infection or treating respiratory diseases or disorders associated with viral infection, comprising administering to a subject in need thereof: (i) a first pharmaceutical composition comprising a first recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from a membrane glycoprotein (M), and a sequence comprising an epitope sequence from a nucleocapsid phosphoprotein (N); and (ii) a second pharmaceutical composition comprising a second recombinant polynucleotide encoding the 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; The ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is 1:50 to 50:

1.

21. A method for treating or preventing viral infection or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject in need thereof a pharmaceutical composition comprising nanoparticles, wherein the nanoparticles comprise: (i) a first recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from a membrane glycoprotein (M), and a sequence comprising an epitope sequence from a nucleocapsid phosphoprotein (N); and (ii) a second recombinant polynucleotide encoding the 2019 SARS-CoV 2 spike protein or a variant or fragment thereof.

22. The method of claim 21, wherein the nanoparticles are present in the pharmaceutical composition at a dose of 100 ng to 500 micrograms.

23. The method of claim 21 or 22, wherein the ratio (eg, mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:50 to 50:

1.

24. A method for treating or preventing viral infection or treating respiratory diseases or disorders associated with viral infection, comprising administering to a subject in need thereof: (i) a first pharmaceutical composition comprising a first nanoparticle, wherein the first nanoparticle comprises a recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from a membrane glycoprotein (M), and a sequence comprising an epitope sequence from a nucleocapsid phosphoprotein (N); and (ii) a second pharmaceutical composition comprising a second nanoparticle, wherein the second nanoparticle comprises a recombinant polynucleotide encoding the 2019 SARS-CoV 2 spike protein or a variant or fragment thereof.

25. The method of claim 24, wherein the ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:50 to 50:

1.

26. The method of claim 24 or 25, wherein the first nanoparticles are present in the first pharmaceutical composition at a dose of about 100 ng to 500 micrograms.

27. The method of any one of claims 24-26, wherein the second nanoparticles are present in the second pharmaceutical composition at a dose of about 100 ng to 500 micrograms.

28. A method for treating or preventing viral infection or treating respiratory diseases or disorders associated with viral infection, comprising administering to a subject in need thereof: (i) A pharmaceutical composition comprising: (a) a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); or (b) a polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii)(a) a pharmaceutical composition comprising: a polypeptide having an amino acid sequence of a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; (b) a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; or a 2019 SARS-CoV 2 spike protein pharmaceutical composition comprising (ii)(a) or (ii)(b); wherein the subject receives a dose of (ii)(a) or (ii)(b) that is lower than the dose that would be received if (ii)(a) or (ii)(b) were administered alone to the subject.

29. A method for treating or preventing viral infection or treating respiratory diseases or disorders associated with viral infection, comprising administering to a subject in need thereof: (i) A pharmaceutical composition comprising: (a) a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); or (b) a polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii)(a) a pharmaceutical composition comprising: a polypeptide having an amino acid sequence of a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; (b) a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; or a 2019 SARS-CoV 2 spike protein pharmaceutical composition comprising (ii)(a) or (ii)(b); wherein the subject receives a number of doses of (ii)(a) or (ii)(b) that is less than the number of doses that would be administered to the subject if (ii)(a) or (ii)(b) were administered alone.

30. The method of claim 28, wherein the subject receives a dose of (ii)(a) or (ii)(b) that is at least 1.1, 1, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100-fold lower than the dose of (ii)(a) or (ii)(b) administered to the subject alone.

31. The method of claim 29, wherein the subject receives 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 fewer doses of (ii)(a) or (ii)(b) than the number of doses of (ii)(a) or (ii)(b) administered alone to the subject.

32. The method of claim 28 or 29, wherein the pharmaceutical composition of (i) is co-formulated with the pharmaceutical composition of (ii), wherein the pharmaceutical composition of (i) is formulated separately from the pharmaceutical composition of (ii), or wherein the pharmaceutical composition of (i) is administered separately from the pharmaceutical composition of (ii).

