Coronavirus vaccines and how to use them

Abstract

Compositions and methods for the prevention and / or treatment of viral infections, particularly of the family Coronaviridae.

Description

[Technical Field]

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS This application claims the benefit of U.S. Provisional Application No. US63 / 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 incorporated herein in their entirety. [Background technology]

[0002] Newly emerged acute respiratory viral infections caused by novel coronaviruses are a major public health concern. Importantly, there are no vaccines or specific antivirals available for the rapid increase in infections, particularly during outbreaks of infections such as the 2015 MERS-CoV or 2019 SARS-CoV-2. The 2019 SARS-CoV-2 epidemic, which broke out in December 2019, claimed more than 2,000 lives less than two months after the first reported case. Therefore, novel and easily scalable therapeutics are needed to combat diseases caused by such viral infections. Summary of the Invention

[0003] Patients who are immunocompromised due to autoimmunity, organ transplantation, or immunosuppressive treatment have a reduced ability to mount an antibody response to vaccination (Rousseau et al., A H1N1v 2009 vaccine in cancer patients treated with cytotoxic chemotherapy and / or targeted therapy: the VACANCE study. Ann Oncol. 2012 Feb;23(2):450-7). Seroprevalence after vaccination is reduced in immunocompromised patients (Haidar et al., Immunogenicity of COVID-19 Vaccination in Immunocompromised Patients: An Observational, Prospective Cohort Study Interim Analysis. medRxiv 2021.06.28.21259576). Although immunocompromised patients were excluded from the original clinical trials testing the current SARS-CoV-2 vaccines targeting the spike protein, follow-up analyses of immunocompromised patients have shown that they have a reduced ability to develop broad and durable anti-spike antibody responses, particularly in older 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 for enhancing both cellular and humoral immunity. Therefore, there is a need for a SARS-CoV-2 vaccine that specifically targets T cell responses. It has been shown that patients receiving anti-CD20 therapy can develop functional T cells upon 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)), indicating that patients with B cell disorders may still develop SARS-CoV2-specific T cells in response to vaccination.

[0004] Provided herein are immunogenic compositions (e.g., vaccines) that specifically target one or more T cell responses against a pathogen (e.g., in some embodiments, a virus), including CD4+ T cell responses and / or CD8+ T cell responses, and / or utilize long-lasting T cell immunity. In some embodiments, the immunogenic compositions (e.g., vaccines) provided herein can specifically target one or more T cell responses against one or more polypeptide antigens of a pathogen (e.g., in some embodiments, one or more viral antigens), including, for example, one or more viral nonstructural proteins, nucleocapsid, membrane proteins, and / or envelope proteins.

[0005] In one aspect, provided herein are SARS-CoV-2 immunogenic compositions (e.g., vaccines) that specifically target one or more T cell responses, including CD4+ T cell responses and / or CD8+ T cell responses, and / or take advantage of long-lasting T cell immunity. In some embodiments, the SARS-CoV-2 vaccines provided herein can specifically target one or more T cell responses against polypeptide antigens of SARS-CoV-2, including, for example, the nucleocapsid, membrane proteins, and / or envelope proteins of SARS-CoV-2. The SARS-CoV-2 immunogenic compositions (e.g., vaccines) provided herein can be useful for eliciting one or more T cell responses against SARS-CoV-2 in all patients. Protection from COVID-19 has been observed in patients lacking humoral immunity when a T cell response was present (Bange, et al., CD8+ T cells contribute to survival in patients with COVID-19 and hematologic cancer. Nat Med 27, 1280-1289 (2021)), and in patients lacking a sustained T cell response derived from a related infection with 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, the particular insight that the SARS-CoV-2 immunogenic compositions (e.g., vaccines) provided herein may be particularly useful, in some embodiments, for eliciting one or more T cell responses against SARS-CoV-2 in patients, e.g., for cancer (e.g., B-cell lymphoma), treatment with rituximab, methotrexate, or other immunosuppressive therapies that target humoral immune responses, or in patients whose humoral immunity is immunocompromised because they have undergone an organ transplant.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-lasting 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 effectiveness of other vaccines, such as those that do not target T cell responses (Davis et al., Reduced neutralization of the Delta (B.1.617.2) SARS-CoV-2 variant of concern following vaccination. PLoS Pathog., 17(12):e 1010022 (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 a subject with or immunize a subject against the SARS-CoV-2 B1.1.529 (Omicron) variant. In some embodiments, the SARS-CoV-2 immunogenic compositions (e.g., vaccines) provided herein can be used to complement 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 through increased CD4+ T cell activation.

[0006] Coronaviruses are positive-stranded single-stranded RNA viruses that occasionally emerge from zoonotic sources and infect human populations. While most human infections cause mild respiratory symptoms, several recent coronavirus infections over the past decade have resulted in severe morbidity and mortality. These include severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and the ongoing SARS-CoV-2 pandemic. Infections caused by these viruses can cause acute respiratory distress and result in high mortality rates. SARS-CoV emerged in southern China in 2002 and its global spread has resulted in 8,096 cases and 774 deaths. The first cases of MERS-CoV emerged in Saudi Arabia in 2012, and since then, a total of 2,494 cases and 858 related deaths have been reported. The 2019 SARS-CoV-2 virus emerged in Wuhan, China, in late December 2019 and by March 8, 2020, had resulted in 118,096 cases worldwide, including 4,262 deaths. The rapid spread of 2019 SARS-CoV-2 led the World Health Organization to declare it a global pandemic of international concern.

[0007] The three coronaviruses SARS-CoV, MERS-CoV, and the recently emerged SARS-CoV-2 all belong to the genus BetaCoronaviridae. SARS-CoV-2 has a 30-kilobase genome encoding at least four structural proteins (spike [S], envelope [E], membrane [M], and nucleocapsid [N]) and at least 16 nonstructural (NSP1-16) proteins. The S protein facilitates viral entry into target cells, and entry depends on the binding of the spike protein to the cellular receptor ACE2 of both SARS-CoV and SARS-CoV-2. Both viruses share 76% amino acid identity across their genomes.

[0008] The field of the disclosure relates to immunotherapeutic peptides, nucleic acids encoding the peptides, peptide binders, and their uses in, for example, immunotherapy of viral diseases. In one aspect, the disclosure provides viral epitopes expressed in virally infected cells that are useful, alone or in combination with other antiviral or immunomodulatory agents, to treat viral infections. The disclosure is useful for immunotherapy of coronavirus infections.

[0009] Provided herein is a method for treating or preventing infection by a virus (e.g., SARS-CoV-2) or treating a respiratory disease or condition associated with infection by a virus (e.g., SARS-CoV-2), comprising administering a pharmaceutical composition to a subject having a B-cell immunodeficiency, the pharmaceutical composition comprising: (i) a polypeptide comprising at least two of the following: (a) a sequence comprising an epitope sequence derived from ORF1ab, (b) a sequence comprising an epitope sequence derived from a membrane glycoprotein (M), and (c) a sequence comprising an epitope sequence derived from a nucleocapsid phosphoprotein (N); and (ii) a polynucleotide encoding the polypeptide, wherein the polypeptide is (i) a polynucleotide comprising at least two of the following: (a) a sequence comprising an epitope sequence derived from a polypeptide of the present invention; (b) a sequence comprising an epitope sequence derived from a membrane glycoprotein (M); and (c) a sequence comprising an epitope sequence derived from a nucleocapsid phosphoprotein (N); (iii) a T cell receptor (TCR) or a T cell comprising the TCR, wherein the TCR forms a complex with a corresponding HLA class I or class II molecule and binds to the epitope sequence of the polypeptide; (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.

[0010] In some embodiments, the subject has a reduced ability to mount an antibody response to an antigen compared to a subject without a B cell immunodeficiency.

[0011] In some embodiments, the subject has a reduced ability to mount an antibody response to vaccination compared to a subject without a B cell immunodeficiency.

[0012] In some embodiments, the subject has a reduced ability to mount an anti-spike protein antibody response and / or an anti-RBD antibody response compared to a subject without a B cell immunodeficiency.

[0013] In some embodiments, the subject is able to mount a T cell response or does not have a reduced ability to mount a T cell response compared to a subject without a B cell immunodeficiency.

[0014] In some embodiments, the pharmaceutical composition protects against variants of 2019 SARS CoV-2.

[0015] In some embodiments, the variant of 2019 SARS CoV-2 is alpha, beta, gamma, delta, epsilon, zeta, eta, theta, iota, kappa, or lambda.

[0016] In some embodiments, the subject mounts a T cell response against an epitope of the polypeptide.

[0017] In some embodiments, the subject mounts a T cell response to an epitope sequence derived from ORF1ab, an epitope sequence derived from membrane glycoprotein (M), and / or an epitope sequence derived from nucleocapsid phosphoprotein (N).

[0018] In some embodiments, the subject is an organ transplant recipient.

[0019] In some embodiments, the organ transplant recipient is a solid organ transplant recipient, a stem cell transplant recipient, or a bone marrow transplant recipient.

[0020] In some embodiments, the subject underwent an organ transplant less than 1 year, less than 6 months, or less than 3 months after the pharmaceutical composition was administered.

[0021] In some embodiments, the subject is scheduled to undergo an organ transplant less than 1 year, less than 6 months, or less than 3 months prior to administration of the pharmaceutical composition.

[0022] In some embodiments, the subject has cancer.

[0023] In some embodiments, the cancer is a B-cell cancer.

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

[0025] In some embodiments, the subject has an autoimmune disease or condition.

[0026] In some embodiments, the autoimmune disease or condition is selected from the group consisting of Addison's disease, anti-NMDA receptor encephalitis, anti-synthetase syndrome, aplastic anemia, autoimmune anemia, autoimmune hemolytic anemia, autoimmune pancreatitis, Behcet's disease, bullous skin diseases, celiac disease (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-Barré syndrome, Hashimoto's thyroiditis, idiopathic rhabdomyosarcoma, ... These diseases include: 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, Sjogren's syndrome, systemic lupus erythematosus, thrombocytopenic purpura, thrombotic thrombocytopenic purpura, type 1 diabetes mellitus, ulcerative colitis, vasculitis, and vitiligo.

[0027] In some embodiments, the subject does not have congenital agammaglobulinemia or congenital IgA deficiency.

[0028] In some embodiments, the subject does not have HIV or AIDS.

[0029] In some embodiments, the subject is 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.

[0030] In some embodiments, the immunosuppressant is abatacept, abrilumab, acalabrutinib, adalimumab, adrenocorticotropic hormone, agatolimod sodium, aldesleukin, alefacept, alemtuzumab, alisertib, alvespimycin hydrochloride, alvocidib, ambrisentan, aminocamptothecin, amiselimod, anakinra, andecaliximab, andrographolide, anifrolumab, antithymocyte Ig, apatinib, apelisib, asparaginase, atacicept, atezolizumab, avelumab, azacitidine, azathioprine , bafetinib, baminocept, baricitinib, basiliximab, becatecarin, begelomab, belatacept, belimumab, bemcentinib, bendamustine, bendamustine, betalutin and rilotomab, bevacizumab, BIIB033, BIIB059, BIIB061, bimekizumab, binimetinib, bleomycin, blinatumomab, bortezomib, brentuximab vedotin, bryostatin 1, bucillamine, bupalisib, busulfan, canakinumab, capecitabine, carboplatin, carfilzomib, carmustine, cediranib maleate , cemiplimab, ceralifimoda, cerduratinib, certolizumab, cetuximab, cidamide, chlorambucil, cilengitide, simtuzumab, cisplatin, cladribine, clazakizumab, clemastine, clioquinol, corticosteroids, cyclophosphamide, cyclosporine, cytarabine, cytotoxic chemotherapy, daclizumab, dalfampridine, daprolizumab pegol, daratumumab, dasatinib, defactinib, defibrotide, denosumab, dexamethasone, diacerein, dimethyl fumarate, dinaciclib, diloxacin cimel, doxorubicin, doxorubicin, durvalumab, duvelisib, duboltukizumab, eculizumab, efalizumab, eftiragimod alfa, methenkefalin and tridecactide neuropeptide combination, elezanumab, elotuzumab, encorafenib, enfuvirtida, entinostat, entospletinib, enzastaurin, epacadostat, epirubicin, epratuzumab, eritoran tetrasodium, etanercept, etoposide, etrolizumab, everolimus, evobrutinib, filgotinib, fingolimod,Frategrast, fludarabine, fluorouracil, fontolizumab, forodesine hydrochloride, fostamatinib, galunisertib, ganetespib, ganitumab, gemcitabine, gemtuzumab ozogamicin, gerilimuzumab, glasdegiv, Gracia, glatiramer acetate, glenbatumumab vedotin, glesatinib, golimumab, guadecitabine, hydrocortisone, hydroxychloroquine sulfate, hydroxyurea, ibritumomab tiuxetan, ibrutinib, ibudilast, idarubicin, idebenone, Idelalisib, ifosfamide, iguratimod, imatinib, imexon, infliximab, inotuzumab ozogamicin, 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, levocaba Sucrine, lipoic acid, 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, mycophenolate, namilumab, natalizumab, navitoclax, neflizumab, Nerispirdine, Neurovax, niraparib, nivolumab, obatoclax mesylate, obinutuzumab, oblimersen sodium, 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, pevonex, pexidartinib, picoplatin, pidilizumab, Pivanex,Pixantrone, Preneva, Probamar acetate, Polatuzumab vedotin, Pomalidomide, Ponatinib, Ponesimod, Prednisone / Prednisolone, Piroxamide, Rabrizimab-CWVZ, Recombinant IL-12, Lelatolimab, Rhigof-1, Rhigom22, Rigosertib, Rilonacept, Ritonavir, Rituximab, Ruxolitinib, Sarilumab, Secukinumab Mab, selumetinib, simvastatin, sintilimab, siplizumab, siponimod, sirolimus (rapamycin), sirukumab, sitravatinib, sonidegib, sorafenib, sotrastaurin acetate, sunitinib, sanphenon epigallocatechin gallate, tabalumab, tacrolimus, talabostat mesylate, talacotuzumab, tanespimycin, tegafur / gimeracil / oteracil, temozolomide, temsirolimus, tenalisib, telameprocol, teriflunomide, thalidomide, thiarabine, thiotepa, tipifarnib, tirabrutinib, tislelizumab, tivozanib, tocilizumab, tofacitinib, tregalizumab, tremelimumab, treosulfan, ublituximab, umbralisib, upadacitinib The agent is selected from the group consisting of rivaroxaban, urelumab, ustekinumab, varlilumab, batelizumab, vedolizumab, veliparib, veltuzumab, venetoclax, vinblastine, vincristine, vinorelbine bitartrate, visilizumab, vismodegib, vistusertib, voriconazole, vorinostat, vosaroxin, ziv-aflibercept, or any combination thereof.

[0031] In some embodiments, the immunosuppressant is an A2aR antagonist, an Akt inhibitor, an anti-CD20, an anti-amyloid (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 The inhibitor is selected from the group consisting of a mAb, a CD1d ligand, a CD40 agonist, a complement C5a inhibitor, a CSF1R inhibitor, an EZH2 inhibitor, an FGFR3 inhibitor, an FGFR4 inhibitor, an FGFrR3 inhibitor, a glucocorticoid-induced tumor necrosis factor receptor-related gene agonist, a glutaminase inhibitor, a human monoclonal antibody against IL-12, an ICOS agonist, an IDO1 inhibitor, an IL2 mutein, an IL2 receptor agonist, a MEK inhibitor, a multitargeted receptor tyrosine kinase inhibitor, a neutrophil elastase inhibitor, a Notch inhibitor, a p38 MAPK inhibitor, a PD-1 inhibitor, a recombinant human Flt3L, a ROCK inhibitor, a selective sphingosine-1-phosphate receptor modulator, a Src kinase inhibitor, a TLR4 agonist, a TLR9 agonist, or any combination thereof.

[0032] In some embodiments, the subject is over 55, 56, 57, 58, 59, 60, 65, 70, 75, or 80 years of age.

[0033] In some embodiments, the polypeptide comprises (a) a sequence comprising an epitope sequence derived from ORF1ab, (b) a sequence comprising an epitope sequence derived from a membrane glycoprotein (M), and (c) a sequence comprising an epitope sequence derived from a nucleocapsid phosphoprotein (N).

[0034] In some embodiments, the sequence comprising the epitope sequence from ORF1ab is C-terminal to the sequence comprising the epitope sequence from nucleocapsid phosphoprotein (N).

[0035] 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).

[0036] In some embodiments, the sequence comprising an epitope sequence derived from a nucleocapsid phosphoprotein (N) is N-terminal to the sequence comprising an epitope sequence derived from a membrane glycoprotein (M).

[0037] In some embodiments, the polypeptide comprises (a) two, three, four, five, six, seven, eight, nine, or ten 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).

[0038] In some embodiments, the epitope sequence derived from ORF1ab is an epitope sequence derived from a nonstructural protein (NSP).

[0039] In some embodiments, the nonstructural protein (NSP) is selected from the group consisting of NSP1, NSP2, NSP3, NSP4, and combinations thereof.

[0040] 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.

[0041] 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.

[0042] In some embodiments, the epitope sequence derived from nucleocapsid glycoprotein (N) is LLLDRLNQL.

[0043] In some embodiments, the epitope sequence derived from membrane phosphoprotein (M) is VATSRTLSY.

[0044] In some embodiments, the polypeptide comprises an epitope sequence from the nucleocapsid glycoprotein (N) that is LLLDRLNQL and an epitope sequence from the membrane phosphoprotein (M) that is VATSRTLSY.

[0045] 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 the nucleocapsid glycoprotein (N) that is LLLDRLNQL, and (c) an epitope sequence from the membrane phosphoprotein (M) that is VATSRTLSY.

[0046] In some embodiments, the sequence comprising an epitope sequence from ORF1ab is selected from the group consisting of the following sequences or fragments thereof: MVTNNTFTLKVPHVGEIPVAYRKVLLKTIQPRVEKYLFDESGEFKLSEVGPEHSLAEYYIFFASFYY, MVTNNFTLKVPHVGEIPVAYRKVLLKTIQPRVEKYLFDESGEFKLSEVGPEHSLAEY, APKEIIFLEGETLFGDDTVIEVAIILASFSAST, APKEIIFLEGETLFGDDTVIEV, HTTDPSFLGRYMSALFADDLNQLTGYHTDFSSEIIGYQLMCQPILLAEAELAKNVSLILGTVSWNL, TTDPSFLGRYMSALFADDLNQLTGYHTDFSSEIIGYQLMCQPILLAEAELAKNVSLILGTVSWNL, LLSAGIFGAITDVFYKENSYKVPTDNYITTY, and combinations thereof.

[0047] In some embodiments, the sequence comprising an epitope sequence from membrane glycoprotein (M) is the following sequence or a fragment thereof: ADSNGTITVEELKKLLEQWNLVIGFLFLTWICLLQFAYANRNRFLYIIKLIFLWLLWPVTLACFVLAAVYRINWITGGIAIAMACLVGLMWLSYFIASFRLFARTRSMWSFNPETNILLNVPLHGTILTRPLLESELVIGAVILRGHLRIAGHHLGRCDIKDLPKEITVATSRTLSYYKLGASQRVAGDSGFAAYSRYRIGNYKLNTDHSSSSDNIALLVQ,

[0048] selected from the group consisting of FAYANRNRFLYIIKLIFLWLLWPVTLACFVLAAVYRINWITGGIAIAMACLVGLMWLSYFIASFRLF, LGRCDIKDLPKEITVATSRTLSYYKLGASQRVA, KLLEQWNLVIGF, NRNRFLYIIKLIFLWLLWPVTLACFVLAAVY, SELVIGAVILRGHLRIAGHHLGR, VATSRTLSYYKLGASQRV, GLMWLSYF, and combinations thereof.

[0049] In some embodiments, the sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N) is the following sequence or a fragment thereof: KDLSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGTTLPKGFYAEGSRGGSQASSRSSSRSRNSSRNSTPGSSRGTSPARMAGNGGDAALALLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDKKKKAD ETQALPQRQKKQQTVTLLPAADLDDFSKQLQQSMSSADSTQA, RMAGNGGDAALALLLLDRLNQLESKMSGKGQQQ, YKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFP, SPARMAGNGGDAALALLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDK, and combinations thereof.

[0050] In some embodiments, the polypeptide comprises one or more linker sequences.

[0051] In some embodiments, the one or more linker sequences are selected from the group consisting of GGSGGGGSGG, GGSLGGGGSG.

[0052] In some embodiments, one or more linker sequences comprises a cleavage sequence.

[0053] 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.

[0054] In some embodiments, the polypeptide comprises a transmembrane domain sequence.

[0055] In some embodiments, the transmembrane domain sequence is C-terminal to a sequence comprising an epitope sequence derived from ORF1ab, a sequence comprising an epitope sequence derived from a membrane glycoprotein (M), and a sequence comprising an epitope sequence derived from a nucleocapsid phosphoprotein (N).

[0056] In some embodiments, the transmembrane domain sequence is EQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT.

[0057] In some embodiments, the polypeptide comprises a SEC sequence.

[0058] In some embodiments, the SEC sequence is N-terminal to a sequence comprising an epitope sequence derived from ORF1ab, a sequence comprising an epitope sequence derived from membrane glycoprotein (M), and a sequence comprising an epitope sequence derived from nucleocapsid phosphoprotein (N).

[0059] In some embodiments, the SEC sequence is MFVFLVLLPLVSSQCVNLT.

[0060] In some embodiments, the composition comprises a polynucleotide encoding the polypeptide.

[0061] In some embodiments, the polynucleotide is mRNA.

[0062] In some embodiments, the polynucleotide comprises a codon-optimized sequence for expression in humans.

[0063] In some embodiments, the polynucleotide comprises a dEarI-hAg sequence.

[0064] In some embodiments, the dEarI-hAg sequence is ATTCTTCTGGTCCCCACAGACTCAGAGAGAACCC, where optionally each T is U.

[0065] In some embodiments, the polynucleotide comprises a Kozak sequence.

[0066] In some embodiments, the Kozak sequence is GCCACC.

[0067] In some embodiments, the polynucleotide comprises an F element sequence.

[0068] In some embodiments, the F element sequence is the 3UTR of the amino-terminal enhancer of splitting (AES).

[0069] In some embodiments, the F element sequence is CTGGTACTGCATGCACGCAATGCTAGCTGCCCCTTTCCCGTCCTGGGTACCCCGAGTCTCCCCCGACCTCGGGTCCCAGGTATGCTCCCACCTCCACCTGCCCCACTCACCACCTCTGCTAGTTCCAGACACCTCC, and optionally each T is U.

[0070] In some embodiments, the polynucleotide comprises an I element sequence.

[0071] In some embodiments, the I element sequence is the 3'UTR of mitochondrially encoded 12S rRNA (mtRNR1).

[0072] In some embodiments, the I element sequence is CAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACACC, and optionally each T is U.

[0073] In some embodiments, the polynucleotide comprises a polyA sequence.

[0074] In some embodiments, the poly A sequence is AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGCATATGACTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA, and optionally each T is U.

[0075] In some embodiments, each of the epitope sequences derived from ORF1ab, membrane glycoprotein, and nucleocapsid phosphoprotein are derived from 2019 SARS-CoV-2.

[0076] In some embodiments, one or more of the epitopes or each epitope elicits a T cell response.

[0077] In some embodiments, one or more epitopes or each epitope was observed by mass spectrometry as being presented by an HLA molecule.

[0078] 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 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, RS C7p4full, RS C8p1, RS C8p2, and RS C8p2full; (ii) 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; or (iii) 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 SEQ ID NOs: 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.

[0079] 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 RS C7p1, 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 NOs: RS C7n1, RS C7n2, RS C7n2full, RS C7n4, and RS C7n4full.

[0080] In some embodiments, the pharmaceutical composition comprises a pharmaceutically acceptable excipient, carrier, or diluent.

[0081] Provided herein are methods for treating or preventing a viral infection or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject with B-cell immunodeficiency a pharmaceutical composition comprising: (i) a polypeptide comprising an epitope sequence of Table 1A, Table IB, 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 IB, Table 1C, Table 2Ai, Table 2Aii, Table 2B, and / or Table 16; (iii) a T cell receptor (TCR) or a T cell comprising the TCR, where the TCR binds to the epitope sequence in a 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, where the antibody binds to the epitope sequence.

[0082] 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.

[0083] 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.

[0084] In some embodiments, the epitope sequence is derived from the orf1ab protein.

[0085] In some embodiments, the epitope sequence is derived from the orf1a protein.

[0086] In some embodiments, the epitope sequence is derived from the surface glycoprotein (S) or a shifted reading frame thereof.

[0087] In some embodiments, the epitope sequence is derived from the nucleocapsid phosphoprotein (N).

[0088] In some embodiments, the epitope sequence is derived from the ORF3a protein.

[0089] In some embodiments, the epitope sequence is derived from the membrane glycoprotein (M).

[0090] In some embodiments, the epitope sequence is derived from the ORF7a protein.

[0091] In some embodiments, the epitope sequence is derived from the ORF8 protein.

[0092] In some embodiments, the epitope sequence is derived from the envelope protein (E).

[0093] In some embodiments, the epitope sequence is derived from the ORF6 protein.

[0094] In some embodiments, the epitope sequence is derived from the ORF7b protein.

[0095] In some embodiments, the epitope sequence is derived from the ORF10 protein.

[0096] In some embodiments, the epitope sequence is derived from the ORF9b protein.

[0097] Provided herein are methods of treating or preventing a viral infection or treating a respiratory disease or condition associated with a viral infection, comprising administering to a subject with a B-cell immunodeficiency a pharmaceutical composition comprising a recombinant polynucleotide encoding a polypeptide having an amino acid 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 one of the sequences set forth in column 2 of Table 11, column 2 of Table 12, or column 3 of Table 15, or a polypeptide having an amino acid 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 one of the sequences set forth in column 2 of Table 11, column 2 of Table 12, or column 3 of Table 15.

[0098] 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 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, RS C7p4full, RS C8p1, RS C8p2, and RS C8p2full; or 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 RS C1p1full, RS C2p1full, RS C3p1full, RS C4p1full, RS C5p1, RS C5p2, RS C5p2full, RS C6p1, RS C6p2, RS The present invention also includes polynucleotides encoding polypeptides 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 C6p2full, RS C7p1, RS C7p2, RS C7p2full, RS C7p4, RS C7p4full, RS C8p1, RS C8p2, and RS C8p2full.

[0099] 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 NOs: 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, and RS C7n4full.

[0100] In some embodiments, the polynucleotide is mRNA.

[0101] In some embodiments, the pharmaceutical composition further comprises one or more lipid components.

[0102] In some embodiments, the one or more lipid components comprise lipid nanoparticles (LNPs).

[0103] In some embodiments, the LNP encapsulates a recombinant polynucleotide construct.

[0104] In some embodiments, the polypeptide is synthetic.

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

[0106] In some embodiments, the polypeptide is between 8 and 1000 amino acids in length.

[0107] 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.

[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 500 nM or less.

[0109] In some embodiments, the epitope sequence comprises a sequence of a viral protein expressed by virus-infected cells of the subject.

[0110] In some embodiments, the virus is a coronavirus.

[0111] In some embodiments, the virus is 2019 SARS-CoV2.

[0112] In some embodiments, the HLA molecules expressed by the subject are unknown at the time of administration.

[0113] In some embodiments, the ability of the virus to evade recognition by the subject's immune system is reduced compared to the ability of the virus to evade recognition by the immune system of a subject administered a pharmaceutical composition that contains epitopes from a single protein or epitopes from fewer proteins than the pharmaceutical compositions administered by the methods described herein.

[0114] 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 epitope sequence that is matched by the HLA allele.

[0115] 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.

[0116] In some embodiments, the method further comprises administering to the subject an additional therapy for 2019 SARS-CoV2 virus infection.

[0117] In some embodiments, the method further comprises administering to the subject (a) a polypeptide having an amino acid sequence of a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, (b) a recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, or a 2019 SARS-CoV2 spike protein pharmaceutical composition comprising (a) or (b).

[0118] In some embodiments, the vaccine or therapeutic agent of (a) or (b) is administered once to the subject.

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

[0120] In some embodiments, the vaccine or therapeutic is administered at least twice, the first administered dose being a priming dose and the second and subsequent doses being booster dose(s).

[0121] In some embodiments, the priming dose and the booster dose are administered at least 21 days apart.

[0122] In some embodiments, the interval between two booster doses is at least 30 days, at least 60 days, or at least 90 days.

[0123] In some embodiments, the vaccine or treatment is administered once a year.

[0124] In some embodiments, the vaccine or treatment is administered twice yearly.

[0125] In some embodiments, the vaccine or therapeutic is administered as a high priming or loading dose for the first dose and reduced boosting or maintenance doses for subsequent doses.

[0126] In some embodiments, subjects receive a lower dose or less frequently of the SARS-CoV spike vaccine than subjects receiving the SARS-CoV spike vaccine alone.

[0127] Provided herein is 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 recombinant polynucleotide encoding a polypeptide comprising at least two of a sequence comprising an epitope sequence derived from ORF1ab, a sequence comprising an epitope sequence derived from a membrane glycoprotein (M), and a sequence comprising an epitope sequence derived from a nucleocapsid phosphoprotein (N); and (ii) a pharmaceutical composition comprising a recombinant polynucleotide encoding a 2019 SARS-CoV2 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.

[0128] 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.

[0129] 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.

[0130] 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: (i) a first pharmaceutical composition comprising a first recombinant polynucleotide encoding a polypeptide comprising at least two of a sequence comprising an epitope sequence derived from ORF1ab, a sequence comprising an epitope sequence derived from a membrane glycoprotein (M), and a sequence comprising an epitope sequence derived from a nucleocapsid phosphoprotein (N); and (ii) a second pharmaceutical composition comprising a second recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, wherein the ratio (e.g., mass ratio) of the recombinant polynucleotide of (i) to the recombinant polynucleotide of (ii) is 1:50 to 50:1.

[0131] In some embodiments, the ratio (eg, mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is about 1:25 to 25:1.

[0132] In some embodiments, the ratio (e.g., mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is about 1:10 to 10:1.

[0133] In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotides of (i) to the recombinant polynucleotides of (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, 2.5:1, 3.5:1, 4.5 In some embodiments, the ratio (e.g., mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is about 1:6. In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotides of (i) to the recombinant polynucleotides of (ii) is about 1:3. In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotides of (i) to the recombinant polynucleotides of (ii) is about 1:2.

[0134] In some embodiments, the recombinant polynucleotide of (i) is present in the pharmaceutical composition at a dose of 0.1 micrograms to 100 micrograms, or 1 micrograms to 50 micrograms, or 1 micrograms to 30 micrograms, or 1 micrograms to 20 micrograms, or 3 micrograms to 20 micrograms, or 5 micrograms to 15 micrograms. In some embodiments, the recombinant polynucleotide of (i) is present in the pharmaceutical composition at a dose of 0.05 micrograms to 10 micrograms, or 0.1 micrograms to 5 micrograms, or 0.3 micrograms to 5 micrograms. In some embodiments, the recombinant polynucleotide of (i) is present in the pharmaceutical composition at a dose of 0.1 micrograms to 20 micrograms, or 0.5 micrograms to 15 micrograms.

[0135] In some embodiments, the recombinant polynucleotide of (ii) is present in the pharmaceutical composition at a dose of 0.1 micrograms to 100 micrograms, or 1 micrograms to 100 micrograms, or 1 micrograms to 30 micrograms, or 1 micrograms to 20 micrograms, or 3 micrograms to 30 micrograms.

[0136] In some embodiments, the recombinant polynucleotide of (i) is present in the pharmaceutical composition at a dose of about 5 micrograms and the recombinant polynucleotide of (ii) is present in the pharmaceutical composition at a dose of about 30 micrograms. In some embodiments, the recombinant polynucleotide of (i) is present in the pharmaceutical composition at a dose of about 10 micrograms and the recombinant polynucleotide of (ii) is present in the pharmaceutical composition at a dose of about 30 micrograms. In some embodiments, the recombinant polynucleotide of (i) is present in the pharmaceutical composition at a dose of about 15 micrograms and the recombinant polynucleotide of (ii) is present in the pharmaceutical composition at a dose of about 30 micrograms.

[0137] In some embodiments, the recombinant polynucleotide of (ii) comprises 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, the RBD) of a different strain or variant thereof. For example, in some embodiments, the recombinant polynucleotide of (ii) comprises a recombinant polynucleotide encoding a SARS-CoV-2 S protein, or an immunogenic variant or fragment thereof (e.g., in some embodiments, the RBD) of an ancestral strain (e.g., the Wuhan strain), and a recombinant polynucleotide encoding a SARS-CoV-2 S protein of a SARS-CoV-2 variant strain that is prevalent or rapidly spreading at the time of administration. For example, in some embodiments, the recombinant polynucleotides of (ii) include a recombinant polynucleotide encoding a SARS-CoV-2 S protein of an ancestral strain (e.g., the Wuhan strain) or an immunogenic variant or fragment thereof (e.g., in some embodiments, the RBD), and a recombinant polynucleotide encoding a SARS-CoV-2 S protein 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), or a variant strain having one or more mutations characteristic of an immunogenic variant or fragment thereof. In some embodiments, at least two recombinant polynucleotides, each encoding a SARS-CoV-2 S protein of a different strain or variant thereof, or an immunogenic variant or fragment thereof, can be present in the pharmaceutical composition in a ratio (e.g., by mass) of 3:1 to 1:3, or 2:1 to 1:2, or 1:1.

[0138] In some embodiments, the pharmaceutical compositions described herein may further comprise (iii) a recombinant polynucleotide encoding a peptide or polypeptide antigen derived 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 (flu) and / or respiratory syncytial virus.

[0139] Provided herein are methods 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 nanoparticles, the nanoparticles comprising: (i) a first recombinant polynucleotide encoding a polypeptide comprising at least two 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); and (ii) a second recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof. In some embodiments, the first recombinant polynucleotide encodes a polypeptide comprising all 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).

[0140] In some embodiments, the nanoparticles are present in the pharmaceutical composition in a dose of 100 ng to 500 micrograms.

[0141] In some embodiments, the nanoparticles are present in the pharmaceutical composition in a dose of between 1 microgram and 100 micrograms.

[0142] In some embodiments, the nanoparticles are present in the pharmaceutical composition in a dose of 1 microgram to 30 micrograms, 5 micrograms to 40 micrograms, or 10 micrograms to 50 micrograms.

[0143] 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.

[0144] In some embodiments, the ratio (e.g., mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:50 to 50:1.

[0145] 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.

[0146] In some embodiments, the ratio (e.g., mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:10 to 10:1.

[0147] 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 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. 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.

[0148] In some embodiments, the first recombinant polynucleotide is present in the pharmaceutical composition at a dose of 0.1 micrograms to 100 micrograms, or 1 micrograms to 50 micrograms, or 1 micrograms to 30 micrograms, or 1 micrograms 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 micrograms 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 micrograms to 20 micrograms, or 0.5 micrograms to 15 micrograms.

[0149] In some embodiments, the second recombinant polynucleotide is present in the pharmaceutical composition at a dose of 0.1 micrograms to 100 micrograms, or 1 micrograms to 100 micrograms, or 1 micrograms to 30 micrograms, or 1 micrograms to 20 micrograms, or 3 micrograms to 30 micrograms.

[0150] In some embodiments, the second recombinant polynucleotide comprises 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, the RBD) of a different strain or variant thereof. For example, in some embodiments, the second recombinant polynucleotide comprises a recombinant polynucleotide encoding a SARS-CoV-2 S protein, or an immunogenic variant or fragment thereof (e.g., in some embodiments, the RBD) of an ancestral strain (e.g., the Wuhan strain), and a recombinant polynucleotide encoding a SARS-CoV-2 S protein of a SARS-CoV-2 variant strain that is prevalent or rapidly spreading at the time of administration. For example, in some embodiments, the second recombinant polynucleotide includes a recombinant polynucleotide encoding a SARS-CoV-2 S protein of an ancestral strain (e.g., the Wuhan strain) or an immunogenic variant or fragment thereof (e.g., in some embodiments, the RBD), and a recombinant polynucleotide encoding a SARS-CoV-2 S protein 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), or a variant strain having one or more mutations characteristic of an immunogenic variant or fragment thereof. In some embodiments, two recombinant polynucleotides, each encoding a SARS-CoV-2 S protein of a different strain or variant thereof, or an immunogenic variant or fragment thereof, can be present in the pharmaceutical composition in a ratio (e.g., by mass) of 3:1 to 1:3, or 2:1 to 1:2, or 1:1.

[0151] In some embodiments, the pharmaceutical compositions described herein may include 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 a non-SARS-CoV-2 respiratory disease may be, but is not limited to, influenza (influenza), and / or respiratory syncytial virus.

[0152] 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: (i) a first pharmaceutical composition comprising first nanoparticles, wherein the first nanoparticles comprise a recombinant polynucleotide encoding a polypeptide comprising at least two of a sequence comprising an epitope sequence derived from ORF1ab, a sequence comprising an epitope sequence derived from membrane glycoprotein (M), and a sequence comprising an epitope sequence derived from nucleocapsid phosphoprotein (N); and (ii) a second pharmaceutical composition comprising second nanoparticles, wherein the second nanoparticles comprise a recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof. In some embodiments, the first pharmaceutical composition comprises first nanoparticles, and the first nanoparticles comprise a recombinant polynucleotide encoding a polypeptide comprising all of a sequence comprising an epitope sequence derived from ORF1ab, a sequence comprising an epitope sequence derived from membrane glycoprotein (M), and a sequence comprising an epitope sequence derived from nucleocapsid phosphoprotein (N).

[0153] In some embodiments, the ratio (e.g., mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is about 1:50 to 50:1.

[0154] In some embodiments, the ratio (eg, mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is about 1:25 to 25:1.

[0155] In some embodiments, the ratio (e.g., mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is about 1:10 to 10:1.

[0156] In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotides of (i) to the recombinant polynucleotides of (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, 2.5:1, 3.5:1, 4.5 In some embodiments, the ratio (e.g., mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is about 1:6. In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotides of (i) to the recombinant polynucleotides of (ii) is about 1:3. In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotides of (i) to the recombinant polynucleotides of (ii) is about 1:2.

[0157] In some embodiments, the recombinant polynucleotide of (i) is present in the pharmaceutical composition at a dose of 0.1 micrograms to 100 micrograms, or 1 micrograms to 50 micrograms, or 1 micrograms to 30 micrograms, or 1 micrograms to 20 micrograms, or 3 micrograms to 20 micrograms, or 5 micrograms to 15 micrograms. In some embodiments, the recombinant polynucleotide of (i) is present in the pharmaceutical composition at a dose of 0.05 micrograms to 10 micrograms, or 0.1 micrograms to 5 micrograms, or 0.3 micrograms to 5 micrograms. In some embodiments, the recombinant polynucleotide of (i) is present in the pharmaceutical composition at a dose of 0.1 micrograms to 20 micrograms, or 0.5 micrograms to 15 micrograms.

[0158] In some embodiments, the recombinant polynucleotide of (ii) is present in the pharmaceutical composition at a dose of 0.1 micrograms to 100 micrograms, or 1 micrograms to 100 micrograms, or 1 micrograms to 30 micrograms, or 1 micrograms to 20 micrograms, or 3 micrograms to 30 micrograms.

[0159] In some embodiments, the recombinant polynucleotide of (ii) comprises 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, the RBD) of a different strain or variant thereof. For example, in some embodiments, the recombinant polynucleotide of (ii) comprises a recombinant polynucleotide encoding a SARS-CoV-2 S protein, or an immunogenic variant or fragment thereof (e.g., in some embodiments, the RBD) of an ancestral strain (e.g., the Wuhan strain), and a recombinant polynucleotide encoding a SARS-CoV-2 S protein of a SARS-CoV-2 variant strain that is prevalent or rapidly spreading at the time of administration. For example, in some embodiments, the recombinant polynucleotides of (ii) include a recombinant polynucleotide encoding a SARS-CoV-2 S protein of an ancestral strain (e.g., the Wuhan strain) or an immunogenic variant or fragment thereof (e.g., in some embodiments, the RBD), and a recombinant polynucleotide encoding a SARS-CoV-2 S protein 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), or a variant strain having one or more mutations characteristic of an immunogenic variant or fragment thereof. In some embodiments, at least two recombinant polynucleotides, each encoding a SARS-CoV-2 S protein of a different strain or variant thereof, or an immunogenic variant or fragment thereof, can be present in the pharmaceutical composition in a ratio (e.g., by mass) of 3:1 to 1:3, or 2:1 to 1:2, or 1:1.

[0160] In some embodiments, a third pharmaceutical composition (iii) comprising third nanoparticles may be administered to a subject in need thereof, wherein the third nanoparticles comprise a recombinant polynucleotide encoding a peptide or polypeptide antigen derived 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.

[0161] In some embodiments, the first nanoparticles are present in the first pharmaceutical composition at a dose of about 100 ng to 500 micrograms.

[0162] In some embodiments, the first nanoparticles are present in the first pharmaceutical composition in a dose of about 1 microgram to 100 micrograms.

[0163] In some embodiments, the first nanoparticles are present in the first pharmaceutical composition in a dose of about 1 microgram to 30 micrograms, 5 micrograms to 40 micrograms, or 10 micrograms to 50 micrograms.