33. A method for treating or preventing viral infection or treating respiratory diseases or disorders associated with viral infection, comprising administering to a subject in need thereof: (i) A pharmaceutical composition comprising: (a) a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); or (b) a polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a pharmaceutical composition comprising: (a) a polypeptide having an amino acid sequence of a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; (b) a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; or a 2019 SARS-CoV 2 spike protein pharmaceutical composition comprising (ii)(a) or (ii)(b); wherein the subject receives a dose of (i)(a) or (i)(b) that is lower than the dose of (i)(a) or (i)(b) administered alone to the subject.

34. A method for treating or preventing viral infection or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject in need thereof: (i) A pharmaceutical composition comprising: (a) a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); or (b) a polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a pharmaceutical composition comprising: (a) a polypeptide having an amino acid sequence of a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; (b) a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; or a 2019 SARS-CoV 2 spike protein pharmaceutical composition comprising (ii)(a) or (ii)(b); wherein the subject receives a number of doses of (i)(a) or (i)(b) that is less than the number of doses that would be administered to the subject if (i)(a) or (i)(b) were administered alone.

35. The method of claim 33, wherein the subject receives a dose of (i)(a) or (i)(b) that is at least 1.1, 1, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100-fold lower than the dose of (i)(a) or (i)(b) administered to the subject alone.

36. The method of claim 34, wherein the subject receives 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 fewer doses of (i)(a) or (i)(b) than the number of doses of (i)(a) or (i)(b) administered alone to the subject.

37. The method of claim 33 or 34, wherein the pharmaceutical composition of (i) is co-formulated with the pharmaceutical composition of (ii), wherein the pharmaceutical composition of (i) is formulated separately from the pharmaceutical composition of (ii), or wherein the pharmaceutical composition of (i) is administered separately from the pharmaceutical composition of (ii).

38. A method for treating or preventing viral infection or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject in need thereof: (i) A pharmaceutical composition comprising: (a) a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); or (b) a polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); wherein the pharmaceutical composition is administered at a first time point, a second time point, and a third time point, wherein the second time point is at least about 2 days after the first time point and the third time point is at least about 2 days after the second time point.

39. The method of claim 38, wherein the second time point is at least about, at most about, or about 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, or 35 days after the first time point, and wherein the second time point is at least about, at most about, or about 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, or 35 days after the first time point. 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, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 40. The method of claim 38 or 39, wherein the third time point is at least about, at most about, or about 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, or 35 days after the second time point, and wherein the third time point is at least about, at most about, or about 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, or 35 days after the second time point. 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, 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, 99, 41. The method of any one of claims 38-40, wherein the third time point is at least about, at most about, or about 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, or 36 days after the first time point, and wherein the third time point is at least about, at most about, or about 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, or 36 days after the first time point. 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34 or 35 weeks after, or at least about 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 or 35 months after, said first time point.

42. A pharmaceutical composition comprising: (i) a recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from a membrane glycoprotein (M), and a sequence comprising an epitope sequence from a nucleocapsid phosphoprotein (N); and (ii) a recombinant polynucleotide encoding the 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; The ratio (eg, mass ratio) of (i):(ii) is greater than 20:1 or less than 1:

20.

43. A composition comprising: (i) a first pharmaceutical composition comprising a first recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from a membrane glycoprotein (M), and a sequence comprising an epitope sequence from a nucleocapsid phosphoprotein (N); and (ii) a second pharmaceutical composition comprising a second recombinant polynucleotide encoding the 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; The ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is 1:50 to 50:

1.

44. A pharmaceutical composition comprising nanoparticles, wherein the nanoparticles comprise: (i) a first recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from a membrane glycoprotein (M), and a sequence comprising an epitope sequence from a nucleocapsid phosphoprotein (N); and (ii) a second recombinant polynucleotide encoding the 2019 SARS-CoV 2 spike protein or a variant or fragment thereof.

45. The pharmaceutical composition of claim 44, wherein the nanoparticles are present in the pharmaceutical composition at a dose of 100 ng to 500 micrograms.

46. ​​The pharmaceutical composition of claim 44 or 45, wherein the ratio (eg, mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:50 to 50:

1.

47. A composition comprising: (i) a first pharmaceutical composition comprising a first nanoparticle, wherein the first nanoparticle comprises a recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from a membrane glycoprotein (M), and a sequence comprising an epitope sequence from a nucleocapsid phosphoprotein (N); and (ii) a second pharmaceutical composition comprising a second nanoparticle, wherein the second nanoparticle comprises a recombinant polynucleotide encoding the 2019 SARS-CoV 2 spike protein or a variant or fragment thereof.

48. The composition of claim 47, wherein the ratio (e.g., mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:50 to 50:

1.

49. The composition of claim 47 or 48, wherein the first nanoparticles are present in the first pharmaceutical composition at a dose of about 100 ng to 500 micrograms.

50. The composition of any one of claims 47-49, wherein the second nanoparticles are present in the second pharmaceutical composition at a dose of about 100 ng to 500 micrograms.

51. The composition of any one of claims 47-50, wherein the recombinant polynucleotide in (i) is present in the first pharmaceutical composition at a dose of about 50 ng to 250 micrograms.

52. The composition of any one of claims 47-51, wherein the recombinant polynucleotide in (ii) is present in the second pharmaceutical composition at a dose of about 50 ng to 250 micrograms.

53. The composition of any one of claims 21-27 and 44-52, wherein the nanoparticle is a lipid nanoparticle.

54. A method for treating or preventing viral infection or treating respiratory diseases or disorders associated with viral infection, comprising administering to a subject in need thereof a pharmaceutical composition comprising: (i) a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, (b) a sequence comprising an epitope sequence from a membrane glycoprotein (M), and (c) a sequence comprising an epitope sequence from a nucleocapsid phosphoprotein (N); (ii) a polynucleotide encoding a polypeptide, wherein the polypeptide comprises at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, (b) a sequence comprising an epitope sequence from a membrane glycoprotein (M), and (c) a sequence comprising an epitope sequence from a nucleocapsid phosphoprotein (N); (iii) a T cell receptor (TCR) or a T cell comprising said TCR, wherein said TCR binds to an epitope sequence of said polypeptide in complex with a corresponding HLA class I or class II molecule; (iv) an antigen presenting cell comprising (i) or (ii); or (v) an antibody or a B cell comprising the antibody, wherein the antibody binds to an epitope sequence of the polypeptide.

55. The method of claim 54, wherein the subject is immunodeficient.

56. The method of claim 55, wherein the subject suffers from B cell immunodeficiency.

57. The method of claim 54, wherein the composition comprises (i) a polypeptide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% sequence identity to a sequence selected from the group consisting of RS C1p1full, RS C2p1full, RS C3p1full, RS C4p1full, RS C5p1, RS C5p2, RS C5p2full, RS C6p1, RS C6p2, RS C6p2full, RS C7p1, RS C7p2, RS C7p2full, RS C7p4, RSC7p4full, RS C8p1, RS C8p2, and RS C8p2full; and (ii) a polynucleotide encoding a polypeptide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% sequence identity to a sequence selected from the group consisting of RS RS C4n1, RS C5n1, RS C6n1, RS C7n1, RS C8n1, RS C5n2, RS C6n2, RS C7n1, RS C7p2, RS C7p2full, RS C7p4, RS C7p4full, RS C8p1, RS C8p2, and RS C8p2full; or (iii) a polynucleotide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% sequence identity to a sequence selected from the group consisting of SEQ ID NO: RS C1n1, RS C2n1, RS C3n1, RS C4n1, RS C5n1, RS C6n1, RS C7n1, RS C8n1, RS C5n2, RS C6n2, RS C7n2, RS C8n2, RS C5n2full, RS C6n2full, RS C7n2full, RSC8n2full, RS C7n4 and RS C7n4full.

58. A method as described in claim 54, wherein the composition comprises (i) a polypeptide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% sequence identity to a sequence selected from the group consisting of: RS C7p1, RS C7p2, RS C7p2full, RS C7p4 and RS C7p4full; or (iii) a polynucleotide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% sequence identity to a sequence selected from the group consisting of: SEQ ID NO: RS C7n1, RS C7n2, RS C7n2full, RS C7n4 and RSC7n4full.