[0164] 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.

[0165] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition at a dose of about 100 ng to 500 micrograms.

[0166] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition in a dose of about 1 microgram to 100 micrograms.

[0167] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition in a dose of about 1 microgram to 30 micrograms, 5 micrograms to 40 micrograms, or 10 micrograms to 50 micrograms.

[0168] 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.

[0169] Provided herein is a method for treating or preventing an infection by a virus or treating a respiratory disease or condition associated with an infection by a virus, comprising administering to a subject in need thereof: (i) a pharmaceutical composition comprising a polynucleotide encoding (a) a polypeptide comprising at least two of 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); or (b) a polypeptide comprising at least two of 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 pharmaceutical composition comprising a recombinant polynucleotide encoding (a) a polypeptide having the amino acid sequence of a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, or (b) a 2019 SARS-CoV2 spike protein or a variant or fragment thereof; or (ii) a 2019 SARS-CoV2 spike protein comprising (a) or (ii)(b). and a SARS-CoV2 spike protein pharmaceutical composition, wherein the subject receives a dose of (ii)(a) or (ii)(b) that is less than the dose of (ii)(a) or (ii)(b) administered to the subject alone.

[0170] Provided herein are methods for treating or preventing infection by a virus or treating a respiratory disease or condition associated with infection by a virus, comprising administering to a subject in need thereof: (i) a pharmaceutical composition comprising a polynucleotide encoding (a) a polypeptide comprising at least two 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); or (b) a polypeptide comprising at least two 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); and (ii) a pharmaceutical composition comprising a recombinant polynucleotide encoding (a) a polypeptide having the amino acid sequence of a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, or (b) a 2019 SARS-CoV2 spike protein or a variant or fragment thereof; or (ii) a 2019 SARS-CoV2 spike protein comprising (a) or (ii)(b). The method comprises administering a SARS-CoV2 spike protein pharmaceutical composition.

[0171] Provided herein is a method for treating or preventing an infection by a virus or treating a respiratory disease or condition associated with an infection by a virus, comprising administering to a subject in need thereof: (i) a pharmaceutical composition comprising a polynucleotide encoding (a) a polypeptide comprising at least two of 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); or (b) a polypeptide comprising at least two of 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 pharmaceutical composition comprising (a) a polypeptide having the amino acid sequence of a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, (b) a recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, or (ii) a recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, or (ii) a recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, comprising (ii)(a) or (ii)(b). and a SARS-CoV2 spike protein pharmaceutical composition, wherein the subject receives a number of doses of (ii)(a) or (ii)(b) that are fewer than the number of doses of (ii)(a) or (ii)(b) administered to the subject alone.

[0172] 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 times less than the dose of (ii)(a) or (ii)(b) administered to the subject alone.

[0173] 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 are administered to the subject alone.

[0174] In some embodiments, the pharmaceutical composition of (i) is co-formulated with the pharmaceutical composition of (ii).

[0175] In some embodiments, the pharmaceutical composition of (i) is formulated separately from the pharmaceutical composition of (ii).

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

[0177] Provided herein is a method for treating or preventing an infection by a virus or treating a respiratory disease or condition associated with an infection by a virus, comprising administering to a subject in need thereof: (i) a pharmaceutical composition comprising a polynucleotide encoding (a) a polypeptide comprising at least two of 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); or (b) a polypeptide comprising at least two of 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 pharmaceutical composition comprising (a) a polypeptide having the amino acid sequence of a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, (b) a recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, or (ii) a recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, or (ii) a recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, comprising (ii)(a) or (ii)(b). and a SARS-CoV2 spike protein pharmaceutical composition, wherein the subject receives fewer doses of (i)(a) or (i)(b) than are administered to the subject alone.

[0178] Provided herein is a method for treating or preventing an infection by a virus or treating a respiratory disease or condition associated with an infection by a virus, comprising administering to a subject in need thereof: (i) a pharmaceutical composition comprising a polynucleotide encoding (a) a polypeptide comprising at least two of 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); or (b) a polypeptide comprising at least two of 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 pharmaceutical composition comprising (a) a polypeptide having the amino acid sequence of a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, (b) a recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, or (ii) a recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, or (ii) a recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, comprising (ii)(a) or (ii)(b). and a SARS-CoV2 spike protein pharmaceutical composition, wherein the subject receives several doses of (i)(a) or (i)(b) that are fewer than the several doses of (i)(a) or (i)(b) administered to the subject alone.

[0179] 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 times less than the dose of (i)(a) or (i)(b) administered to the subject alone.

[0180] 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 are administered to the subject alone.

[0181] In some embodiments, the pharmaceutical composition of (i) is co-formulated with the pharmaceutical composition of (ii).

[0182] In some embodiments, the pharmaceutical composition of (i) is formulated separately from the pharmaceutical composition of (ii).

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

[0184] In some embodiments, the pharmaceutical composition is a co-formulation.

[0185] In some embodiments, the first pharmaceutical composition is administered together with or on the same day as the second pharmaceutical composition.

[0186] In some embodiments, the first pharmaceutical composition is administered simultaneously with the second pharmaceutical composition.

[0187] In some embodiments, a first pharmaceutical composition is administered at a first location in a subject, and a second pharmaceutical composition is administered at a second location in the subject that is different from the first location.

[0188] In some embodiments, the first location is on an appendage of the subject and the second location is on a contralateral appendage of the subject.

[0189] In some embodiments, the first appendage is an arm and the second appendage is an arm.

[0190] In some embodiments, the first pharmaceutical composition and the second pharmaceutical composition are administered to the subject at the same location.

[0191] 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, 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. 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 weeks or at least about, up to 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.

[0192] 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, 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 second time point. 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 weeks or at least about, up to 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.

[0193] In some embodiments, the third time point is at least about, up to 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, up to 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 days after the first time point. , 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 weeks later, or at least about, up to 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.

[0194] 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, 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 days after the first time point. 1, 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 weeks or at least about, up to 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 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, 31, 32, 33, 34, 35, or 36 days after the second 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, 35, or 36 weeks later, or at least about, up to 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.

[0196] In some embodiments, the third time point is at least about, up to 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, up to about or about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 days after the first time point. , 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 weeks later, or at least about, up to 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.

[0197] In some embodiments, the second pharmaceutical composition is administered at the first time point.

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

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

[0200] In some embodiments, the second pharmaceutical composition is administered 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 36 weeks later, or at least about, up to 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.

[0201] In some embodiments, the second pharmaceutical composition is administered 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 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, or 36 weeks later, or at least about, up to 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.

[0202] Provided herein are methods 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 polynucleotide encoding (a) a polypeptide comprising at least two 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), or (b) a polypeptide comprising at least two 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), 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 two days after the first time point and the third time point is at least about two days after the second time point.

[0203] 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, 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 days after the first time point. 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35 weeks 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.

[0204] In some embodiments, the second time point is up to 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, up to about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or 18 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 later, 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.

[0205] 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, 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 days after the first time point. 8, 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.

[0206] 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, or at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or 18 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 later, 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.

[0207] In some embodiments, the third time point is up to 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, 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 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 later, 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.

[0208] 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, 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 days after the second time point. 8, 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.

[0209] 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, 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, 35, or 36 days after the first time point. 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35 weeks 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.

[0210] In some embodiments, the third time point is up to 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, 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, 35, or 36 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 later, 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.

[0211] 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, 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. 8, 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.

[0212] In some embodiments, the method further comprises administering to the subject (ii)(a) a polypeptide having the amino acid sequence of a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, (b) a recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, or a 2019 SARS-CoV2 spike protein pharmaceutical composition comprising (ii)(a) or (ii)(b).

[0213] In some embodiments, the subject has an immunodeficiency.

[0214] In some embodiments, the subject has a B-cell immunodeficiency.

[0215] In some embodiments, the pharmaceutical composition is administered prophylactically.

[0216] Provided herein is a pharmaceutical composition comprising: (i) a recombinant polynucleotide encoding a polypeptide comprising at least two of a sequence comprising an epitope sequence derived from ORF1ab, a sequence comprising an epitope sequence derived from a membrane glycoprotein (M), and a sequence comprising an epitope sequence derived from a nucleocapsid phosphoprotein (N); and (ii) a recombinant polynucleotide encoding a 2019 SARS-CoV2 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.

[0217] 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.

[0218] 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.

[0219] Provided herein are compositions comprising: (i) a first pharmaceutical composition comprising a first recombinant polynucleotide encoding a polypeptide comprising at least two of a sequence comprising an epitope sequence derived from ORF1ab, a sequence comprising an epitope sequence derived from a membrane glycoprotein (M), and a sequence comprising an epitope sequence derived from a nucleocapsid phosphoprotein (N); and (ii) a second pharmaceutical composition comprising a second recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, wherein the ratio (e.g., mass ratio) of the recombinant polynucleotide of (i) to the recombinant polynucleotide of (ii) is 1:50 to 50:1.

[0220] In some embodiments, the ratio (eg, mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is about 1:25 to 25:1. In some embodiments, the ratio (e.g., mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is about 1:10 to 10:1.

[0221] In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotides of (i) to the recombinant polynucleotides of (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, 2.5:1, 3.5:1, 4.5 In some embodiments, the ratio (e.g., mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is about 1:6. In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotides of (i) to the recombinant polynucleotides of (ii) is about 1:3. In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotides of (i) to the recombinant polynucleotides of (ii) is about 1:2.

[0222] In some embodiments, the recombinant polynucleotide of (i) is present at a dose of 0.1 micrograms to 100 micrograms, or 1 micrograms to 50 micrograms, or 1 micrograms to 30 micrograms, or 1 micrograms to 20 micrograms, or 3 micrograms to 20 micrograms, or 5 micrograms to 15 micrograms. In some embodiments, the recombinant polynucleotide of (i) is present at a dose of 0.05 micrograms to 10 micrograms, or 0.1 micrograms to 5 micrograms, or 0.3 micrograms to 5 micrograms. In some embodiments, the recombinant polynucleotide of (i) is present at a dose of 0.1 micrograms to 20 micrograms, or 0.5 micrograms to 15 micrograms.

[0223] In some embodiments, the recombinant polynucleotide of (ii) is present at a dose of 0.1 micrograms to 100 micrograms, or 1 micrograms to 100 micrograms, or 1 micrograms to 30 micrograms, or 1 micrograms to 20 micrograms, or 3 micrograms to 30 micrograms.

[0224] In some embodiments, the recombinant polynucleotide of (ii) includes 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 of (ii) includes 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).

[0225] In some embodiments, the recombinant polynucleotide of (i) is present in a dose of about 5 micrograms and the recombinant polynucleotide of (ii) is present in a dose of about 30 micrograms. In some embodiments, the recombinant polynucleotide of (i) is present in a dose of about 10 micrograms and the recombinant polynucleotide of (ii) is present in a dose of about 30 micrograms. In some embodiments, the recombinant polynucleotide of (i) is present in a dose of about 15 micrograms and the recombinant polynucleotide of (ii) is present in a dose of about 30 micrograms.

[0226] Provided herein is a pharmaceutical composition comprising nanoparticles, the nanoparticles comprising: (i) a first recombinant polynucleotide encoding a polypeptide comprising at least two of 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-CoV2 spike protein or a variant or fragment thereof.

[0227] In some embodiments, the nanoparticles are present in the pharmaceutical composition in a dose of 100 ng to 500 micrograms.

[0228] In some embodiments, the nanoparticles are present in the pharmaceutical composition in a dose of between 1 microgram and 100 micrograms.

[0229] In some embodiments, the nanoparticles are present in the pharmaceutical composition in a dose of 1 microgram to 30 micrograms, 5 micrograms to 40 micrograms, or 10 micrograms to 50 micrograms.

[0230] 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.

[0231] In some embodiments, the ratio (e.g., mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:50 to 50:1.

[0232] 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.

[0233] In some embodiments, the ratio (e.g., mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:10 to 10:1.

[0234] 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. 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.

[0235] In some embodiments, the first recombinant polynucleotide is present in the pharmaceutical composition at a dose of 0.1 micrograms to 100 micrograms, or 1 micrograms to 50 micrograms, or 1 micrograms to 30 micrograms, or 1 micrograms 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 micrograms 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 micrograms to 20 micrograms, or 0.5 micrograms to 15 micrograms.

[0236] In some embodiments, the second recombinant polynucleotide is present in the pharmaceutical composition at a dose of 0.1 micrograms to 100 micrograms, or 1 micrograms to 100 micrograms, or 1 micrograms to 30 micrograms, or 1 micrograms to 20 micrograms, or 3 micrograms to 30 micrograms.

[0237] In some embodiments, the second recombinant polynucleotide includes 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 includes 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, for example, an Omicron BA.1, BA.2, BA.4, or BA.5 variant).

[0238] Provided herein are compositions comprising: (i) a first pharmaceutical composition comprising first nanoparticles, wherein the first nanoparticles comprise a recombinant polynucleotide encoding a polypeptide comprising at least two 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), and (ii) a second pharmaceutical composition comprising second nanoparticles, wherein the second nanoparticles comprise a recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof.

[0239] In some embodiments, the ratio (e.g., mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is about 1:50 to 50:1.

[0240] In some embodiments, the ratio (eg, mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is about 1:25 to 25:1.

[0241] In some embodiments, the ratio (e.g., mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is about 1:10 to 10:1.

[0242] In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotides of (i) to the recombinant polynucleotides of (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, 2.5:1, 3.5:1, 4.5 In some embodiments, the ratio (e.g., mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is about 1:6. In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotides of (i) to the recombinant polynucleotides of (ii) is about 1:3. In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotides of (i) to the recombinant polynucleotides of (ii) is about 1:2.

[0243] In some embodiments, the recombinant polynucleotide of (i) is present at a dose of 0.1 micrograms to 100 micrograms, or 1 micrograms to 50 micrograms, or 1 micrograms to 30 micrograms, or 1 micrograms to 20 micrograms, or 3 micrograms to 20 micrograms, or 5 micrograms to 15 micrograms. In some embodiments, the recombinant polynucleotide of (i) is present at a dose of 0.05 micrograms to 10 micrograms, or 0.1 micrograms to 5 micrograms, or 0.3 micrograms to 5 micrograms. In some embodiments, the recombinant polynucleotide of (i) is present at a dose of 0.1 micrograms to 20 micrograms, or 0.5 micrograms to 15 micrograms.

[0244] In some embodiments, the recombinant polynucleotide of (ii) is present at a dose of 0.1 micrograms to 100 micrograms, or 1 micrograms to 100 micrograms, or 1 micrograms to 30 micrograms, or 1 micrograms to 20 micrograms, or 3 micrograms to 30 micrograms.

[0245] In some embodiments, the recombinant polynucleotide of (ii) includes 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 of (ii) includes 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).

[0246] In some embodiments, the first nanoparticles are present in the first pharmaceutical composition at a dose of about 100 ng to 500 micrograms.

[0247] In some embodiments, the first nanoparticles are present in the first pharmaceutical composition in a dose of about 1 microgram to 100 micrograms.

[0248] In some embodiments, the first nanoparticles are present in the first pharmaceutical composition in a dose of about 1 microgram to 30 micrograms, 5 micrograms to 40 micrograms, or 10 micrograms to 50 micrograms.

[0249] 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.

[0250] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition at a dose of about 100 ng to 500 micrograms.

[0251] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition in a dose of about 1 microgram to 100 micrograms.

[0252] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition in a dose of about 1 microgram to 30 micrograms, 5 micrograms to 40 micrograms, or 10 micrograms to 50 micrograms.

[0253] 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.

[0254] 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.

[0255] In some embodiments, the recombinant polynucleotide of (i) is present in the first pharmaceutical composition in a dose of about 0.5 to 50 micrograms.

[0256] 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.

[0257] 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.

[0258] 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.

[0259] In some embodiments, the recombinant polynucleotide of (ii) is present in the second pharmaceutical composition in a dose of about 0.5 to 50 micrograms.

[0260] In some embodiments, the recombinant polynucleotide of (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.

[0261] 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.

[0262] In some embodiments, the nanoparticles are lipid nanoparticles.

[0263] 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: (i) a polypeptide comprising at least two of (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 the polypeptide, wherein the polypeptide comprises a sequence comprising an epitope sequence from (a) ORF1ab; (i) a sequence comprising at least two of the following: (a) a sequence comprising an epitope sequence derived from a membrane glycoprotein (M); and (b) a sequence comprising an epitope sequence derived from a nucleocapsid phosphoprotein (N); (iii) a T cell receptor (TCR) or a T cell comprising the TCR (the TCR forms a complex with a corresponding HLA class I or class II molecule and binds to the epitope sequence of the polypeptide); (iv) an antigen-presenting cell comprising (i) or (ii); or (v) an antibody or a B cell comprising the antibody (the antibody binds to the epitope sequence of the polypeptide).

[0264] In some embodiments, the subject has an immunodeficiency.

[0265] In some embodiments, the subject has a B-cell immunodeficiency.

[0266] In some embodiments, the subject has a reduced ability to mount an antibody response to an antigen compared to a subject without an immunodeficiency.

[0267] In some embodiments, the subject has a reduced ability to mount an antibody response to vaccination compared to a non-immunocompromised subject.

[0268] In some embodiments, the subject has a reduced ability to mount an anti-spike protein antibody response and / or an anti-RBD antibody response compared to a subject without an immunodeficiency.

[0269] In some embodiments, the subject is able to mount a T cell response or does not have a reduced ability to mount a T cell response compared to a subject without an immunodeficiency.

[0270] In some embodiments, the pharmaceutical composition protects against variants of 2019 SARS CoV-2.

[0271] In some embodiments, the variant of 2019 SARS CoV-2 is alpha, beta, gamma, delta, epsilon, zeta, eta, theta, iota, kappa, or lambda.

[0272] In some embodiments, the subject mounts a T cell response against an epitope of the polypeptide.

[0273] In some embodiments, the subject mounts a T cell response to an epitope sequence derived from ORF1ab, an epitope sequence derived from membrane glycoprotein (M), and / or an epitope sequence derived from nucleocapsid phosphoprotein (N).

[0274] In some embodiments, the subject is an organ transplant recipient.

[0275] In some embodiments, the organ transplant recipient is a solid organ transplant recipient, a stem cell transplant recipient, or a bone marrow transplant recipient.

[0276] In some embodiments, the subject underwent an organ transplant less than 1 year, less than 6 months, or less than 3 months after the pharmaceutical composition was administered.

[0277] In some embodiments, the subject is scheduled to undergo an organ transplant less than 1 year, less than 6 months, or less than 3 months prior to administration of the pharmaceutical composition.

[0278] In some embodiments, the subject has cancer.

[0279] In some embodiments, the cancer is a B-cell cancer.

[0280] In some embodiments, the B cell cancer is a B cell lymphoma or a B cell leukemia.

[0281] In some embodiments, the subject has an autoimmune disease or condition.

[0282] In some embodiments, the autoimmune disease or condition is selected from the group consisting of Addison's disease, anti-NMDA receptor encephalitis, anti-synthetase syndrome, aplastic anemia, autoimmune anemia, autoimmune hemolytic anemia, autoimmune pancreatitis, Behcet's disease, bullous skin diseases, celiac disease (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-Barré syndrome, Hashimoto's thyroiditis, idiopathic rhabdomyosarcoma, ... These diseases include: 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, Sjogren's syndrome, systemic lupus erythematosus, thrombocytopenic purpura, thrombotic thrombocytopenic purpura, type 1 diabetes mellitus, ulcerative colitis, vasculitis, and vitiligo.

[0283] In some embodiments, the subject has congenital agammaglobulinemia or congenital IgA deficiency.

[0284] In some embodiments, the subject has HIV or AIDS. In some embodiments, the subject has age-related decline in immunity, immunosenescence, multifactorial immunodeficiency, or is an elderly or geriatric subject with age-related immunodeficiency.

[0285] In some embodiments, the subject is 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.