59. A method for treating or preventing viral infection or treating respiratory diseases or disorders associated with viral infection, comprising administering to a subject in need thereof a pharmaceutical composition comprising: (i) a polypeptide comprising an epitope sequence of Table 1A, Table 1B, Table 1C, Table 2Ai, Table 2Aii, Table 2B and / or Table 16; (ii) a polynucleotide encoding a polypeptide comprising an epitope sequence of Table 1A, Table 1B, Table 1C, Table 2Ai, Table 2Aii, Table 2B and / or Table 16; (iii) a T cell receptor (TCR) or a T cell comprising said TCR, wherein said TCR binds to said epitope sequence in complex with a corresponding HLA class I or class II molecule; (iv) an antigen presenting cell comprising (i) or (ii); or (v) an antibody or a B cell comprising the antibody, wherein the antibody binds to the epitope sequence.

60. The method of claim 59, wherein the subject is immunodeficient.

61. The method of claim 60, wherein the subject suffers from B cell immunodeficiency.

62. A method for treating or preventing viral infection or treating respiratory diseases or disorders associated with viral infection, comprising administering a pharmaceutical composition to a subject in need thereof, the pharmaceutical composition comprising: a polypeptide having an amino acid sequence that has at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% sequence identity to any of the sequences depicted in Column 2 of Table 11, Column 2 of Table 12, or Column 3 of Table 15; or a recombinant polynucleotide encoding a polypeptide having an amino acid sequence that has at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% sequence identity to any of the sequences depicted in Column 2 of Table 11, Column 2 of Table 12, or Column 3 of Table 15.

63. The method of claim 62, wherein the subject is immunodeficient.

64. The method of claim 63, wherein the subject suffers from B cell immunodeficiency.

65. The method of claim 62, wherein the pharmaceutical composition comprises: a polypeptide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% sequence identity to a sequence selected from the group consisting of RS C1p1full, RS C2p1full, RS C3p1full, RS C4p1full, RS C5p1, RS C5p2, RS C5p2full, RS C6p1, RS C6p2, RS C6p2full, RS C7p1, RS C7p2, RS C7p2full, RS C7p4, RSC7p4full, RS C8p1, RS C8p2, and RS C8p2full; or a polynucleotide encoding a polypeptide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% sequence identity to a sequence selected from the group consisting of RS C1p1full, RS C2p1full, RS C3p1full, RS C4p1full, RS C5p1, RS C5p2, RSC5p2full, RS C6p1, RS C6p2, RS C6p2full, RS C7p1, RS C7p2, RS C7p2full, RS C7p4, RSC7p4full, RS C8p1, RS C8p2, and RS C8p2full.

66. The method of claim 62, wherein the pharmaceutical composition comprises a polynucleotide having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or 100% sequence identity to a sequence selected from the group consisting of SEQ ID NO: RS C1n1, RS C2n1, RS C3n1, RS C4n1, RS C5n1, RS C6n1, RS C7n1, RS C8n1, RS C5n2, RS C6n2, RS C7n2, RS C8n2, RS C5n2full, RS C6n2full, RS C7n2full, RS C8n2full, RS C7n4, RS C7n4full.

67. The method of any one of claims 54, 59 or 62, wherein the polynucleotide is mRNA.

68. The method of any one of claims 54, 59 or 62, wherein the pharmaceutical composition further comprises one or more lipids.

69. The method of claim 68, wherein the one or more lipids comprise lipid nanoparticles (LNPs).

70. The method of claim 69, wherein the LNP encapsulates a recombinant polynucleotide construct.

71. A method for treating or preventing a viral infection or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject in need thereof a pharmaceutical composition comprising: (i) a recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from a membrane glycoprotein (M), and a sequence comprising an epitope sequence from a nucleocapsid phosphoprotein (N); and (ii) a recombinant polynucleotide encoding the 2019 SARS-CoV 2 spike protein or a variant or fragment thereof.

72. A method for treating or preventing a viral infection or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject in need thereof: (i) a first pharmaceutical composition comprising a first recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from a membrane glycoprotein (M), and a sequence comprising an epitope sequence from a nucleocapsid phosphoprotein (N); and (ii) a second pharmaceutical composition comprising a second recombinant polynucleotide encoding the 2019 SARS-CoV 2 spike protein or a variant or fragment thereof.

73. The method of claim 71 or 72, wherein the ratio (e.g., mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is 20:1 to 1:

20.

74. A method for treating or preventing a viral infection or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject in need thereof a pharmaceutical composition comprising: (i) a first recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from a membrane glycoprotein (M), and a sequence comprising an epitope sequence from a nucleocapsid phosphoprotein (N); and (ii) a second recombinant polynucleotide encoding the 2019 SARS-CoV 2 spike protein or a variant or fragment thereof.

75. The method of claim 71 or 74, wherein the pharmaceutical composition comprises nanoparticles, wherein the nanoparticles comprise the first recombinant polynucleotide and the second recombinant polynucleotide.

76. The method of claim 75, wherein the nanoparticles are present in the pharmaceutical composition at a dose of 100 ng to 500 micrograms.

77. The method of any one of claims 74-76, wherein the ratio (e.g., mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:50 to 50:

1.

78. A method of treating or preventing a viral infection or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject in need thereof: (i) a first pharmaceutical composition comprising a recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from a membrane glycoprotein (M), and a sequence comprising an epitope sequence from a nucleocapsid phosphoprotein (N); and (ii) a second pharmaceutical composition comprising a recombinant polynucleotide encoding the 2019 SARS-CoV 2 spike protein or a variant or fragment thereof.

79. The method of claim 78, wherein the ratio (e.g., mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:50 to 50:

1.

80. A method as described in claim 72 or 78, wherein the first pharmaceutical composition comprises a first nanoparticle, wherein the first nanoparticle comprises a recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from a membrane glycoprotein (M), and a sequence comprising an epitope sequence from a nucleocapsid phosphoprotein (N); and wherein the second pharmaceutical composition comprises a second nanoparticle, wherein the second nanoparticle comprises a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof.

81. The method of claim 80, wherein the first nanoparticles are present in the first pharmaceutical composition at a dose of about 100 ng to 500 micrograms.

82. The method of claim 80, wherein the second nanoparticles are present in the second pharmaceutical composition at a dose of about 100 ng to 500 micrograms.

83. A method of treating or preventing a viral infection or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject in need thereof: (i) A pharmaceutical composition comprising: (a) a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); or (b) a polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii)(a) a pharmaceutical composition comprising: a polypeptide having an amino acid sequence of a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; (b) a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; or a 2019 SARS-CoV 2 spike protein pharmaceutical composition comprising (ii)(a) or (ii)(b); wherein the subject receives a dose of (ii)(a) or (ii)(b) that is lower than the dose that would be received if (ii)(a) or (ii)(b) were administered alone to the subject.

84. A method of treating or preventing a viral infection or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject in need thereof: (i) A pharmaceutical composition comprising: (a) a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); or (b) a polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii)(a) a pharmaceutical composition comprising: a polypeptide having an amino acid sequence of a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; (b) a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; or a 2019 SARS-CoV 2 spike protein pharmaceutical composition comprising (ii)(a) or (ii)(b); wherein the subject receives a number of doses of (ii)(a) or (ii)(b) that is less than the number of doses that would be administered to the subject if (ii)(a) or (ii)(b) were administered alone.

85. The method of claim 83, wherein the subject receives a dose of (ii)(a) or (ii)(b) that is at least 1.1, 1, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100-fold lower than the dose of (ii)(a) or (ii)(b) administered alone to the subject.

86. The method of claim 84, wherein the subject receives 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 doses of (ii)(a) or (ii)(b) less than the number of doses of (ii)(a) or (ii)(b) administered alone to the subject.

87. The method of claim 83 or 84, wherein the pharmaceutical composition of (i) is co-formulated with the pharmaceutical composition of (ii), wherein the pharmaceutical composition of (i) is formulated separately from the pharmaceutical composition of (ii), or wherein the pharmaceutical composition of (i) is administered separately from the pharmaceutical composition of (ii).

88. A method of treating or preventing a viral infection or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject in need thereof: (i) A pharmaceutical composition comprising: (a) a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); or (b) a polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a pharmaceutical composition comprising: (a) a polypeptide having an amino acid sequence of a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; (b) a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; or a 2019 SARS-CoV 2 spike protein pharmaceutical composition comprising (ii)(a) or (ii)(b); wherein the subject receives a dose of (i)(a) or (i)(b) that is lower than the dose of (i)(a) or (i)(b) administered alone to the subject.