[0286] In some embodiments, the immunosuppressant is abatacept, abrilumab, acalabrutinib, adalimumab, adrenocorticotropic hormone, agatolimod sodium, aldesleukin, alefacept, alemtuzumab, alisertib, alvespimycin hydrochloride, alvocidib, ambrisentan, aminocamptothecin, amiselimod, anakinra, andecaliximab, andrographolide, anifrolumab, antithymocyte Ig, apatinib, apelisib, asparaginase, atacicept, atezolizumab, avelumab, azacitidine, azathioprine , bafetinib, baminocept, baricitinib, basiliximab, becatecarin, begelomab, belatacept, belimumab, bemcentinib, bendamustine, bendamustine, betalutin and rilotomab, bevacizumab, BIIB033, BIIB059, BIIB061, bimekizumab, binimetinib, bleomycin, blinatumomab, bortezomib, brentuximab vedotin, bryostatin 1, bucillamine, bupalisib, busulfan, canakinumab, capecitabine, carboplatin, carfilzomib, carmustine, cediranib maleate , cemiplimab, ceralifimoda, cerduratinib, certolizumab, cetuximab, cidamide, chlorambucil, cilengitide, simtuzumab, cisplatin, cladribine, clazakizumab, clemastine, clioquinol, corticosteroids, cyclophosphamide, cyclosporine, cytarabine, cytotoxic chemotherapy, daclizumab, dalfampridine, daprolizumab pegol, daratumumab, dasatinib, defactinib, defibrotide, denosumab, dexamethasone, diacerein, dimethyl fumarate, dinaciclib, diloxacin cimel, doxorubicin, doxorubicin, durvalumab, duvelisib, duboltukizumab, eculizumab, efalizumab, eftiragimod alfa, methenkefalin and tridecactide neuropeptide combination, elezanumab, elotuzumab, encorafenib, enfuvirtida, entinostat, entospletinib, enzastaurin, epacadostat, epirubicin, epratuzumab, eritoran tetrasodium, etanercept, etoposide, etrolizumab, everolimus, evobrutinib, filgotinib, fingolimod,Frategrast, fludarabine, fluorouracil, fontolizumab, forodesine hydrochloride, fostamatinib, galunisertib, ganetespib, ganitumab, gemcitabine, gemtuzumab ozogamicin, gerilimuzumab, glasdegiv, Gracia, glatiramer acetate, glenbatumumab vedotin, glesatinib, golimumab, guadecitabine, hydrocortisone, hydroxychloroquine sulfate, hydroxyurea, ibritumomab tiuxetan, ibrutinib, ibudilast, idarubicin, idebenone, Idelalisib, ifosfamide, iguratimod, imatinib, imexon, infliximab, inotuzumab ozogamicin, 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, levocaba Sucrine, lipoic acid, 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, mycophenolate, namilumab, natalizumab, navitoclax, neflizumab, Nerispirdine, Neurovax, niraparib, nivolumab, obatoclax mesylate, obinutuzumab, oblimersen sodium, 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, pevonex, pexidartinib, picoplatin, pidilizumab, Pivanex,Pixantrone, Preneva, Probamar acetate, Polatuzumab vedotin, Pomalidomide, Ponatinib, Ponesimod, Prednisone / Prednisolone, Piroxamide, Rabrizimab-CWVZ, Recombinant IL-12, Lelatolimab, Rhigof-1, Rhigom22, Rigosertib, Rilonacept, Ritonavir, Rituximab, Ruxolitinib, Sarilumab, Secukinumab Mab, selumetinib, simvastatin, sintilimab, siplizumab, siponimod, sirolimus (rapamycin), sirukumab, sitravatinib, sonidegib, sorafenib, sotrastaurin acetate, sunitinib, sanphenon epigallocatechin gallate, tabalumab, tacrolimus, talabostat mesylate, talacotuzumab, tanespimycin, tegafur / gimeracil / oteracil, temozolomide, temsirolimus, tenalisib, telameprocol, teriflunomide, thalidomide, thiarabine, thiotepa, tipifarnib, tirabrutinib, tislelizumab, tivozanib, tocilizumab, tofacitinib, tregalizumab, tremelimumab, treosulfan, ublituximab, umbralisib, upadacitinib The agent is selected from the group consisting of rivaroxaban, urelumab, ustekinumab, varlilumab, batelizumab, vedolizumab, veliparib, veltuzumab, venetoclax, vinblastine, vincristine, vinorelbine bitartrate, visilizumab, vismodegib, vistusertib, voriconazole, vorinostat, vosaroxin, ziv-aflibercept, or any combination thereof.

[0287] In some embodiments, the immunosuppressant is an A2aR antagonist, an Akt inhibitor, an anti-CD20, an anti-amyloid (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 The inhibitor is selected from the group consisting of a mAb, a CD1d ligand, a CD40 agonist, a complement C5a inhibitor, a CSF1R inhibitor, an EZH2 inhibitor, an FGFR3 inhibitor, an FGFR4 inhibitor, an FGFrR3 inhibitor, a glucocorticoid-induced tumor necrosis factor receptor-related gene agonist, a glutaminase inhibitor, a human monoclonal antibody against IL-12, an ICOS agonist, an IDO1 inhibitor, an IL2 mutein, an IL2 receptor agonist, a MEK inhibitor, a multitargeted receptor tyrosine kinase inhibitor, a neutrophil elastase inhibitor, a Notch inhibitor, a p38 MAPK inhibitor, a PD-1 inhibitor, a recombinant human Flt3L, a ROCK inhibitor, a selective sphingosine-1-phosphate receptor modulator, a Src kinase inhibitor, a TLR4 agonist, a TLR9 agonist, or any combination thereof.

[0288] In some embodiments, the subject is over 55, 56, 57, 58, 59, 60, 65, 70, 75, or 80 years of age.

[0289] In some embodiments, the polypeptide comprises (a) a sequence comprising an epitope sequence derived from ORF1ab, (b) a sequence comprising an epitope sequence derived from a membrane glycoprotein (M), and (c) a sequence comprising an epitope sequence derived from a nucleocapsid phosphoprotein (N).

[0290] In some embodiments, the sequence comprising the epitope sequence from ORF1ab is C-terminal to the sequence comprising the epitope sequence from nucleocapsid phosphoprotein (N).

[0291] 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).

[0292] In some embodiments, the sequence comprising an epitope sequence derived from a nucleocapsid phosphoprotein (N) is N-terminal to the sequence comprising an epitope sequence derived from a membrane glycoprotein (M).

[0293] In some embodiments, the polypeptide comprises (a) two, three, four, five, six, seven, eight, nine, or ten 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).

[0294] In some embodiments, the epitope sequence derived from ORF1ab is an epitope sequence derived from a nonstructural protein (NSP).

[0295] In some embodiments, the nonstructural protein (NSP) is selected from the group consisting of NSP1, NSP2, NSP3, NSP4, and combinations thereof.

[0296] 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.

[0297] 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.

[0298] In some embodiments, the epitope sequence derived from nucleocapsid glycoprotein (N) is LLLDRLNQL.

[0299] In some embodiments, the epitope sequence derived from membrane phosphoprotein (M) is VATSRTLSY.

[0300] In some embodiments, the polypeptide comprises an epitope sequence from the nucleocapsid glycoprotein (N) that is LLLDRLNQL and an epitope sequence from the membrane phosphoprotein (M) that is VATSRTLSY.

[0301] 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 the nucleocapsid glycoprotein (N) that is LLLDRLNQL, and (c) an epitope sequence from the membrane phosphoprotein (M) that is VATSRTLSY.

[0302] In some embodiments, the sequence comprising an epitope sequence from ORF1ab is selected from the group consisting of the following sequences or fragments thereof: MVTNNTFTLKVPHVGEIPVAYRKVLLKTIQPRVEKYLFDESGEFKLSEVGPEHSLAEYYIFFASFYY, MVTNNFTLKVPHVGEIPVAYRKVLLKTIQPRVEKYLFDESGEFKLSEVGPEHSLAEY, APKEIIFLEGETLFGDDTVIEVAIILASFSAST, APKEIIFLEGETLFGDDTVIEV, HTTDPSFLGRYMSALFADDLNQLTGYHTDFSSEIIGYQLMCQPILLAEAELAKNVSLILGTVSWNL, TTDPSFLGRYMSALFADDLNQLTGYHTDFSSEIIGYQLMCQPILLAEAELAKNVSLILGTVSWNL, LLSAGIFGAITDVFYKENSYKVPTDNYITTY, and combinations thereof.

[0303] In some embodiments, the sequence comprising an epitope sequence from membrane glycoprotein (M) is the following sequence or a fragment thereof: ADSNGTITVEELKKLLEQWNLVIGFLFLTWICLLQFAYANRNRFLYIIKLIFLWLLWPVTLACFVLAAVYRINWITGGIAIAMACLVGLMWLSYFIASFRLFARTRSMWSFNPETNILLNVPLHGTILTRPLLESELVIGAVILRGHLRIAGHHLGRCDIKDLPKEITVATSRTLSYYKLGASQRVAGDSGFAAYS RYRIGNYKLNTDHSSSSDNIALLVQ, FAYANRNRFLYIIKLIFLWLLWPVTLACFVLAAVYRINWITGGIAIAMACLVGLMWLSYFIASFRLF;LGRCDIKDLPKEITVATSRTLSYYKLGASQRVA, KLLEQWNLVIGF, NRNRFLYIIKLIFLWLLWPVTLACFVLAAVY, SELVIGAVILRGHLRIAGHHLGR, VATSRTLSYYKLGASQRV, GLMWLSYF, and combinations thereof.

[0304] In some embodiments, the sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N) is the following sequence or a fragment thereof: KDLSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGTTLPKGFYAEGSRGGSQASSRSSSRSRNSSRNSTPGSSRGTSPARMAGNGGDAALALLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDKKKKAD ETQALPQRQKKQQTVTLLPAADLDDFSKQLQQSMSSADSTQA, RMAGNGGDAALALLLLDRLNQLESKMSGKGQQQ, YKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFP, SPARMAGNGGDAALALLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDK, and combinations thereof.

[0305] In some embodiments, the polypeptide comprises one or more linker sequences.

[0306] In some embodiments, the one or more linker sequences are selected from the group consisting of GGSGGGGSGG, GGSLGGGGSG.

[0307] In some embodiments, one or more linker sequences comprises a cleavage sequence.

[0308] 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.

[0309] In some embodiments, the polypeptide comprises a transmembrane domain sequence.

[0310] In some embodiments, the transmembrane domain sequence is C-terminal to a sequence comprising an epitope sequence derived from ORF1ab, a sequence comprising an epitope sequence derived from a membrane glycoprotein (M), and a sequence comprising an epitope sequence derived from a nucleocapsid phosphoprotein (N).

[0311] In some embodiments, the transmembrane domain sequence is EQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT.

[0312] In some embodiments, the polypeptide comprises a secretory signal sequence (SEC sequence).

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

[0314] In some embodiments, the SEC sequence is MFVFLVLLPLVSSQCVNLT.

[0315] In some embodiments, the composition comprises a polynucleotide encoding the polypeptide.

[0316] In some embodiments, the polynucleotide is mRNA.

[0317] In some embodiments, the polynucleotide comprises a codon-optimized sequence for expression in humans.

[0318] In some embodiments, the polynucleotide comprises a dEarI-hAg sequence.

[0319] In some embodiments, the dEarI-hAg sequence is ATTCTTCTGGTCCCCACAGACTCAGAGAGAACCC, where optionally each T is U.

[0320] In some embodiments, the polynucleotide comprises a Kozak sequence.

[0321] In some embodiments, the Kozak sequence is GCCACC.

[0322] In some embodiments, the polynucleotide comprises an F element sequence.

[0323] In some embodiments, the F element sequence is the 3UTR of the amino-terminal enhancer of splitting (AES).

[0324] In some embodiments, the F element sequence is CTGGTACTGCATGCACGCAATGCTAGCTGCCCCTTTCCCGTCCTGGGTACCCCGAGTCTCCCCCGACCTCGGGTCCCAGGTATGCTCCCACCTCCACCTGCCCCACTCACCACCTCTGCTAGTTCCAGACACCTCC, and optionally each T is U.

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

[0326] In some embodiments, the I element sequence is the 3'UTR of mitochondrially encoded 12S rRNA (mtRNR1).

[0327] In some embodiments, the I element sequence is CAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACACC, and optionally each T is U.

[0328] In some embodiments, the polynucleotide comprises a polyA sequence.

[0329] In some embodiments, the poly A sequence is AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGCATATGACTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA, and optionally each T is U.

[0330] In some embodiments, each of the epitope sequences derived from ORF1ab, membrane glycoprotein, and nucleocapsid phosphoprotein are derived from 2019 SARS-CoV-2.

[0331] In some embodiments, one or more of the epitopes or each epitope elicits a T cell response.

[0332] In some embodiments, one or more epitopes or each epitope was observed by mass spectrometry as being presented by an HLA molecule.

[0333] 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 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, RS C7p4full, RS C8p1, RS C8p2, and RS C8p2full; (ii) 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; or (iii) 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 SEQ ID NOs: 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.

[0334] 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 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 NOs: RS C7n1, RS C7n2, RS C7n2full, RS C7n4, RS, and C7n4full.

[0335] In some embodiments, the pharmaceutical composition comprises a pharmaceutically acceptable excipient, carrier, or diluent.

[0336] Provided herein are methods 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 IB, 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 IB, Table 1C, Table 2Ai, Table 2Aii, Table 2B, and / or Table 16; (iii) a T cell receptor (TCR) or a T cell comprising the TCR, where the TCR binds to the epitope sequence in a 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, where the antibody binds to the epitope sequence.

[0337] In some embodiments, the subject has an immunodeficiency.

[0338] In some embodiments, the subject has a B-cell immunodeficiency.

[0339] 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.

[0340] 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.

[0341] In some embodiments, the epitope sequence is derived from the orf1ab protein.

[0342] In some embodiments, the epitope sequence is derived from the orf1a protein.

[0343] In some embodiments, the epitope sequence is derived from the surface glycoprotein (S) or a shifted reading frame thereof.

[0344] In some embodiments, the epitope sequence is derived from the nucleocapsid phosphoprotein (N).

[0345] In some embodiments, the epitope sequence is derived from the ORF3a protein.

[0346] In some embodiments, the epitope sequence is derived from the membrane glycoprotein (M).

[0347] In some embodiments, the epitope sequence is derived from the ORF7a protein.

[0348] In some embodiments, the epitope sequence is derived from the ORF8 protein.

[0349] In some embodiments, the epitope sequence is derived from the envelope protein (E).

[0350] In some embodiments, the epitope sequence is derived from the ORF6 protein.

[0351] In some embodiments, the epitope sequence is derived from the ORF7b protein.

[0352] In some embodiments, the epitope sequence is derived from the ORF10 protein.

[0353] In some embodiments, the epitope sequence is derived from the ORF9b protein.

[0354] Provided herein are methods 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 a pharmaceutical composition comprising a recombinant polynucleotide encoding a polypeptide having an amino acid 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 one of the sequences set forth in column 2 of Table 11, column 2 of Table 12, or column 3 of Table 15, or a polypeptide having an amino acid 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 one of the sequences set forth in column 2 of Table 11, column 2 of Table 12, or column 3 of Table 15.

[0355] In some embodiments, the subject has an immunodeficiency.

[0356] In some embodiments, the subject has a B-cell immunodeficiency.

[0357] 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 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, RS C7p4full, RS C8p1, RS C8p2, and RS C8p2full; or 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 The present invention also includes polynucleotides encoding polypeptides 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 C6p2full, RS C7p1, RS C7p2, RS C7p2full, RS C7p4, RS C7p4full, RS C8p1, RS C8p2, and RS C8p2full.

[0358] 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 NOs: 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, and RS C7n4full.

[0359] In some embodiments, the polynucleotide is mRNA.

[0360] In some embodiments, the pharmaceutical composition further comprises one or more lipids.

[0361] In some embodiments, the one or more lipids comprise a lipid nanoparticle (LNP).

[0362] In some embodiments, the LNP encapsulates a recombinant polynucleotide construct.

[0363] In some embodiments, the polypeptide is synthetic.

[0364] In some embodiments, the polypeptide is recombinant.

[0365] In some embodiments, the polypeptide is between 8 and 1000 amino acids in length.

[0366] 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.

[0367] 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.

[0368] In some embodiments, the epitope sequence comprises a sequence of a viral protein expressed by virus-infected cells of the subject.

[0369] In some embodiments, the virus is a coronavirus.

[0370] In some embodiments, the virus is 2019 SARS-CoV2.

[0371] In some embodiments, the HLA molecules expressed by the subject are unknown at the time of administration.

[0372] In some embodiments, the ability of the virus to evade recognition by the subject's immune system is reduced compared to the ability of the virus to evade recognition by the immune system of a subject administered a pharmaceutical composition that contains epitopes from a single protein or epitopes from fewer proteins than the pharmaceutical compositions administered by the methods described herein.

[0373] 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 epitope sequence that is matched by the HLA allele.

[0374] 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.

[0375] In some embodiments, the method further comprises administering to the subject an additional therapy for 2019 SARS-CoV2 virus infection.

[0376] In some embodiments, the method further comprises administering to the subject (a) a polypeptide having an amino acid sequence of a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, (b) a recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, or a 2019 SARS-CoV2 spike protein pharmaceutical composition comprising (a) or (b).

[0377] In some embodiments, the vaccine or therapeutic agent of (a) or (b) is administered once to the subject.

[0378] In some embodiments, the vaccine or therapeutic agent of (a) or (b) is administered to the subject more than once.

[0379] In some embodiments, the vaccine or therapeutic agent of (a) or (b) is administered at least twice, the first administered dose being a priming dose and the second and subsequent doses being booster dose(s). In some embodiments, the vaccine or therapeutic agent of (a) or (b) is administered at least three times, the first administered dose being a priming dose and the second, third, and subsequent doses being booster dose(s).

[0380] In some embodiments, the priming dose and the booster dose are administered at least 21 days apart.

[0381] In some embodiments, the interval between two booster doses is at least 30 days, at least 60 days, or at least 90 days.

[0382] In some embodiments, the vaccine or treatment is administered once a year.

[0383] In some embodiments, the vaccine or treatment is administered twice yearly.

[0384] In some embodiments, the vaccine or therapeutic is administered as a high priming or loading dose for the first dose and reduced boosting or maintenance doses for subsequent doses.

[0385] In some embodiments, subjects receive a lower dose or less frequently of the SARS-CoV spike vaccine than subjects receiving the SARS-CoV spike vaccine alone.

[0386] Provided herein are methods 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) a recombinant polynucleotide encoding a polypeptide comprising at least two of a sequence comprising an epitope sequence derived from ORF1ab, a sequence comprising an epitope sequence derived from a membrane glycoprotein (M), and a sequence comprising an epitope sequence derived from a nucleocapsid phosphoprotein (N); and (ii) a recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof.

[0387] In some embodiments, provided herein are methods of treating or preventing infection by a virus or treating a respiratory disease or condition associated with infection by a virus, comprising administering to a subject in need thereof: (i) a first pharmaceutical composition comprising: (a) a first recombinant polynucleotide encoding a polypeptide comprising at least two of 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 a 2019 SARS-CoV2 spike protein or a variant or fragment thereof.

[0388] In some embodiments, the ratio (eg, mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is between 20:1 and 1:20.

[0389] In some embodiments, the ratio (e.g., mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is 1:10 to 10:1.

[0390] In some embodiments, the ratio (eg, mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is about 1:5 to 5:1.

[0391] In some embodiments, the ratio (eg, mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is about 1:3 to 3:1.

[0392] In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotides of (i) to the recombinant polynucleotides of (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, 2.5:1, 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.

[0393] In some embodiments, the method of treating or preventing an infection comprises administering a first pharmaceutical composition (i) and a second pharmaceutical composition (ii) to a subject who has previously received 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 an infection comprises administering the first pharmaceutical composition (i) and the second pharmaceutical composition (ii) to a subject who has previously received two or more (e.g., three) doses of a SARS-CoV-2 vaccine.

[0394] In some embodiments, provided herein are methods for treating or preventing infection by a virus or treating a respiratory disease or condition associated with infection by a virus, 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: (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-CoV2 spike protein or a variant or fragment thereof.

[0395] In some embodiments, the pharmaceutical composition comprises nanoparticles, the nanoparticles comprising a first recombinant polynucleotide and a second recombinant polynucleotide.

[0396] In some embodiments, the nanoparticles are present in the pharmaceutical composition in a dose of 100 ng to 500 micrograms.

[0397] In some embodiments, the nanoparticles are present in the pharmaceutical composition in a dose of between 1 microgram and 100 micrograms.

[0398] In some embodiments, the nanoparticles are present in the pharmaceutical composition in a dose of 1 microgram to 30 micrograms, 5 micrograms to 40 micrograms, or 10 micrograms to 50 micrograms.

[0399] 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.

[0400] In some embodiments, the ratio (e.g., mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:50 to 50:1.

[0401] 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.

[0402] In some embodiments, the ratio (e.g., mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:10 to 10:1.

[0403] 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.

[0404] Provided herein are methods 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) a recombinant polynucleotide encoding a polypeptide comprising at least two of a sequence comprising an epitope sequence derived from ORF1ab, a sequence comprising an epitope sequence derived from a membrane glycoprotein (M), and a sequence comprising an epitope sequence derived from a nucleocapsid phosphoprotein (N); and (ii) a second pharmaceutical composition comprising a recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof.