89. A method for treating or preventing a viral infection or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject in need thereof: (i) A pharmaceutical composition comprising: (a) a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); or (b) a polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); and (ii) a pharmaceutical composition comprising: (a) a polypeptide having an amino acid sequence of a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; (b) a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; or a 2019 SARS-CoV 2 spike protein pharmaceutical composition comprising (ii)(a) or (ii)(b); wherein the subject receives a number of doses of (i)(a) or (i)(b) that is less than the number of doses that would be administered to the subject if (i)(a) or (i)(b) were administered alone.

90. The method of claim 88, wherein the subject receives a dose of (i)(a) or (i)(b) that is at least 1.1, 1, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100-fold lower than the dose of (i)(a) or (i)(b) administered to the subject alone.

91. The method of claim 89, wherein the subject receives 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 doses of (i)(a) or (i)(b) less than the number of doses of (i)(a) or (i)(b) administered alone to the subject.

92. The method of claim 88 or 89, wherein the pharmaceutical composition of (i) is co-formulated with the pharmaceutical composition of (ii), wherein the pharmaceutical composition of (i) is formulated separately from the pharmaceutical composition of (ii), or wherein the pharmaceutical composition of (i) is administered separately from the pharmaceutical composition of (ii).

93. The method of any one of claims 28-41, 54-71, 73-77, and 83-92, wherein the pharmaceutical composition is administered at a first time point and a second time point, wherein the second time point is at least about, at most about, or about 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, or 36 days after the first time point; or at least about, at most about, or about 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, or 36 months after said first time point.

94. The method of claim 93, wherein the pharmaceutical composition is administered at a third time point, wherein the third time point is at least about, at most about, or about 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, or 36 days after the second time point; or at least about, at most about, or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or at least about, at most about, or about 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 or 36 months after the second time point.

95. The method of claim 94, wherein the third time point is at least about, at most about, or about 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 50 days after the first time point; or at least about, at most about, or about 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, or 36 months after said first time point.

96. The method of any one of claims 20-27, 72, 73, and 78-82, wherein the first pharmaceutical composition is administered at a first time point and a second time point, wherein the second time point is at least about, at most about, or about 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, or 36 days after the first time point; or at least about, at most about, or about 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 or 36 months after said first time point.

97. The method of claim 96, wherein the first pharmaceutical composition is administered at a third time point, wherein the third time point is at least about, at most about, or about 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, or 36 days after the second time point; and at least about, at most about, or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or at least about, at most about, or about 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 or 36 months after the second time point.

98. The method of claim 97, wherein the third time point is at least about, at most about, or about 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 50 days after the first time point; or at least about, at most about, or about 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, or 36 months after said first time point.

99. The method of any one of claims 96-98, wherein the second pharmaceutical composition is administered at the first time point.

100. The method of any one of claims 96-99, wherein the second pharmaceutical composition is administered at the second time point.

101. The method of any one of claims 96-100, wherein the second pharmaceutical composition is administered at the third time point.

102. The method of any one of claims 96-98, 100 or 101, wherein at least about, at most about, or about 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 or 36 days after the first time point; at least about, at most about, or about 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 or 36 days after the first time point; or at least about, at most about, or about 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, or 36 months after said first time point.

103. The method of any one of claims 96-98 or 101, wherein at least about, at most about, or about 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, or 36 days after the second time point; at least about, at most about, or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or at least about, at most about, or about 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, or 36 months after said second time point.

104. A method of treating or preventing a viral infection or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject in need thereof: (i) A pharmaceutical composition comprising: (a) a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); or (b) a polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from membrane glycoprotein (M), and a sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N); wherein the pharmaceutical composition is administered at a first time point and a second time point, wherein the second time point is at least about 2 days after the first time point.

105. The method of claim 104, wherein the pharmaceutical composition is administered at a third time point, wherein the third time point is at least about 2 days after the second time point.

106. The method of claim 104 or 105, wherein the second time point is at least about, at most about, or about 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, or 35 days after the first time point, and the second time point is at least about, at most about, or about 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, or 35 days after the first time point. 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, or 35 months after said first time point.

107. The method of claim 105 or 106, wherein the third time point is at least about, at most about, or about 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, or 35 days after the second time point, and the third time point is at least about, at most about, or about 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, or 35 days after the second time point. 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34 or 35 weeks after the second time point, or at least about 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 or 35 months after the second time point.