[0405] In some embodiments, the ratio (e.g., mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is about 1:50 to 50:1.

[0406] In some embodiments, the ratio (eg, mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is about 1:25 to 25:1.

[0407] In some embodiments, the ratio (e.g., mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is about 1:10 to 10:1.

[0408] In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotides of (i) to the recombinant polynucleotides of (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, 2.5:1, 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.

[0409] In some embodiments, the first pharmaceutical composition comprises first nanoparticles, the first nanoparticles comprising a recombinant polynucleotide encoding a polypeptide comprising at least two of (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 the second pharmaceutical composition comprises second nanoparticles, the second nanoparticles comprising a recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof.

[0410] In some embodiments, the first nanoparticles are present in the first pharmaceutical composition at a dose of about 100 ng to 500 micrograms.

[0411] In some embodiments, the first nanoparticles are present in the first pharmaceutical composition in a dose of about 1 microgram to 100 micrograms.

[0412] In some embodiments, the first nanoparticles are present in the first pharmaceutical composition in a dose of about 1 microgram to 30 micrograms, 5 micrograms to 40 micrograms, or 10 micrograms to 50 micrograms.

[0413] 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.

[0414] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition at a dose of about 100 ng to 500 micrograms.

[0415] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition in a dose of about 1 microgram to 100 micrograms.

[0416] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition in a dose of about 1 microgram to 30 micrograms, 5 micrograms to 40 micrograms, or 10 micrograms to 50 micrograms.

[0417] 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.

[0418] Provided herein is a method for treating or preventing an infection by a virus or treating a respiratory disease or condition associated with an infection by a virus, comprising administering to a subject in need thereof: (i) a pharmaceutical composition comprising: (a) a polypeptide comprising at least two of 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); or (b) a polynucleotide encoding a polypeptide comprising at least two of (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 pharmaceutical composition comprising: (a) a polypeptide having the amino acid sequence of a 2019 SARS-CoV2 spike protein or a variant or fragment thereof; (b) a recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof; or (ii) a recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof; and a SARS-CoV2 spike protein pharmaceutical composition,

[0419] The subject receives a dose of (ii)(a) or (ii)(b) that is lower than the dose of (ii)(a) or (ii)(b) administered to the subject alone.

[0420] Provided herein is a method for treating or preventing an infection by a virus or treating a respiratory disease or condition associated with an infection by a virus, comprising administering to a subject in need thereof: (i) a pharmaceutical composition comprising: (a) a polypeptide comprising at least two of 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); or (b) a polynucleotide encoding a polypeptide comprising at least two of (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 pharmaceutical composition comprising: (a) a polypeptide having the amino acid sequence of a 2019 SARS-CoV2 spike protein or a variant or fragment thereof; (b) a recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof; or (ii) a recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof; and a SARS-CoV2 spike protein pharmaceutical composition,

[0421] The subject receives some doses of (ii)(a) or (ii)(b) that are lower than some doses of (ii)(a) or (ii)(b) administered to the subject alone.

[0422] 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 times less than the dose of (ii)(a) or (ii)(b) administered to the subject alone.

[0423] 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 are administered to the subject alone.

[0424] In some embodiments, the pharmaceutical composition of (i) is co-formulated with the pharmaceutical composition of (ii).

[0425] In some embodiments, the pharmaceutical composition of (i) is formulated separately from the pharmaceutical composition of (ii).

[0426] In some embodiments, the pharmaceutical composition of (i) is administered separately from the pharmaceutical composition of (ii).

[0427] Provided herein is a method for treating or preventing an infection by a virus or treating a respiratory disease or condition associated with an infection by a virus, comprising administering to a subject in need thereof: (i) a pharmaceutical composition comprising a polynucleotide encoding a polypeptide comprising at least two of (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); or (b) a polypeptide comprising at least two of (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 pharmaceutical composition comprising a recombinant polynucleotide encoding (a) a polypeptide having the amino acid sequence of a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, (b) a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, or (ii) a 2019 SARS-CoV2 spike protein comprising (a) or (ii)(b). and a SARS-CoV2 spike protein pharmaceutical composition, wherein the subject receives a dose of (i)(a) or (i)(b) that is less than the dose of (i)(a) or (i)(b) administered to the subject alone.

[0428] Provided herein is a method for treating or preventing an infection by a virus or treating a respiratory disease or condition associated with an infection by a virus, comprising administering to a subject in need thereof: (i) a pharmaceutical composition comprising a polynucleotide encoding a polypeptide comprising at least two of (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); or (b) a polypeptide comprising at least two of (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 pharmaceutical composition comprising a recombinant polynucleotide encoding (a) a polypeptide having the amino acid sequence of a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, (b) a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, or (ii) a 2019 SARS-CoV2 spike protein comprising (a) or (ii)(b). and a SARS-CoV2 spike protein pharmaceutical composition, wherein the subject receives some doses of (i)(a) or (i)(b) that are lower than some doses of (i)(a) or (i)(b) administered to the subject alone.

[0429] 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 times less than the dose of (i)(a) or (i)(b) administered to the subject alone.

[0430] 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 are administered to the subject alone.

[0431] In some embodiments, the pharmaceutical composition of (i) is co-formulated with the pharmaceutical composition of (ii).

[0432] In some embodiments, the pharmaceutical composition of (i) is formulated separately from the pharmaceutical composition of (ii).

[0433] In some embodiments, the pharmaceutical composition of (i) is administered separately from the pharmaceutical composition of (ii).

[0434] In some embodiments, the pharmaceutical composition is a co-formulation.

[0435] In some embodiments, the first pharmaceutical composition is administered together with or on the same day as the second pharmaceutical composition.

[0436] In some embodiments, the first pharmaceutical composition is administered simultaneously with the second pharmaceutical composition.

[0437] In some embodiments, a first pharmaceutical composition is administered at a first location in a subject, and a second pharmaceutical composition is administered at a second location in the subject that is different from the first location.

[0438] In some embodiments, the first location is on an appendage of the subject and the second location is on a contralateral appendage of the subject.

[0439] In some embodiments, the first appendage is an arm and the second appendage is an arm.

[0440] In some embodiments, the first pharmaceutical composition and the second pharmaceutical composition are administered to the subject at the same location.

[0441] 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, 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. 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 weeks or at least about, up to 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.

[0442] 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, 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 second time point. 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 weeks or at least about, up to 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.

[0443] In some embodiments, the third time point is at least about, up to 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, up to 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 days after the first time point. , 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 weeks later, or at least about, up to 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.

[0444] 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, 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 days after the first time point. 1, 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 weeks or at least about, up to 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 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, 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 days after the second 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, 35, or 36 weeks later, or at least about, up to 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, up to 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, up to about or about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 days after the first time point. , 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 weeks later, or at least about, up to 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 second pharmaceutical composition is administered at the first time point.

[0448] In some embodiments, a second pharmaceutical composition is administered at a second time point.

[0449] In some embodiments, a second pharmaceutical composition is administered at a third time point.

[0450] In some embodiments, the second pharmaceutical composition is administered 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 36 weeks later, or at least about, up to 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.

[0451] In some embodiments, the second pharmaceutical composition is administered 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 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, or 36 weeks later, or at least about, up to 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.

[0452] 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: (i) (a) a pharmaceutical composition comprising a polynucleotide encoding a polypeptide comprising at least two of: (a) a sequence comprising an epitope sequence derived from ORF1ab, a sequence comprising an epitope sequence derived from membrane glycoprotein (M), and a sequence comprising an epitope sequence derived from nucleocapsid phosphoprotein (N); or (b) a polypeptide comprising at least two of: (a) a sequence comprising an epitope sequence derived from ORF1ab, a sequence comprising an epitope sequence derived from membrane glycoprotein (M), and a sequence comprising an epitope sequence derived from nucleocapsid phosphoprotein (N), wherein the pharmaceutical composition is administered at a first time point and a second time point, the second time point being at least about 2 days after the first time point.

[0453] In some embodiments, the pharmaceutical composition is administered at a third time point, the third time point being at least about 2 days after the second time point.

[0454] 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, 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 days after the first time point. 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35 weeks 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.

[0455] In some embodiments, the second time point is up to 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, up to about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or 18 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 later, 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.

[0456] 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, 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 days after the first time point. 8, 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.

[0457] 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, or at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or 18 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 later, 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.

[0458] In some embodiments, the third time point is up to 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, 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 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 later, 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.

[0459] 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, 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 days after the second time point. 8, 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.

[0460] 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, 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, 35, or 36 days after the first time point. 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35 weeks 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.

[0461] In some embodiments, the third time point is up to 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, 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, 35, or 36 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 later, 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.

[0462] 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, 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. 8, 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.

[0463] In some embodiments, the method further comprises administering to the subject (ii)(a) a polypeptide having the amino acid sequence of a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, (b) a recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, or a 2019 SARS-CoV2 spike protein pharmaceutical composition comprising (ii)(a) or (ii)(b).

[0464] In some embodiments, the subject has an immunodeficiency.

[0465] In some embodiments, the subject has a B-cell immunodeficiency.

[0466] In some embodiments, the pharmaceutical composition is administered prophylactically.

[0467] Provided herein is a pharmaceutical composition comprising: (i) a recombinant polynucleotide encoding a polypeptide comprising at least two of (a) a sequence comprising an epitope sequence derived from ORF1ab, a sequence comprising an epitope sequence derived from membrane glycoprotein (M), and a sequence comprising an epitope sequence derived from nucleocapsid phosphoprotein (N); and (ii) a recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof.

[0468] In some embodiments, the ratio (eg, mass ratio) of (i):(ii) is from 20:1 to 1:20.

[0469] 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.

[0470] 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.

[0471] Provided herein are compositions comprising: (i) a first pharmaceutical composition comprising: (a) a first recombinant polynucleotide encoding a polypeptide comprising at least two of 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 a 2019 SARS-CoV2 spike protein or a variant or fragment thereof.

[0472] In some embodiments, the ratio (e.g., mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is 1:50 to 50:1.

[0473] In some embodiments, the ratio (eg, mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is about 1:25 to 25:1.

[0474] In some embodiments, the ratio (e.g., mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is about 1:10 to 10:1.

[0475] In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotides of (i) to the recombinant polynucleotides of (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, 2.5:1, 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.

[0476] Provided herein is a pharmaceutical composition comprising: (i) a first recombinant polynucleotide encoding a polypeptide comprising at least two of (a) a sequence comprising an epitope sequence derived from ORF1ab, a sequence comprising an epitope sequence derived from membrane glycoprotein (M), and a sequence comprising an epitope sequence derived from nucleocapsid phosphoprotein (N); and (ii) a second recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof.

[0477] In some embodiments, the pharmaceutical composition comprises nanoparticles, the nanoparticles comprising a first recombinant polynucleotide and a second recombinant polynucleotide.

[0478] In some embodiments, the nanoparticles are present in the pharmaceutical composition in a dose of 100 ng to 500 micrograms.

[0479] In some embodiments, the nanoparticles are present in the pharmaceutical composition in a dose of between 1 microgram and 100 micrograms.

[0480] In some embodiments, the nanoparticles are present in the pharmaceutical composition in a dose of 1 microgram to 30 micrograms, 5 micrograms to 40 micrograms, or 10 micrograms to 50 micrograms.

[0481] 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.

[0482] In some embodiments, the ratio (e.g., mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:50 to 50:1.

[0483] 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.

[0484] In some embodiments, the ratio (e.g., mass ratio) of the first recombinant polynucleotide to the second recombinant polynucleotide is about 1:10 to 10:1.

[0485] 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.

[0486] Provided herein are compositions comprising: (i) a first pharmaceutical composition comprising: (a) a recombinant polynucleotide encoding a polypeptide comprising at least two of 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 a 2019 SARS-CoV2 spike protein or a variant or fragment thereof.

[0487] In some embodiments, the first pharmaceutical composition comprises first nanoparticles, the first nanoparticles comprising a recombinant polynucleotide encoding a polypeptide comprising at least two of (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 the second pharmaceutical composition comprises second nanoparticles, the second nanoparticles comprising a recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof.

[0488] In some embodiments, the ratio (e.g., mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is about 1:50 to 50:1.

[0489] In some embodiments, the ratio (eg, mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is about 1:25 to 25:1.

[0490] In some embodiments, the ratio (e.g., mass ratio) of (i) recombinant polynucleotide to (ii) recombinant polynucleotide is about 1:10 to 10:1.

[0491] In some embodiments, the ratio (e.g., mass ratio) of the recombinant polynucleotides of (i) to the recombinant polynucleotides of (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, 2.5:1, 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.

[0492] In some embodiments, the first nanoparticles are present in the first pharmaceutical composition at a dose of about 100 ng to 500 micrograms.

[0493] In some embodiments, the first nanoparticles are present in the first pharmaceutical composition in a dose of about 1 microgram to 100 micrograms.

[0494] In some embodiments, the first nanoparticles are present in the first pharmaceutical composition in a dose of about 1 microgram to 30 micrograms, 5 micrograms to 40 micrograms, or 10 micrograms to 50 micrograms.

[0495] 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.

[0496] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition at a dose of about 100 ng to 500 micrograms.

[0497] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition in a dose of about 1 microgram to 100 micrograms.

[0498] In some embodiments, the second nanoparticles are present in the second pharmaceutical composition in a dose of about 1 microgram to 30 micrograms, 5 micrograms to 40 micrograms, or 10 micrograms to 50 micrograms.

[0499] 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.

[0500] 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.

[0501] In some embodiments, the recombinant polynucleotide of (i) is present in the first pharmaceutical composition in a dose of about 0.5 to 50 micrograms.

[0502] 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.

[0503] 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.

[0504] 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.

[0505] In some embodiments, the recombinant polynucleotide of (ii) is present in the second pharmaceutical composition in a dose of about 0.5 to 50 micrograms.

[0506] In some embodiments, the recombinant polynucleotide of (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.

[0507] 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.

[0508] In some embodiments, the nanoparticles are lipid nanoparticles.

[0509] Provided herein are (i) a polypeptide comprising at least two of (a) a sequence comprising an epitope sequence derived from ORF1ab, (b) a sequence comprising an epitope sequence derived from membrane glycoprotein (M), and (c) a sequence comprising an epitope sequence derived from nucleocapsid phosphoprotein (N); (ii) a polynucleotide encoding the polypeptide, wherein the polypeptide is a sequence comprising at least two of (a) a sequence comprising an epitope sequence derived from ORF1ab, (b) a sequence comprising an epitope sequence derived from membrane glycoprotein (M), and (c) a sequence comprising an epitope sequence derived from nucleocapsid phosphoprotein (N); (iii) a T cell receptor (TCR) or a T cell comprising the TCR (the TCR forms a complex with a corresponding HLA class I or class II molecule and binds to the epitope sequence of the polypeptide), (iv) an antigen-presenting cell comprising (i) or (ii), or (v) an antibody or a B cell comprising the antibody (the antibody binds to the epitope sequence of the polypeptide), and a pharmaceutically acceptable excipient.

[0510] 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). In some embodiments, the sequence comprising the epitope sequence from ORF1ab is C-terminal to the sequence comprising the epitope sequence from nucleocapsid phosphoprotein (N). 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). In some embodiments, the sequence comprising the epitope sequence from nucleocapsid phosphoprotein (N) is N-terminal to the sequence comprising the epitope sequence from membrane glycoprotein (M).

[0511] In some embodiments, the polypeptide comprises at least two of: (a) a sequence comprising an epitope sequence derived from ORF1ab; (b) a sequence comprising an epitope sequence derived from membrane glycoprotein (M); and (c) a sequence comprising an epitope sequence derived from nucleocapsid phosphoprotein (N).

[0512] In some embodiments, the polypeptide comprises (a) two, three, four, five, six, seven, eight, nine, or ten 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).

[0513] 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.

[0514] 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.

[0515] In some embodiments, the epitope sequence derived from nucleocapsid glycoprotein (N) is LLLDRLNQL. In some embodiments, the epitope sequence derived from membrane phosphoprotein (M) is VATSRTLSY. In some embodiments, the polypeptide comprises an epitope sequence derived from nucleocapsid glycoprotein (N) that is LLLDRLNQL and an epitope sequence derived from membrane phosphoprotein (M) that is VATSRTLSY.

[0516] 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 the nucleocapsid glycoprotein (N) that is LLLDRLNQL, and (c) an epitope sequence from the membrane phosphoprotein (M) that is VATSRTLSY.

[0517] In some embodiments, the sequence comprising an epitope sequence from ORF1ab is selected from the group consisting of the following sequences or fragments thereof: MVTNNTFTLKVPHVGEIPVAYRKVLLKTIQPRVEKYLFDESGEFKLSEVGPEHSLAEYYIFFASFYY, MVTNNFTLKVPHVGEIPVAYRKVLLKTIQPRVEKYLFDESGEFKLSEVGPEHSLAEY, APKEIIFLEGETLFGDDTVIEVAIILASFSAST, APKEIIFLEGETLFGDDTVIEV, HTTDPSFLGRYMSALFADDLNQLTGYHTDFSSEIIGYQLMCQPILLAEAELAKNVSLILGTVSWNL, TTDPSFLGRYMSALFADDLNQLTGYHTDFSSEIIGYQLMCQPILLAEAELAKNVSLILGTVSWNL, LLSAGIFGAITDVFYKENSYKVPTDNYITTY, and combinations thereof.

[0518] In some embodiments, the sequence comprising an epitope sequence from membrane glycoprotein (M) is the following sequence or a fragment thereof: ADSNGTITVEELKKLLEQWNLVIGFLFLTWICLLQFAYANRNRFLYIIKLIFLWLLWPVTLACFVLAAVYRINWITGGIAIAMACLVGLMWLSYFIASFRLFARTRSMWSFNPETNILLNVPLHGTILTRPLLESELVIGAVILRGHLRIAGHHLGRCDIKDLPKEITVATSRTLSYYKLGASQRVAGDSGFAAYS RYRIGNYKLNTDHSSSSDNIALLVQ, FAYANRNRFLYIIKLIFLWLLWPVTLACFVLAAVYRINWITGGIAIAMACLVGLMWLSYFIASFRLF;LGRCDIKDLPKEITVATSRTLSYYKLGASQRVA, KLLEQWNLVIGF, NRNRFLYIIKLIFLWLLWPVTLACFVLAAVY, SELVIGAVILRGHLRIAGHHLGR, VATSRTLSYYKLGASQRV, GLMWLSYF, and combinations thereof.

[0519] In some embodiments, the sequence comprising an epitope sequence from nucleocapsid phosphoprotein (N) is the following sequence or a fragment thereof: KDLSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGTTLPKGFYAEGSRGGSQASSRSSSRSRNSSRNSTPGSSRGTSPARMAGNGGDAALALLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDKKKKAD ETQALPQRQKKQQTVTLLPAADLDDFSKQLQQSMSSADSTQA, RMAGNGGDAALALLLLDRLNQLESKMSGKGQQQ, YKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFP, SPARMAGNGGDAALALLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDK, and combinations thereof.

[0520] 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.

[0521] In some embodiments, the polypeptide comprises a transmembrane domain sequence. In some embodiments, the transmembrane 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). In some embodiments, the transmembrane sequence is EQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT.

[0522] In some embodiments, the polypeptide comprises a SEC sequence. In some embodiments, the SEC sequence is N-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). In some embodiments, the SEC sequence is MFVFLVLLPLVSSQCVNLT.

[0523] In some embodiments, the composition comprises a polynucleotide encoding a polypeptide. In some embodiments, the polynucleotide is mRNA. In some embodiments, the polynucleotide comprises a codon-optimized sequence for expression in humans.

[0524] In some embodiments, the polynucleotide comprises a dEarI-hAg sequence. In some embodiments, the dEarI-hAg sequence is ATTCTTCTCTGGTCCCCACAGACTCAGAGAGAACCC, where optionally each T is U.

[0525] In some embodiments, the polynucleotide comprises a Kozak sequence. In some embodiments, the Kozak sequence is GCCACC.

[0526] In some embodiments, the polynucleotide comprises an F element sequence. In some embodiments, the F element sequence is the 3UTR of the amino terminal enhancer of splitting (AES). In some embodiments, the F element sequence is CTGGTACTGCATGCACGCAATGCTAGCTGCCCCTTTCCCGTCCTGGGTACCCCGAGTCTCCCCCGACCTCGGGTCCCAGGTATGCTCCCACCTCCACCTGCCCCACTCACCACCTCTGCTAGTTCCAGACACCTCC, where optionally each T is U.

[0527] In some embodiments, the polynucleotide comprises an I element sequence. In some embodiments, the I element sequence is the 3'UTR of mitochondrially encoded 12S rRNA (mtRNR1). In some embodiments, the I element sequence is CAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACACC, where optionally each T is U.

[0528] In some embodiments, the polynucleotide comprises a poly A sequence. In some embodiments, the poly A sequence is AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGCATATGACTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA, and optionally each T is U.

[0529] In some embodiments, each of the epitope sequences derived from ORF1ab, membrane glycoprotein, and nucleocapsid phosphoprotein are derived from 2019 SARS-CoV-2.

[0530] In some embodiments, one or more of the epitopes or each epitope elicits a T cell response.

[0531] In some embodiments, one or more epitopes or each epitope was observed by mass spectrometry as being presented by an HLA molecule.

[0532] 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 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, RS C7p4full, RS C8p1, RS C8p2, and RS C8p2full; (ii) 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; or (iii) 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 SEQ ID NOs: 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.

[0533] Also described herein are pharmaceutical compositions comprising any of the compositions described herein.

[0534] Also provided herein are pharmaceutical compositions comprising (i) a polypeptide comprising an epitope sequence of Table 1A, Table IB, 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 the TCR, wherein the TCR binds to the epitope sequence in a 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.

[0535] 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.

[0536] In some embodiments, the epitope sequence is derived from the orf1ab protein. In some embodiments, the epitope sequence is derived from the orf1a protein. In some embodiments, the epitope sequence is derived from the surface glycoprotein (S) or a shifted reading frame thereof. In some embodiments, the epitope sequence is derived from the nucleocapsid phosphoprotein (N). In some embodiments, the epitope sequence is derived from the ORF3a protein. In some embodiments, the epitope sequence is derived from the membrane glycoprotein (M). In some embodiments, the epitope sequence is derived from the ORF7a protein. In some embodiments, the epitope sequence is derived from the ORF8 protein. In some embodiments, the epitope sequence is derived from the envelope protein (E). In some embodiments, the epitope sequence is derived from the ORF6 protein. In some embodiments, the epitope sequence is derived from the ORF7b protein. In some embodiments, the epitope sequence is derived from the ORF10 protein. In some embodiments, the epitope sequence is derived from the ORF9b protein.

[0537] Also provided herein is a pharmaceutical composition comprising a recombinant polynucleotide encoding a polypeptide having an amino acid sequence with at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% sequence identity to any one of the sequences set forth in column 2 of Table 11, column 2 of Table 12, or column 3 of Table 15; or a polypeptide having an amino acid sequence with at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% sequence identity to any one of the sequences set forth in column 2 of Table 11, column 2 of Table 12, or column 3 of Table 15.

[0538] 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 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, RS C7p4full, RS C8p1, RS C8p2, and RS C8p2full; or 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 The present invention also includes polynucleotides encoding polypeptides 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 C6p2full, RS C7p1, RS C7p2, RS C7p2full, RS C7p4, RS C7p4full, RS C8p1, 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 NOs: 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, and RS C7n4full.

[0539] In some embodiments, the polynucleotide is mRNA.

[0540] In some embodiments, the pharmaceutical composition further comprises one or more lipid components. In some embodiments, the one or more lipids comprise lipid nanoparticles (LNPs). In some embodiments, the LNPs encapsulate the recombinant polynucleotide construct.

[0541] In some embodiments, the polypeptide is synthetic. In some embodiments, the polypeptide is recombinant.

[0542] In some embodiments, the polypeptide is between 8 and 1000 amino acids in length.

[0543] 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, hi 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.

[0544] In some embodiments, the epitope sequence comprises a sequence of a viral protein expressed by virus-infected cells of the subject.

[0545] Also provided herein is 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 a pharmaceutical composition described herein.

[0546] In some embodiments, the virus is a coronavirus. In some embodiments, the virus is 2019 SARS-CoV2. In some embodiments, the HLA molecules expressed by the subject are unknown at the time of administration. In some embodiments, the virus has a reduced ability to evade recognition by the subject's immune system compared to the ability of a virus to evade recognition by the immune system of a subject administered a pharmaceutical composition containing epitopes from a single protein or epitopes from fewer proteins than the pharmaceutical compositions described herein. In some embodiments, the subject expresses an HLA molecule encoded by an HLA allele in any one 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.

[0547] 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.

[0548] Also provided herein is a method of treating or preventing 2019 SARS-CoV2 infection in a subject in need thereof, comprising administering to the subject a pharmaceutical composition described herein.

[0549] In some embodiments, the pharmaceutical composition is administered in addition to one or more therapeutic agents for a 2019 SARS-CoV2 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-CoV2 spike protein or a variant or fragment thereof, (b) a recombinant polynucleotide encoding a 2019 SARS-CoV2 spike protein or a variant or fragment thereof, or a 2019 SARS-CoV2 spike protein pharmaceutical composition comprising (a) or (b). In some embodiments, the 2019 SARS-CoV2 spike protein or variant or fragment thereof is a SARS-CoV-2 spike protein or fragment thereof.

[0550] In some embodiments, the pharmaceutical composition is administered 1 to 10 weeks after the initial administration of the 2019 SARS-CoV2 spike protein pharmaceutical composition. In some embodiments, the pharmaceutical composition is administered 1 to 6 weeks, 1 to 6 months, or 1 to 2 years or later after the initial administration of the 2019 SARS-CoV2 spike protein pharmaceutical composition. In some embodiments, the pharmaceutical composition is administered on the same day as or simultaneously with the administration of the 2019 SARS-CoV2 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-CoV2 spike protein, or a variant or fragment thereof, or a recombinant polynucleotide encoding the 2019 SARS-CoV2 spike protein, or a variant or fragment thereof. In some embodiments, the pharmaceutical composition is administered prior to the administration of the 2019 SARS-CoV2 spike protein pharmaceutical composition, such as 2 to 10 weeks prior to the administration of the 2019 SARS-CoV2 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 to 7, 7 to 14, 14 to 21, 21 to 28, or 28 to 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.

[0551] Also provided herein is the use of a composition described herein for the preparation of a therapeutic agent for treating or preventing a respiratory viral infection caused by the 2019 SARS CoV-2 virus.

[0552] Also provided herein is a composition described herein or a pharmaceutical composition described herein for use as a medicament.

[0553] Also provided herein is a composition described herein or a pharmaceutical composition described herein for use in treating or preventing a respiratory viral infection caused by the 2019 SARS CoV-2 virus.

[0554] Provided herein are antigenic peptides comprising an epitope sequence from Table 1A, Table IB, Table 1C, Table 2Ai, Table 2Aii, or Table 2B. Also provided herein are polynucleotides encoding antigenic peptides comprising an epitope sequence from Table 1A, Table IB, Table 1C, Table 2Ai, Table 2Aii, or Table 2B. The antigenic peptides and / or polynucleotides may be recombinant. The antigenic peptides and / or polynucleotides may be isolated or purified. The antigenic peptides may be synthetic or expressed from a polynucleotide.

[0555] Also provided herein are antibodies or B cells comprising antibodies that bind to antigenic peptides comprising epitope sequences from Table 1A, Table 1B, Table 1C, Table 2Ai, Table 2Aii, or Table 2B.

[0556] Also provided herein are T cell receptors (TCRs) or T cells comprising the TCR that bind epitope sequences from Table 1A or Table 1B in complex with a corresponding MHC class I molecule according to Table 1A or Table 1B. For example, the TCR can bind epitope sequences from column 2 (Set 1) of Table 1A in complex with a corresponding MHC class I molecule from the same row, column 3 (Set 1) of Table 1A. For example, the TCR can bind epitope sequences from column 4 (Set 2) of Table 1A in complex with a corresponding MHC class I molecule from the same row, column 5 (Set 2) of Table 1A. For example, the TCR can bind epitope sequences from column 6 (Set 3) of Table 1A in complex with a corresponding MHC class I molecule from the same row, column 7 (Set 3) of Table 1A. For example, a TCR can bind to an epitope sequence from column 2 (Set 1) of Table 1B in a complex with a corresponding MHC class I molecule from the same row, column 3 (Set 1) of Table 1B. For example, a TCR can bind to an epitope sequence from column 4 (Set 2) of Table 1B in a complex with a corresponding MHC class I molecule from the same row, column 5 (Set 2) of Table 1B.

[0557] Also provided herein are T cell receptors (TCRs) or T cells comprising such TCRs that bind to epitope sequences from Table 2Ai or Table 2Aii in a complex with a corresponding MHC class II molecule according to Table 2Ai or Table 2Aii. For example, a TCR can bind to an epitope sequence from column 2 (Set 1) of Table 2Ai in a complex with a corresponding MHC class II molecule from the same row, column 3 (Set 1) of Table 2Ai. For example, a TCR can bind to an epitope sequence from column 4 (Set 2) of Table 2Ai in a complex with a corresponding MHC class II molecule from the same row, column 5 (Set 2) of Table 2Ai. Similarly, a TCR can bind to an epitope sequence from the left column of Table 2Aii in a complex with a corresponding MHC class II molecule from the right column of Table 2Aii.

[0558] Provided herein is a method of 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 IB, Table 1C, Table 2Ai, Table 2Aii, or Table 2B. 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 polynucleotide encoding an antigenic peptide comprising an epitope sequence from Table 1A, Table IB, Table 1C, Table 2Ai, Table 2Aii, or Table 2B.

[0559] 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 containing 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.

[0560] 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 said TCR that binds an epitope sequence from Table 1A or Table 1B in complex with a corresponding MHC class I molecule according to Table 1A or Table 1B.

[0561] For example, the method can include administering to a subject a TCR or T cells comprising a TCR capable of binding to an epitope sequence from column 2 (Set 1) of Table 1A in a complex with a corresponding MHC class I molecule from the same row, column 3 (Set 1) of Table 1A. For example, the method can include administering to a subject a TCR or T cells comprising a TCR capable of binding to an epitope sequence from column 2 (Set 1) of Table 1A in a complex with a corresponding MHC class I molecule from the same row, column 3 (Set 1) of Table 1A to a subject expressing the corresponding MHC class I molecule from column 3 (Set 1). For example, the method can include administering to a subject a TCR or T cells comprising a TCR capable of binding to an epitope sequence from column 4 (Set 2) of Table 1A in a complex with a corresponding MHC class I molecule from the same row, column 5 (Set 2) of Table 1A. For example, the method can include administering a TCR or T cells comprising a TCR capable of binding to an epitope sequence from column 4 (Set 2) of Table 1A in a complex with a corresponding MHC class I molecule from the same row, column 5 (Set 2) of Table 1A to a subject expressing the corresponding MHC class I molecule from column 5 (Set 2). For example, the method can include administering a TCR or T cells comprising a TCR capable of binding to an epitope sequence from column 6 (Set 3) of Table 1A in a complex with a corresponding MHC class I molecule from the same row, column 7 (Set 3) of Table 1A to a subject expressing the corresponding MHC class I molecule from column 7 (Set 3).

[0562] For example, the method can include administering to a subject a TCR or T cells comprising a TCR capable of binding to an epitope sequence from column 2 (Set 1) of Table 1B in a complex with a corresponding MHC class I molecule from the same row, column 3 (Set 1) of Table 1B. For example, the method can include administering to a subject a TCR or T cells comprising a TCR capable of binding to an epitope sequence from column 2 (Set 1) of Table 1B in a complex with a corresponding MHC class I molecule from the same row, column 3 (Set 1) of Table 1B to a subject expressing the corresponding MHC class I molecule from column 3 (Set 1). For example, the method can include administering to a subject a TCR or T cells comprising a TCR capable of binding to an epitope sequence from column 4 (Set 2) of Table 1B in a complex with a corresponding MHC class I molecule from the same row, column 5 (Set 2) of Table 1B. For example, the method can include administering a TCR or a T cell comprising a TCR capable of binding to an epitope sequence from column 4 (Set 2) of Table 1B in a complex with a corresponding MHC class I molecule from column 5 (Set 2) of the same row of Table 1B to a subject expressing the corresponding MHC class I molecule from column 5 (Set 2).

[0563] For example, the method can include administering to a subject a TCR or T cells comprising a TCR capable of binding to an epitope sequence from column 2 (Set 1) of Table 2Ai in a complex with a corresponding MHC class II molecule from the same row, column 3 (Set 1) of Table 2Ai. For example, the method can include administering to a subject a TCR or T cells comprising a TCR capable of binding to an epitope sequence from column 2 (Set 1) of Table 2Ai in a complex with a corresponding MHC class II molecule from the same row, column 3 (Set 1) of Table 2Ai to a subject expressing the corresponding MHC class II molecule from column 3 (Set 1). For example, the method can include administering to a subject a TCR or T cells comprising a TCR capable of binding to an epitope sequence from column 4 (Set 2) of Table 2Ai in a complex with a corresponding MHC class II molecule from the same row, column 5 (Set 2) of Table 2Ai. For example, the method can include administering a TCR or T cells comprising a TCR capable of binding to an epitope sequence from column 4 (Set 2) of Table 2Ai in a complex with a corresponding MHC class II molecule from the same row, column 5 (Set 2) of Table 2Ai to a subject expressing a corresponding MHC class II molecule from column 5 (Set 2). For example, the method can include administering to a subject a TCR or T cells comprising a TCR capable of binding to an epitope sequence from the left column of Table 2Aii in a complex with a corresponding MHC class II molecule from the same row, right column of Table 2Aii.

[0564] In one embodiment, the antigenic peptide is a viral antigen. In another embodiment, the antigenic peptide is an overexpressed antigen that is not mutated. In some embodiments, the viral antigen is derived from publicly disclosed information regarding viral genetic information. In some embodiments, the viral antigen is derived from analysis of a viral genome to predict preferred epitopes for T cell activation. In some embodiments, the viral antigen is derived from analysis of the sequence of the viral genome in an MHC-peptide presentation prediction algorithm implemented on a computer processor. In some embodiments, the viral antigen is derived from analysis of the viral sequence in an MHC-peptide presentation prediction algorithm implemented on a computer processor trained with machine learning software that predicts the likelihood of epitope binding and presentation by MHC class I antigens or MHC class II antigens. In some embodiments, the MHC-peptide presentation predictor is neonmhc2.

[0565] In some embodiments, the MHC and peptide presentation prediction algorithm or MHC and peptide presentation predictor is NetMHCpan or NetMHCIIpan, and further analysis is performed with the MHC and peptide presentation predictor NetMHCpan or NetMHCIIpan for comparison. In some embodiments, one skilled in the art may use a hidden Markov model approach for MHC and peptide presentation prediction. In some embodiments, the peptide prediction model MARIA may be utilized. In some embodiments, the MHC and peptide presentation prediction algorithm or MHC and peptide presentation predictor used is not NetMHCpan or NetMHCIIpan. In some embodiments, the viral sequence is analyzed with an MHC and peptide presentation prediction algorithm implemented on a computer processor, where the MHC and peptide presentation predictor is neonmhc1 or neonmhc2, which refer to class I and class II binding predictions, respectively. In some embodiments, the MHC and peptide presentation predictor model is RECON, which provides high-quality MHC and peptide presentation predictions based on expression, processing, and binding capacity.

[0566] In one aspect, provided herein is a method of 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 to the subject's T cells by antigen-presenting cells to mount an antiviral response in the subject. In some embodiments, the viral antigens are derived from analysis of the sequence of the viral genome in an MHC-peptide presentation prediction algorithm implemented on a computer processor. In some embodiments, the viral antigens are derived from analysis of the viral sequence in an MHC-peptide presentation prediction algorithm implemented on a computer processor trained with machine learning software that predicts the likelihood of epitope binding and presentation by MHC class I or MHC class II antigens. In some embodiments, the MHC-peptide presentation predictor is neonmhc2. In some embodiments, the method further comprises analyzing a nucleic acid sequence from the viral genome with an MHC-peptide presentation prediction model, the MHC-peptide presentation prediction model comprising an algorithm implemented on a computer processor trained by machine learning software, wherein the MHC-peptide presentation prediction model predicts the likelihood of binding and presentation of epitopes encoded by the viral genome by MHC class I or MHC class II antigens. In some embodiments, the method further comprises analyzing a biological sample from the subject for identification of an MHC class I and MHC class II repertoire, wherein analyzing comprises analyzing by genome or whole exome sequencing or analyzing by analyzing proteins encoded by HLA genes.In some embodiments, the method further includes matching epitopes predicted by the MHC-peptide presentation prediction model with high affinity for MHC class I or MHC class II peptides encoded by the subject's HLA genes, and selecting one or more peptides predicted to bind to the MHC peptides encoded by the subject's HLA genes with high affinity as ranked by the MHC-peptide presentation prediction model. In some embodiments, the one or more selected peptides are predicted to bind the MHC peptides encoded by the subject's HLA genes with an affinity of at least 1000 nM. In some embodiments, the one or more selected peptides are predicted to bind the MHC class I peptides encoded by the subject's HLA genes with an affinity of at least 500 nM. In some embodiments, the one or more selected peptides are predicted to bind the MHC class II peptides encoded by the subject's HLA genes with an affinity of at least 1000 nM.

[0567] In some embodiments, the MHC-peptide presentation prediction model is programmed to provide a rank order of the likelihood of a particular epitope or antigenic peptide binding to an HLA allele that presents the peptide to a T cell receptor. In some embodiments, the epitope sequence most likely to be bound and presented by an HLA is selected for preparing a therapeutic. In some embodiments, the selection of an HLA may be constrained by the HLA expressed in the subject. In some embodiments, the selection of an HLA may be based on the prevalence (e.g., higher prevalence) of the allele in a population. In some embodiments, an epitope may be selected for preparing a therapeutic based on the peptide (epitope) being more likely to be bound and presented by an HLA allele, e.g., an HLA allele of interest. In some embodiments, this % rank value may be determined by evaluating the percentile at which a query peptide scores for a particular allele compared to a fixed set of reference peptides (a different set of class I and class II reference peptides). In some embodiments, the top 10% of epitopes most likely to bind to an HLA allele may be selected. In some embodiments, the top 2% of epitopes most likely to bind to an HLA allele may be selected. In some embodiments, the top 5% of epitopes most likely to bind to an HLA allele may be selected. In some embodiments, the top 8% of epitopes most likely to bind to an HLA allele may be selected. In some embodiments, the top 1% of epitopes most likely to bind to an HLA allele may be selected. In some embodiments, the top 0.5% of epitopes most likely to bind to an HLA allele may be selected. In some embodiments, the top 0.1% of epitopes most likely to bind to an HLA allele may be selected. In some embodiments, the top 0.01% of epitopes most likely to bind to an HLA allele may be selected.In some embodiments, the choice of cutoff may depend on the availability and number of epitopes predicted to have a high probability of binding to the HLA allele as determined by a predictive model.

[0568] In some embodiments, the subject may be infected with a virus. In some embodiments, the subject may be at risk for infection with a virus. In some embodiments, the virus is a coronavirus. In some embodiments, the coronavirus is selected from SARS virus, MERS coronavirus, or 2019 SARS CoV-2 virus. In some embodiments, the one or more viral peptide antigens comprise a peptide comprising at least 8 consecutive amino acids of a sequence in Table 1A, Table IB, 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 comprise a peptide comprising at least 7 consecutive amino acids of a sequence in Table 1A, Table IB, 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 comprise a peptide comprising at least 6 consecutive amino acids of a sequence in Table 1A, Table IB, 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.

[0569] In one embodiment, the antigenic peptide is between about 5 and about 50 amino acids in length. In another embodiment, the antigenic peptide is between about 15 and about 35 amino acids in length. In another embodiment, the antigenic peptide is about 15 or less amino acids in length. In another embodiment, the antigenic peptide is between about 8 and about 11 amino acids in length. In another embodiment, the antigenic peptide is 9 or 10 amino acids in length. In one embodiment, the antigenic peptide binds to major histocompatibility complex (MHC) class I. In another embodiment, the antigenic peptide binds to MHC class I with a binding affinity of less than about 500 nM. In one embodiment, the antigenic peptide is about 30 amino acids or less in length. In another embodiment, the antigenic peptide is between about 6 and about 25 amino acids in length. In another embodiment, the antigenic peptide is between about 15 and about 24 amino acids in length. In another embodiment, the antigenic peptide is between about 9 and about 15 amino acids in length. In one embodiment, the antigenic peptide binds MHC class II. In another embodiment, the antigenic peptide binds MHC class II with a binding affinity of less than about 1000 nM.

[0570] In one embodiment, the antigenic peptide further comprises flanking amino acids. In another embodiment, the flanking amino acids are not naturally occurring flanking amino acids. In one embodiment, the antigenic peptide is linked to at least a second antigenic peptide. In another embodiment, the peptides are linked using a polyglycine linker or a polyserine linker. In another embodiment, the second antigenic peptide binds MHC class I or class II with a binding affinity of less than about 1000 nM. In another embodiment, the second antigenic peptide binds MHC class I or class II with a binding affinity of less than about 500 nM. In another embodiment, both epitopes bind human leukocyte antigen (HLA)-A, -B, -C, -DP, -DQ, or -DR. In another embodiment, the antigenic peptide binds class I HLA and the second antigenic peptide binds class II HLA. In another embodiment, the antigenic peptide binds class II HLA and the second antigenic peptide binds class I HLA.