108. The method of any one of claims 105-107, wherein the third time point is at least about, at most about, or about 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, or 36 days after the first time point, and wherein the third time point is at least about, at most about, or about 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, or 36 days after the first time point. 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34 or 35 weeks after, or at least about 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 or 35 months after, said first time point.

109. The method of any one of claims 104-108, wherein the method further comprises administering to the subject: (ii)(a) a polypeptide having an amino acid sequence of a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; (b) a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof; or a 2019 SARS-CoV 2 spike protein pharmaceutical composition comprising (ii)(a) or (ii)(b).

110. The method of any one of claims 71-109, wherein the subject has an immunodeficiency.

111. The method of any one of claims 71-110, wherein the subject suffers from B cell immunodeficiency.

112. A pharmaceutical composition comprising: (i) a recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from a membrane glycoprotein (M), and a sequence comprising an epitope sequence from a nucleocapsid phosphoprotein (N); and (ii) a recombinant polynucleotide encoding the 2019 SARS-CoV 2 spike protein or a variant or fragment thereof.

113. A pharmaceutical composition as described in claim 112, wherein the ratio (e.g., mass ratio) of (i):(ii) is 20:1 to 1:

20.

114. A composition comprising: (i) a first pharmaceutical composition comprising a first recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from a membrane glycoprotein (M), and a sequence comprising an epitope sequence from a nucleocapsid phosphoprotein (N); and (ii) a second pharmaceutical composition comprising a second recombinant polynucleotide encoding the 2019 SARS-CoV 2 spike protein or a variant or fragment thereof.

115. The composition of claim 114, wherein the ratio (eg, mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is 1:50 to 50:

1.

116. A pharmaceutical composition comprising: (i) a first recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from a membrane glycoprotein (M), and a sequence comprising an epitope sequence from a nucleocapsid phosphoprotein (N); and (ii) a second recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof.

117. The pharmaceutical composition of claim 116, wherein the pharmaceutical composition comprises nanoparticles, wherein the nanoparticles comprise the first recombinant polynucleotide and the second recombinant polynucleotide.

118. The pharmaceutical composition of claim 117, wherein the nanoparticles are present in the pharmaceutical composition at a dose of 100 ng to 500 micrograms.

119. The pharmaceutical composition of any one of claims 116-118, wherein the ratio (e.g., mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:50 to 50:

1.

120. A composition comprising: (i) a first pharmaceutical composition comprising a recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from a membrane glycoprotein (M), and a sequence comprising an epitope sequence from a nucleocapsid phosphoprotein (N); and (ii) a second pharmaceutical composition comprising a recombinant polynucleotide encoding the 2019 SARS-CoV 2 spike protein or a variant or fragment thereof.

121. A composition as described in claim 120, wherein the first pharmaceutical composition comprises a first nanoparticle, wherein the first nanoparticle comprises a recombinant polynucleotide encoding a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence from ORF1ab, a sequence comprising an epitope sequence from a membrane glycoprotein (M), and a sequence comprising an epitope sequence from a nucleocapsid phosphoprotein (N); and wherein the second pharmaceutical composition comprises a second nanoparticle, wherein the second nanoparticle comprises a recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof.

122. The composition of claim 121, wherein the ratio (e.g., mass ratio) of the recombinant polynucleotide in (i) to the recombinant polynucleotide in (ii) is about 1:50 to 50:

1.

123. The composition of claim 121 or 122, wherein the first nanoparticles are present in the first pharmaceutical composition at a dose of about 100 ng to 500 micrograms.

124. The composition of any one of claims 121-123, wherein the second nanoparticles are present in the second pharmaceutical composition at a dose of about 100 ng to 500 micrograms.

125. The composition of any one of claims 121-124, wherein the recombinant polynucleotide in (i) is present in the first pharmaceutical composition at a dose of about 50 ng to 250 micrograms.

126. The composition of any one of claims 121-125, wherein the recombinant polynucleotide in (ii) is present in the second pharmaceutical composition at a dose of about 50 ng to 250 micrograms.