[0571] In one embodiment, the antigen peptide further comprises a modification that increases in vivo half-life, cellular targeting, antigen uptake, antigen processing, MHC affinity, MHC stability, or antigen presentation. In another embodiment, the modification is conjugation to a carrier protein, conjugation to a ligand, conjugation to an antibody, PEGylation, polysialylation, HESylation, recombinant PEG mimic, Fc fusion, albumin fusion, nanoparticle conjugation, nanoparticle encapsulation, cholesterol fusion, iron fusion, acylation, amidation, glycosylation, side chain oxidation, phosphorylation, biotinylation, addition of surfactants, addition of amino acid mimics, or addition of unnatural amino acids, e.g., synthetic amino acids, 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 the DEC205, XCR1, CD197, CD80, CD86, CD123, CD209, CD273, CD283, CD289, CD184, CD85h, CD85j, CD85k, CD85d, CD85g, CD85a, CD141, CD11c, CD83, TSLP receptor, or CD1a markers. In another embodiment, dendritic cells are targeted using the CD141, DEC205, or XCR1 markers.

[0572] In one embodiment, provided herein is an in vivo delivery system comprising an antigenic peptide described herein. In another embodiment, the delivery system comprises a cell-penetrating peptide, nanoparticle encapsulation, virus-like particle, or liposome. In another embodiment, the cell-penetrating peptide is TAT ​​peptide, herpes simplex virus VP22, transportan, or Antp.

[0573] In one embodiment, provided herein is a cell comprising an antigenic peptide described herein. In another embodiment, the cell is an antigen-presenting cell. In another embodiment, the cell is a dendritic cell.

[0574] In one embodiment, provided herein is a composition comprising an antigenic peptide 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 1B. 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 to a coronavirus.

[0575] In one embodiment, provided herein is a polynucleotide encoding an antigenic peptide described herein. In another embodiment, the polynucleotide is RNA, optionally a self-amplifying RNA. In some embodiments, the polynucleotide is DNA. In another embodiment, the RNA is modified to enhance stability, enhance cellular targeting, translation efficiency, adjuvant activity, cytosolic accessibility, and / or reduce cytotoxicity. In another embodiment, the modification is conjugation to a carrier protein, conjugation to a ligand, conjugation to an antibody, codon optimization, increased GC content, incorporation of modified nucleosides, incorporation of a 5'-cap or cap analog, and / or incorporation of a polyA sequence, e.g., an unmasked polyA sequence or a disrupted polyA sequence in which two segments of adjacent A sequences are joined by a linker.

[0576] In one embodiment, provided herein is a cell comprising a polynucleotide described herein.

[0577] In one embodiment, provided herein is a vector comprising the polynucleotide described herein. In another embodiment, the polynucleotide is operably linked to a promoter. In another embodiment, the vector is a self-amplifying RNA replicon, a plasmid, a phage, a transposon, a cosmid, a virus, or a virion. In another embodiment, the vector is an adeno-associated virus, a herpes virus, a lentivirus, or a pseudotype thereof.

[0578] In one embodiment, provided herein is an in vivo delivery system comprising a polynucleotide 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.

[0579] In one embodiment, provided herein is a cell comprising a vector or delivery system 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.

[0580] In some embodiments, provided herein are compositions comprising at least one polynucleotide described herein. In some embodiments, provided herein are compositions comprising one or more antigenic peptides described herein in combination with one or more 2019 SARS CoV-2 vaccines (e.g., mRNA-based vaccines, DNA-based vaccines, AAV-based vaccines, protein-based vaccines). In some embodiments, provided herein are compositions comprising one or more polynucleotides encoding at least one antigenic peptide described herein in combination with one or more 2019 SARS CoV-2 vaccines (e.g., mRNA-based vaccines, DNA-based vaccines, AAV-based vaccines, protein-based vaccines). In some embodiments, provided herein are single polynucleotides encoding more than one antigenic peptide described herein. In some embodiments, provided herein are single polynucleotides encoding (i) at least one antigenic peptide described herein and (ii) a 2019 SARS CoV-2 protein (e.g., S protein) and / or an immunogenic fragment thereof (e.g., receptor binding domain (RBD) of the 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 of the 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 and the additional antigenic polynucleotide are linked. In another embodiment, the polynucleotides are linked using nucleic acids encoding a polyglycine linker or a polyserine linker.

[0581] In one embodiment, provided herein is a T cell receptor (TCR) capable of binding at least one antigenic peptide described herein. In another embodiment, the TCR is capable of binding the antigenic peptide in the context of MHC class I or class II.

[0582] In one embodiment, provided herein is a chimeric antigen receptor comprising (i) a T cell activation molecule, (ii) a transmembrane region, and (iii) an antigen recognition portion capable of binding to an antigenic peptide described herein. In another embodiment, CD3 zeta is the 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 Fc epsilon RI-gamma. In another embodiment, the antigen recognition portion is capable of binding an antigenic peptide in the context of MHC class I or class II. In another embodiment, the chimeric antigen receptor comprises the transmembrane region of CD3-zeta, CD28, CTLA-4, ICOS, BTLA, KIR, LAG3, CD137, OX40, CD27, CD4OL, Tim-3, A2aR, or PD-1.

[0583] In one embodiment, provided herein is a T cell comprising a T cell receptor or chimeric antigen receptor described herein. In one embodiment, the T cell is a helper T cell or a cytotoxic T cell.

[0584] In one embodiment, provided herein is a nucleic acid comprising a promoter operably linked to a polynucleotide encoding a T cell receptor described herein. In another embodiment, the TCR is capable of binding at least one antigenic peptide in the context of 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 described herein. In another embodiment, the antigen recognition moiety is capable of binding at least one antigenic peptide in the context of major histocompatibility complex (MHC) class I or class II.

[0585] In one embodiment, provided herein is an antibody capable of binding a peptide comprising an epitope in Table 1A, Table IB, 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 capable of binding a peptide comprising an epitope in Table 1B. In one embodiment, provided herein is an antibody capable of binding a peptide comprising an epitope in Table 2Ai or Table 2Aii.

[0586] In one embodiment, provided herein are modified cells transfected or transduced with a nucleic acid described herein. In one embodiment, the modified cells are T cells, tumor-infiltrating lymphocytes, NK-T cells, TCR-expressing cells, CD4+ T cells, CD8+ T cells, or NK cells.

[0587] In one embodiment, provided herein is a composition comprising a T cell receptor or chimeric antigen receptor described herein. In another embodiment, the composition comprises a patient's autologous T cells containing a T cell receptor or chimeric antigen receptor 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 ligand, 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 a B-7 family ligand, or a combination thereof.

[0588] In one embodiment, the composition further comprises an immunomodulatory agent or adjuvant. In another embodiment, the immunomodulatory agent is a costimulatory 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 immunomodulatory agent is at least one infected cell extract. In another embodiment, the infected cells are autologous to the subject in need of the composition. In another embodiment, the infected cells have been lysed or exposed to ultraviolet light. In another embodiment, the composition further comprises an adjuvant. In another embodiment, the adjuvant is Poly(I:C), Poly-ICLC, STING agonist, 1018ISS, aluminum salts, Amplivax, AS15, BCG, CP-870,893, CpG7909, CyaA, dSLIM, GM-CSF, IC30, IC31, Imiquimod, or ImuFact. In another embodiment, the adjuvant is selected from the group consisting of IMP321, IS patch, ISS, ISCOMATRIX, JuvImmune, LipoVac, MF59, monophosphoryl lipid A, Montanide IMS1312VG, Montanide ISA206VG, ​​Montanide ISA50V2, Montanide ISA51VG, OK-432, OM-174, OM-197-MP-EC, ISA-TLR2 agonist, ONTAK, PepTel®, vector systems, PLG microparticles, resiquimod, SRL172, virosomes and other virus-like particles, YF-17D, VEGF trap, R848, beta-glucan, Pam3Cys, Pam3CSK4, acrylic or methacrylic polymers, copolymers of maleic anhydride, and QS21 stimulon. In another embodiment, the adjuvant induces humoral immunity when administered to a subject. In another embodiment, the adjuvant induces type 1 helper T cells when administered to a subject.

[0589] In one embodiment, provided herein is a method of inhibiting viral infection by administering to a subject susceptible to infection with the virus a vaccine composition comprising one or more peptides comprising at least 8 consecutive amino acids from an epitope defined in Table 1A, Table IB, Table 1C, Table 2Ai, Table 2Aii, or Table 2B, comprising contacting the cell with a peptide, polynucleotide, delivery system, vector, composition, antibody, or cell of the disclosure.

[0590] In one embodiment, provided herein is a method of treating a viral infection, particularly a coronavirus infection, e.g., a 2019 SARS CoV-2 infection, by enhancing or prolonging an antiviral response in a subject in need thereof, comprising administering to the subject a peptide, polynucleotide, vector, composition, antibody, or cell described herein.

[0591] In one embodiment, the subject is a human. In another embodiment, the subject has a viral infection. In one embodiment, the subject is infected with an acute respiratory virus, such as a SARS-like virus or a MERS or MERS-like virus, or more specifically, a respiratory virus such as a 2019 SARS CoV-2 strain of coronavirus. In some embodiments, the subject is infected with the 2019 SARS CoV-2 coronavirus. In some embodiments, the subject is detectably infected with the 2019 SARS CoV-2 coronavirus. In some embodiments, the subject is asymptomatic. In some embodiments, the subject exhibits symptoms. In some embodiments, the subject has not been detected as having been infected with the 2019 SARS CoV-2 virus or a related virus, but the subject has been near an infected person, in an infected area, or otherwise at risk of infection.

[0592] 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, optionally RNA, is administered. 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, cells are administered. In another embodiment, the cells are T cells or dendritic cells. In another embodiment, the peptide or polynucleotide comprises a moiety that targets antigen-presenting cells.

[0593] In one embodiment, the peptide, polynucleotide, vector, composition, or cells are administered prior to coadministration with another therapy, such as another antiviral therapy. In another embodiment, the peptide, polynucleotide, vector, composition, or cells are administered before or after another antiviral therapy. In another embodiment, the administration of the other antiviral therapy is continued throughout the antigen peptide therapy, polynucleotide therapy, vector therapy, composition therapy, or cell therapy.

[0594] In one embodiment of the method, an additional agent is administered. In another embodiment, the agent is a chemotherapeutic agent, an immunomodulatory agent, an immunometabolic modulating agent, a targeted therapy, radiation, an antiangiogenic agent, or an agent that reduces immunosuppression. In another embodiment, administration of a pharmaceutical composition described herein induces or promotes a CD4+ T cell immune response. In another embodiment, administration of a pharmaceutical composition described herein induces or promotes a CD4+ T cell immune response and a CD8+ T cell immune response.

[0595] In another embodiment, the patient received chemotherapeutic agents, immunomodulatory agents, immunometabolic modulating agents, targeted therapy, or radiation therapy prior to and / or during receipt of the antigenic peptide or nucleic acid vaccine. In another embodiment, the autologous T cells are obtained from a patient who has already received at least one T cell therapy containing the antigen. 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 a viral antigen. In another embodiment, the adoptive T cell therapy further comprises allogeneic T cells. In another embodiment, the allogeneic T cells target a viral antigen.

[0596] In one embodiment, provided herein is a method for assessing the effectiveness of a treatment, comprising: (i) measuring the number or concentration of target cells in a first sample obtained from a subject before administering modified cells; (ii) measuring the number or concentration of target cells in a second sample obtained from the subject after administering 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 effectiveness of the treatment is determined by monitoring a clinical outcome: an increase, enhancement, or prolongation of antiviral activity by T cells; 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 effectiveness of the treatment is determined by monitoring a biomarker. In another embodiment, the therapeutic effect 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.

[0597] Provided herein are pharmaceutical compositions comprising one or more polypeptides having the amino acid sequence of any one of the sequences set forth in column 2 of Tables 11 and 12; or one or more recombinant polynucleotide constructs each encoding a polypeptide having the amino acid sequence of any one of the sequences set forth in column 2 of Tables 11 and 12.

[0598] In some embodiments, the one or more polypeptides comprise at least 2, 3, 4, 5, 6, 7, or 8 different polypeptides having the amino acid sequence of any one of the sequences set forth in column 2 of Tables 11 and 12; or the one or more recombinant polynucleotide constructs comprise at least 2, 3, 4, 5, 6, 7, or 8 recombinant polynucleotide constructs, each encoding a different polypeptide having the amino acid sequence of any one of the sequences set forth in column 2 of Tables 11 and 12. In some embodiments, the pharmaceutical composition comprises at least 8 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 of sequences set forth in SEQ ID NOs: RSCln, RS C2n, RS C3n, RSC4n, RS C5n, RS C6n, RS C7n, and RS C8n, or a sequence that is at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or 100% sequence identity to any one of the foregoing. In some embodiments, the recombinant polynucleotide construct comprises mRNA. In some embodiments, the recombinant polynucleotide construct is mRNA. In some embodiments, the pharmaceutical composition further comprises one or more lipid components. In some embodiments, the one or more lipids comprise lipid nanoparticles (LNPs). In some embodiments, the LNPs encapsulate the recombinant polynucleotide construct. In some embodiments, the pharmaceutical composition is administered to a subject in need thereof.

[0599] Provided herein are methods for treating COVID in a subject in need thereof, comprising administering the pharmaceutical composition described above to the subject. In some embodiments, the pharmaceutical composition is administered in addition to one or more COVID therapeutics. In some embodiments, the pharmaceutical composition is administered in combination with one or more polypeptides having the amino acid sequence of the 2019 SARS CoV-2 spike protein or fragment thereof, or one or more recombinant polynucleotide constructs encoding the 2019 SARS CoV-2 spike protein or fragment thereof. In some embodiments, the 2019 SARS CoV-2 spike protein or fragment thereof is a SARS-CoV-2 spike protein or fragment thereof. In some embodiments, the pharmaceutical composition is administered 2 to 10 weeks after the first administration of the 2019 SARS CoV-2 spike protein or fragment thereof. In some embodiments, the pharmaceutical composition is administered 1 to 6 months after the first administration of the 2019 SARS CoV-2 spike protein or fragment thereof. In some embodiments, the pharmaceutical composition is administered simultaneously with the administration of the 2019 SARS CoV-2 spike protein or fragment thereof. In some embodiments, the pharmaceutical composition is administered 2 to 10 weeks before the first administration of the 2019 SARS-CoV-2 spike protein or fragment thereof. In some embodiments, the pharmaceutical composition is administered 2 to 10 weeks after the first administration of a vaccine comprising the SARS-CoV-2 spike protein or a polynucleotide encoding same. In some embodiments, the pharmaceutical composition is administered 1 to 6 months after the first administration of the SARS-CoV-2 spike protein or a polynucleotide encoding same. In some embodiments, the pharmaceutical composition is administered simultaneously with the administration of the SARS-CoV-2 spike protein or a polynucleotide encoding same. In some embodiments, the pharmaceutical composition is administered prophylactically. In some embodiments, the pharmaceutical composition is administered once every 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, or more.

[0600] Also provided herein is the use of any one of the compositions described herein for the preparation of a therapeutic medicament for treating or preventing a respiratory viral infection caused by the 2019 SARS CoV-2 virus.

[0601] When aspects or embodiments of the present disclosure are described in terms of a Markush group or other group of alternatives, the present disclosure encompasses not only the entire group listed as a whole, but also each member of the group individually, and all possible subgroups of the main group, and the main group in which one or more group members are not present. The present disclosure also contemplates the explicit exclusion of one or more of any group members in embodiments of the present disclosure. [Brief explanation of the drawings]