127. The composition of any one of claims 121-126 or the pharmaceutical composition of any one of claims 117-119, wherein the nanoparticle is a lipid nanoparticle.

128. The method of claim 78, wherein a certain ratio (e.g., mass ratio) of the first pharmaceutical composition and the second pharmaceutical composition are administered on the first day, and the first pharmaceutical composition and the second pharmaceutical composition are administered on the second day thereafter.

129. The method of claim 128, wherein the recombinant polynucleotide in the first pharmaceutical composition administered on the first day is present in a ratio of about 3:1 to the recombinant polynucleotide in the second pharmaceutical composition administered on the first day.

130. The method of claim 128 or 129, wherein the recombinant polynucleotide in the first pharmaceutical composition administered on the second day is present in a ratio of about 3:1 to the recombinant polynucleotide in the second pharmaceutical composition administered on the second day.

131. The method of any one of claims 78-82, wherein the second pharmaceutical composition is administered at least once prior to administration of the first pharmaceutical composition.

132. The method of claim 128, wherein the second pharmaceutical composition is administered at least twice prior to administration of the first pharmaceutical composition.

133. The method of claim 132, wherein the second pharmaceutical composition is administered at least 2, 3, 4, 5, or 6 months prior to administration of the first pharmaceutical composition.

134. The method of claim 132 or 133, wherein the first administration of the second pharmaceutical composition is administered less than one month prior to the second administration of the second pharmaceutical composition.

135. The method of any one of claims 132-134, wherein the second administration of the second pharmaceutical composition is administered at least 2, 3, 4, 5, or 6 months prior to administration of the first pharmaceutical composition.

136. The method of any one of claims 132-135, wherein the second pharmaceutical composition is administered at least three times prior to administration of the first pharmaceutical composition.

137. The method of any one of claims 128-136, wherein the first pharmaceutical composition is administered at least 6 months after the last administration of the second pharmaceutical composition, wherein the last administration of the second pharmaceutical composition lacks the polynucleotide of the first pharmaceutical composition.

138. The method of any one of claims 128-135 and 137, wherein the second pharmaceutical composition is administered twice prior to administration of the first pharmaceutical composition.

139. The method of claim 138, wherein the first pharmaceutical composition administered after administering the second pharmaceutical composition twice further comprises a second recombinant polynucleotide encoding a 2019 SARS-CoV 2 spike protein or a variant or fragment thereof.

140. The method of claim 139, wherein the first recombinant polynucleotide in the first pharmaceutical composition and the second recombinant polynucleotide in the first pharmaceutical composition are present in a ratio of about 1:

3.

141. The method of claim 138, wherein the ratio (e.g., mass ratio) of the first recombinant polynucleotide in the first pharmaceutical composition to the second recombinant polynucleotide in the second pharmaceutical composition administered for the first time is about 1:

1.

142. The method of claim 138, wherein the ratio (e.g., mass ratio) of the first recombinant polynucleotide in the first pharmaceutical composition to the second recombinant polynucleotide in the second pharmaceutical composition administered a second time is about 1:

1.

143. The method of claim 138, wherein the method comprises administering the first pharmaceutical composition and a third amount of the second pharmaceutical composition on the same day.

144. The method of claim 143, wherein the ratio (e.g., mass ratio) of the first recombinant polynucleotide in the first pharmaceutical composition to the second recombinant polynucleotide in the second pharmaceutical composition administered a third time is about 1:

3.

145. The method of claim 143, wherein the ratio (e.g., mass ratio) of the first recombinant polynucleotide in the first pharmaceutical composition to the second recombinant polynucleotide in the second pharmaceutical composition administered a third time is about 1:

9.

146. The method of any of the above method claims, wherein the first recombinant polynucleotide is administered at a dose of about 1 microgram, 3 micrograms, 5 micrograms, 10 micrograms, 15 micrograms, or 30 micrograms.

147. The method of any of the above method claims, wherein a total amount of about 30 micrograms of the first polynucleotide and / or second polynucleotide is administered to the subject.

148. The method of any of the preceding claims, wherein the pharmaceutical composition is effective against the SARS-CoV-2B1.1.529 (Omicron) variant.

149. The method of any of the preceding claims, wherein the subject has the SARS-CoV-2B1.1.529 (Omicron) variant.

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