[0602] [Figure 1A] 1 shows an exemplary flow diagram of a method for identifying peptides most relevant for generating CD8+ T cell responses against viral epitopes described herein. [Figure 1B] A graphical representation of the SARS-CoV2 genome is shown. [Figure 2] An exemplary graph of the results obtained using the T cell epitope prediction algorithm applied to class I peptide-MHC allele pairs in the validation dataset, and a comparison of the calculated percent ranks of these pairs with the reported MHC binding assay results, is shown. Peptide-MHC allele pairs that showed binary "positive" results in the MHC binding assay had significantly lower percent ranks than pairs that showed "negative" results. For more detailed positive results, stronger assay results (low < medium < high) were associated with significantly lower percent ranks. [Figure 3]Experimental validation of HLA-A02:01 predicted epitopes from 2019 SARS CoV-2 in human T cell induction assays is shown. Twenty-three peptides predicted to be high binders to HLA-A02:01 (see Table 4 in Example 8) were synthesized and assayed in T cell induction assays using PBMCs from three human donors. An epitope was considered immunogenic if it elicited a T cell response against the peptide in at least one donor, as determined by pMHC multimer technology. Representative flow cytometry plots of pMHC staining using peptides from Table 4 in Example 8 are shown. Multimer-positive populations are circled, and the frequency of multimer-positive CD8+ T cells is indicated in the upper right corner of each plot. [Figure 4A] Illustrated are exemplary graphs of cumulative USA population coverage of HLA alleles for the indicated peptides predicted to be MHC class I epitopes (left) and cumulative USA population coverage of HLA alleles for 25mer peptides predicted to be MHC class II epitopes (right). [Figure 4B] This demonstrates that a small number of predicted multi-allelic binding epitopes from individual 2019 SARS-CoV-2 proteins (alternatively referred to as 2019-CoV-2 proteins) can achieve broad population coverage. The top panel shows cumulative HLA-I coverage for the USA, EUR, and API populations relative to the number of preferred HLA-I epitopes contained in each of the M, N, and S proteins. The corresponding peptide sequences for the top panel are shown in Table 6. The bottom panel shows cumulative HLA-II coverage for each population relative to the number of preferred HLA-II 25-mers contained in each of the M, N, and S proteins. The corresponding peptide sequences for the bottom panel are shown in Table 7. [Figure 5]We present the results of an analysis of publicly available proteomic datasets showing relative 2019 SARS CoV-2 protein expression levels that can be leveraged to prioritize potential vaccine targets. Three datasets examining the proteomic response to 2019 SARS CoV-2 infection (also known as 2019 SARS CoV-2 infection) were reanalyzed, and protein abundance was estimated by spectral counts normalized to protein length. Annotated ORFs not shown in the figure were not detected in these proteomic studies. Across all three studies, the nucleocapsid protein is the most abundant protein during 2019 SARS CoV-2 infection. [Figure 6A] 1 shows a graphical representation of the string constructs described as Group 1, which are also described in Tables 9 and 11. [Figure 6B] A detailed enlarged view of the construct of FIG. 6A is provided. [Figure 7A] 1 shows a graphical representation of the string constructs described as Group 2, which are also described in Tables 10 and 12. [Figure 7B] A detailed enlarged view of the construct of FIG. 7A is provided. [Figure 8Ai] Characterization of BNT mRNA vaccine-induced T cells at the single epitope level. Data included demonstrate epitope-responsive T cells to 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. [Figure 8Aii] Characterization of BNT mRNA vaccine-induced T cells at the single epitope level. Data included demonstrate epitope-responsive T cells to 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. [Figure 8B]Multimer-positive CD8+ cells analyzed by flow cytometry for the cell surface markers CCR7, CD45RA, CD3, PD-1, CD38, HLA-DR, CD28 and CD27 are shown. [Figure 8C] An mRNA vaccine containing spike proteins S1 and S2 is shown, with the indicated epitope regions capable of binding to specific MHC molecules indicated by solid shapes along their length, and the corresponding HLA alleles to which they bind are shown below. [Figure 8D] Figure 1 shows T cell responses over time after vaccination of a patient with spike protein mRNA vaccine at different doses (10, 20, and 30 micrograms as indicated). The top panel shows CD4+ T cell responses as indicated by IFN-g expression using an ELISPOT assay. The bottom panel shows CD8+ T cell responses as indicated by IFN-g expression using an ELISPOT assay. CEF and CEFT are pooled controls: CMV, EBV, and influenza. [Figure 8E] 1 shows CD4+ T cell and CD8+ T cell responses over time in an elderly population administered spike protein mRNA vaccine (30 micrograms each). [Figure 9] 1 shows the design of a vaccine string containing the ORF-1ab epitope, specifically using MS-based HLA-I cleavage predictor information in epitope ordering, which utilizes a minimal number of linker sequences. [Figure 10A] 1 shows the experimental design for testing the immunogenicity of string vaccine compositions in animal models. [Figure 10B] A representative experimental setup for an animal model study to determine the immunogenicity of four CorVac2.0 strings when administered in vivo is shown: Five groups (16 animals / 8–10 slaughtered on day 14 and 8–10 slaughtered on day 28). [Figure 11A] FIG. 1 is a schematic diagram of different administration schedules for spike vaccine (BNT162b2) and CorVac2.0. [Figure 11B]FIG. 1 shows a schematic diagram of an animal study to determine the immune response elicited by different combination ratios and doses of CorVac2.0 string and BNT162b2 in HLA-A02 transgenic mice. [Figure 11C] FIG. 1 shows a schematic diagram of an animal study to determine the immune response elicited by different combination ratios and doses of CorVac2.0 string and BNT162b2 in transgenic mice expressing human ACE2. [Figure 12A] Shows the variants and mutations of sequences across the spike protein in different SARS CoV-2 isolates and their respective mapping to vaccine epitope sequences. [Figure 12B] 1 is a chart showing spike variant frequency over time. [Figure 13A] Shows sequence variants and mutations across the nucleocapsid protein in different SARS CoV-2 isolates and their respective mapping to vaccine epitope sequences. [Figure 13B] 1 is a chart showing nucleocapsid variant frequencies over time. [Figure 14] Shows variants and mutations of sequences spanning the membrane protein in different SARS CoV-2 isolates and their respective mapping to vaccine epitope sequences. [Figure 15] Shows variants and mutations of sequences spanning the NSP1 protein in different SARS CoV-2 isolates and their respective mapping to vaccine epitope sequences. [Figure 16] Shown are variants and mutations of sequences spanning the NSP2 protein in different SARS CoV-2 isolates and their respective mapping to vaccine epitope sequences. [Figure 17] Shown are variants and mutations of sequences spanning the NSP3 protein in different SARS CoV-2 isolates and their respective mapping to vaccine epitope sequences. [Figure 18]Shown are variants and mutations of sequences spanning the NSP4 protein in different SARS CoV-2 isolates and their respective mapping to vaccine epitope sequences. [Figure 19A] CorVac2.0 - String design for maximal CD8 and CD4 T cell responses. [Figure 19B] We show that RS-C7 is enriched for known ORF1ab T cell epitopes and avoids most variants of concern / variants of interest (VOC / VOI) mutations. [Figure 19C] We show that RS-C7 is enriched for known nucleocapsid and membrane T-cell epitopes and avoids most variants of concern / variants of interest (VOC / VOI) mutations. [Figure 20] FIG. 1 shows an exemplary experimental setup outlined for testing polynucleotide strings for peptide presentation in complex with MHC proteins. [Figure 21] Representative data are shown showing exemplary target epitope presentation verified by mass spectrometry: endogenous in an experimental setting where the epitope is expressed in A375 cells expressing endogenous HLA, and synthetic in an experimental setting where the epitope is expressed in cells expressing exogenous HLA. [Figure 22] Figure 1 shows a diagrammatic representation of the list of epitopes identified by the above method using mass spectrometry. The identified epitopes span the viral genome and cover epitopes of the nucleocapsid protein, the ORF1ab domain, and membrane proteins. [Figure 23] A map representation of all identified CorVac2.0 epitopes across the viral nucleocapsid, ORF1ab and membrane regions is shown. [Figure 24]Representative data are shown showing that Corvac2.0 string elicits T cell responses from the nucleocapsid region after a single injection on day 0 in BALB / C mice. Immunoreactive T cells are determined by elispot assay (number of spots / 1x10^6 cells). Statistical significance determined by two-way ANOVA with Sidak's multiple comparison test. [Figure 25] Representative data are shown showing that Corvac2.0 string elicits T cell responses from membrane regions after a single injection on day 0 in BALB / C mice. Immunoreactive T cells are determined by elispot assay (number of spots / 1x10^6 cells). Statistical significance determined by two-way ANOVA with Sidak's multiple comparison test. [Figure 26] Figure 1 shows a graphical representation of a summary of the performance of different strings tested to date, with the number of stars proportional to the statistical significance of each string's immunogenicity compared to the vehicle control. [Figure 27] Representative data are shown showing that Corvac2.0 string elicits T cell responses to epitopes from the nucleocapsid region after 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 / 1x10^6 cells). Statistical significance was determined by two-way ANOVA with Sidak's multiple comparison test. Data are from mice 28 days after injection of the string composition. [Figure 28] Representative data are shown showing that Corvac2.0 string elicits T cell responses to epitopes from membrane regions after 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 / 1x10^6 cells). Statistical significance was determined by two-way ANOVA with Sidak's multiple comparison test. Data from mice 28 days after injection of the string composition. [Figure 29]Representative data are shown showing that Corvac2.0 string elicits T cell responses to epitopes from the ORF1ab region after a single injection on day 0 in HLA-A2tg mice (mice expressing humanized HLA-A02:01). T cell immune reactivity was determined by ELISpot assay (number of spots / 1x10^6 cells). Statistical significance was determined by two-way ANOVA with Sidak's multiple comparison test. Data are from mice 28 days after injection of the string composition. [Figure 30] Figure 27 is a graphical representation summarizing the statistical significance of the immunogenicity of the different strings tested in the HLA-A02 transgenic mouse model compared to the vehicle control and the results shown in Figures 27, 28, and 29. This representation shows that RS-C7 has the most T cell response across the pools in the HLA-A02 transgenic mouse model. [Figure 31] 1 shows a graphical representation of the RS-C7 string design, showing the regions of the string that elicited an immune response as determined by ELISpot assay, and the epitopes that were process confirmed and presented by HLA using mass spectrometry. [Figure 32A] 1 shows a graphical representation of a string design in which the encoded nucleocapsid sequence contains, among other things, tiled overlapping 15mer epitope sequences with an 11 amino acid overlap. [Figure 32B] 1 shows a graphical representation of the string design in which the encoded membrane sequences contain, among other things, tiled 15-mer sequences with 11 amino acid overlaps. [Figure 32C] 1 shows a graphical representation of the string design in which the encoded ORF1ab sequence contains, among other things, tiled 15-mer sequences with an 11 amino acid overlap. [Figure 32D]Results from the experimental design shown in Figure 10B show that CorVac2.0 strings do not elevate T cell responses from the ORF1ab region in a BALB / C mouse model. In contrast, results shown in Figure 29 (left, pool 11) and (right, pool 12) show that CorVac2.0 strings elevate T cell responses from the ORF1ab region in an HLA-A02 transgenic mouse model. Statistical significance determined by one-way ANOVA with Sidak's multiple comparison test. [Figure 32E] 1 is a graphical representation of a summary of the performance of different strings tested in the BALB / C mouse model, showing that RS-C7 has the most T cell response across pools in the BALB / C mouse model. The RS-C7 string raised the most T cell response across pools in the BALB / C mouse model. [Figure 33] 1 is a graphical representation showing that the CorVac2.0 string C7 epitope has little to no overlap with regions harboring mutations of variants of concern. [Figure 34A] Using the dosing schedule indicated by Figure 11A, data relating to assessment of B cell responses by ELISA for S1-binding antibodies in mouse serum at the indicated time points and serum dilutions are shown. [Figure 34B] Using the dosing schedule indicated by Figure 11A, data relating to assessment of B cell responses by ELISA for NP-binding antibodies in mouse serum at the indicated time points and serum dilutions are shown. [Figure 35] Figure 11 shows ELISA results for serum IgG concentrations on days 14, 21, and 35 after treatment (injection) with saline control (NaCl), BNT162b2, C7 string, or the combination, as shown using the dosing schedule according to Figure 11A. The results indicate that the inclusion of CorVac2.0 in the co-formulation setting does not affect the development of Spike-specific Abs. [Figure 36]Figure 11A shows the results of a pseudovirus neutralization test (pVNT) using viral particles pseudotyped with a VSV envelope containing the SARS-CoV-2 spike protein on days 14, 21, and 35 after treatment (injection) with saline control (NaCl), BNT162b2, C7 string, or the combination, as shown using the dosing schedule in Figure 11A. The results show that CorVac2.0 does not adversely affect the formation of neutralizing antibodies against SARS-CoV-2 viral proteins (Wuhan strain). [Figure 37A] Figure 11A shows the results of lymph node phenotyping on day 35 using the dosing schedule described above. B cell populations are indicated by the % of CD19+ cells in the CD45+ cell population. The percentage of activated B cells was determined by the % of IgD-CD3-CD4-CD8- cells, the percentage of switched B cells was determined by the % of activated / B220+IgM-CD19+CD138- cells, and the % of GC B cells was determined by the % of activated / B220+IgM-CD19+CD138- cells of total CD45+ cells in the population. The results indicate that the inclusion of CorVac2.0 in the 1:1 co-formulation does not affect, but slightly enhances, BNT162b2-driven B cell responses. [Figure 37B] Using the dosing schedule according to Figure 11A, results of lymph node phenotyping on day 35 are shown. The results demonstrate that packaging CorVac2.0 maintains the frequency of Tfh cells in the lymph nodes. [Figure 38] Figure 11A shows the activation of splenocytes stimulated with peptides present in BNT162b2 on day 35 and assessed by flow cytometry for the presence of the activation marker CD69 on the bulk T cell population (left panel) or CD4 T cells (middle panel) or CD8 T cells (right panel) using the dosing schedule described in Figure 11A. The results show that T cell activation upon restimulation with spike peptide (Spike 1 pool) is increased in the vaccine group with BNT162b2 (Group 2) and is not inhibited in the groups with both CorVac2.0 and BNT162b2 (Groups 4-7). [Figure 39]Figure 11A shows the activation of splenocytes stimulated with peptides present in BNT162b2 on day 35 and assessed by flow cytometry for the presence of the activation marker IFN-gamma on the bulk T cell population (left panel), CD8 T cells (middle panel), or CD4 T cells (right panel) using the dosing schedule described in Figure 11A. The results show that T cell activation upon restimulation with the spike peptide (Spike 1 pool) is increased in the vaccine group with BNT162b2 (Group 2) and is not inhibited in the groups with both CorVac2.0 and BNT162b2 (Groups 4-7) for the CD3 T cell population and the CD8 T cell population, but not significantly increased in any of the groups for the CD4 T cell population. [Figure 40] Using the dosing schedule per Figure 11A, splenocyte activation stimulated with peptides present in BNT162b2 on day 35 and assessed by flow cytometry for the presence of the activation marker CD69 on the bulk T cell population (left panel) or CD4 T cells (middle panel) or CD8 T cells (right panel) is shown. The results show that T cell activation upon restimulation with spike peptide (Spike 2 pool) is most dramatically increased in groups receiving BNT162b2 co-formulated in the same LNP (Groups 5-7). [Figure 41A] Figure 11A shows the activation of splenocytes stimulated with peptides present in the nucleocapsid sequence present in the CorVac2.0 string on day 35 using the dosing schedule according to Figure 11A and assessed by flow cytometry for the presence of the activation marker CD69 on the bulk T cell population (left panel) or CD4 T cells (middle panel) or CD8 T cells (right panel). The results show that T cell activation upon restimulation with nucleocapsid peptide is increased in the CD3 and CD8 T cell populations in the vaccine group with CorVac2.0 (group 3) and in the vaccine groups with both the separately formulated and co-formulated strings of BNT162b2 and CorVac2.0 (groups 4 and 5), with a modest increase in the CD4 T cell population. [Figure 41B]Figure 11A shows the activation of splenocytes stimulated with peptides present in the nucleocapsid sequence present in the CorVac2.0 string on day 35 using the dosing schedule according to Figure 11A and assessed by flow cytometry for the presence of the functional marker IFN-γ on the bulk T cell population (left panel) or CD8 T cells (middle panel) or CD4 T cells (right panel). The results show that the production of IFN-γ in T cells upon restimulation with the nucleocapsid peptide is increased in the CD3 and CD4 T cell populations in the vaccine group with CorVac2.0 (group 3) and in the vaccine group with the co-formulated strings of both BNT162b2 and CorVac2.0 in the same proportions (group 5), and modestly increased in the CD8 T cell population. [Figure 42] Using the dosing schedule according to Figure 11A, results are shown showing spike (N-terminal and C-terminal) antigen-specific T cell responses by ELISpot assay on samples from day 35. The results show that Ag-specific spike T cell responses are not inhibited by the addition of CorVac2.0 and are slightly enhanced by the 1:1 co-formulation. [Figure 43] Using the dosing schedule according to Figure 11A, results are shown showing nucleocapsid, membrane, and Orf1ab antigen-specific T cell responses by ELISpot assay on samples from day 35. The results show that the CorVac2.0 string response was stronger in the CorVac2.0-only group, but was still present when the CorVac2.0 string was combined with BNT162b2. [Figure 44] Using the dosing schedule per Figure 11A, we show the effect of BNT162b2 and CorVac2.0 alone or in combination on anti-spike antigen T cell responses by ELISPOT on days 14 and 35. The kinetic studies presented here demonstrate increased spike T cell responses following boost in all groups. [Figure 45]Using the dosing schedule according to Figure 11A, the effect of booster doses on CorVac2.0 immune responses on days 14 and 35 is shown. The kinetic studies presented here show that CorVac2.0 responses did not increase after the boost. [Figure 46] Figure 11A shows the polyfunctionality of CD4 and CD8 responses elicited by BNT162b2 and CorVac2.0 using the dosing schedule according to Figure 11A after restimulation with cognate peptide groups (spike N-terminus, spike C-terminus, nucleocapsid, and membrane, as noted) assayed by flow cytometry. CD4 and CD8 T cell responses were determined to be polyfunctional by expression of IFNγ+IL-2+TNFα+. [Figure 47] 11A shows a graphical representation summarizing the effect of the different formulations shown in the left column on spike N-terminal antigen-specific responses by CD4 / CD8 cells using the dosing schedule according to FIG. 11A. The number of stars is proportional to the statistical significance and strength of the response compared to the vehicle control. [Figure 48] 11A shows a graphical representation summarizing the effect of the different formulations shown in the left column on spike C-terminal antigen-specific responses by CD4 / CD8 cells using the dosing schedule according to FIG. 11A. The number of stars is proportional to the statistical significance and strength of the response compared to the vehicle control. [Figure 49] 11A shows a graphical representation summarizing the effect of the different formulations shown in the left column on nucleocapsid antigen-specific responses by CD4 / CD8 cells using the dosing schedule according to FIG. 11A. The number of initiations is proportional to the statistical significance and strength of the response compared to the vehicle control. [Figure 50] 11A shows a graphical representation summarizing the effect of the different formulations shown in the left column on membrane antigen-specific responses by CD4 / CD8 cells using the dosing schedule according to FIG. 11A. The number of stars is proportional to the statistical significance and strength of the response compared to the vehicle control. [Figure 51]FIG. 1 shows a schematic diagram of an animal study to determine the immune response elicited by different combination ratios and doses of CorVac2.0 string and BNT162b2 in transgenic mice expressing human ACE2. [Figure 52] Figure 51 shows data from an animal study demonstrating that boosting with separately formulated CorVac2.0 at a dose of 0.3 μg enhances anti-spike IgG production (quantified on day 56). CorVac2.0 alone slightly promotes anti-spike IgG production, separately formulated 3:1 promotes anti-spike IgG production, and the inclusion of multiple doses of separately formulated CorVac2.0 does not adversely affect the anti-spike IgG response. [Figure 53] Figure 51 shows data from an animal study demonstrating that boosting with separately formulated CorVac2.0 at a 0.3 μg dose enhances anti-spike IgG production (as measured by optical density (OD) on day 56). CorVac2.0 alone slightly promotes anti-spike IgG production, separately formulated 3:1 promotes anti-spike IgG production, and inclusion of multiple doses of separately formulated CorVac2.0 does not adversely affect the anti-spike IgG response. [Figure 54] Figure 51 shows data from an animal study demonstrating anti-spike IgG kinetics over time. A third boost increased anti-spike IgG under all CorVac2.0 variations. [Figure 55] ELISA data from the animal study shown in FIG. 51 are shown, showing anti-spike IgG levels in serum on the indicated days using the serum dilutions shown. [Figure 56] Figure 51 shows pseudovirus neutralization test (pVNT) data from an animal study demonstrating that inclusion of CorVac2.0 does not adversely affect neutralization titers on the indicated days after treatment with the indicated dosing regimen. pVNT was performed using viral particles pseudotyped with a VSV envelope containing the SARS-CoV-2 spike protein at the dilutions shown. [Figure 57] Tetramer staining data using PBLs from the animal study shown in Figure 51 show the percentage of CD8+ T cells specific for the indicated membrane and spike epitopes or epitope combinations, demonstrating that the anti-spike response is unaffected by the addition of CorVac2.0. [Figure 58] Tetramer staining data using PBLs from the animal study shown in Figure 51 are shown, showing the percentage of CD8+ T cells specific for the indicated spike epitopes, demonstrating that the anti-spike response is unaffected by the addition of CorVac2.0. [Figure 59] Figure 51 shows a spot formation assay from an animal study depicting the number of spots formed per 1x10^6 cells after treatment with the indicated regimen on day 56, demonstrating that the addition of CorVac2.0 in the third booster shot as a separate formulation slightly improves the anti-spike T-cell response. CorVac2.0 alone slightly enhances the anti-spike T-cell response, separately formulated 3:1 and 9:1 slightly enhance anti-spike T-cells, and the inclusion of multiple doses of separately formulated CorVac2.0 does not adversely affect the anti-spike T-cell response. [Figure 60] Figure 51 shows a spot formation assay from an animal study, depicting the number of spots formed per 1 x 10^6 cells after treatment with the indicated regimens on day 56, demonstrating that a weak anti-nucleocapsid response was seen with a single 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 with a single CorVac2.0 boost. An increased anti-nucleocapsid response was also observed with increasing numbers of CorVac2.0 administrations. [Figure 61]Figure 51 shows a spot formation assay from an animal study, showing the number of spots formed per 1x10^6 cells after treatment with the indicated regimen on day 56, demonstrating that the strongest anti-membrane response was seen in the separately formulated group as a booster, with multiple doses of separately formulated BNT162b2 + CorVac2.0 resulting in an increased response. The strongest anti-membrane response was seen under the separately formulated condition. An increase in the anti-membrane response was observed with increasing numbers of CorVac2.0 administrations. [Figure 62] Figure 51 shows data from the animal study shown in Figure 51 in which harvested inguinal lymph nodes (draining lymph nodes (dLN)) were dissected and viable cell counts determined after treatment with the indicated regimens. Three samples (G5, G7, G9) with 0% viability were removed. The data show that the group with the CorVac2.0 boost in combination with BNT162b2 exhibits an increase in viable LN cell counts. [Figure 63] Figure 51 shows data from an animal study in which harvested lymph nodes were dissected and cell counts of the indicated cell populations as a percentage of CD45.2 cells were determined after treatment with the indicated regimens. The data demonstrate a trend toward an increase in germinal center (GC) cells and CD27+ memory B cells in the group treated with separately formulated CorVac2.0+BNT162. [Figure 64A] Figure 51 shows data from an animal study in which harvested lymph nodes were dissected and cell counts of the indicated cell populations as a percentage of CD45.2 cells were determined after treatment with the indicated regimens. The data show slightly higher class-switched B cells in the group treated with separately formulated CorVac2.0+BNT162. [Figure 64B] Figure 51 shows data from an animal study 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 show slightly higher class-switched B cells in the group treated with separately formulated CorVac2.0+BNT162. [Figure 65]Tetramer-specific staining data from the animal study shown in Figure 51 are shown from harvested lymph node samples showing the percentage of spike- or membrane epitope-specific CD8+ T cells. Also shown are graphs 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 fewer differentiated cells were observed in the CorVac2.0-treated group. [Figure 66-1] FIG. 1 shows a schematic diagram of an animal study to determine the immune response elicited by different combination ratios and doses of CorVac2.0 string and BNT162b2 in HLA-A02 transgenic mice. [Figure 66-2] FIG. 1 shows a schematic diagram of an animal study to determine the immune response elicited by different combination ratios and doses of CorVac2.0 string and BNT162b2 in HLA-A02 transgenic mice. [Figure 67A] Figure 66 shows a spot formation assay from an animal study showing the number of spots formed per 1x10^6 cells after treatment with the indicated regimens on day 14, demonstrating that CorVac2.0 induces the strongest immune response at the highest dose. [Figure 67B] Figure 66 shows a spot formation assay from an animal study showing the number of spots formed per 1x10^6 cells after treatment with the indicated regimens on day 35, demonstrating that spike T cell responses are enhanced with inclusion of CorVac2.0. The 1 μg dose produced the strongest response. [Figure 67C] Figure 66 shows a spot formation assay from the animal study, showing the number of spots formed per 1x10^6 cells over time. After the boost, improved T cell responses to all regions were observed. [Figure 67D]Figure 66 shows a co-culture spot formation assay from the animal study, showing the number of spots formed per 1 x 10^6 cells after treatment with the indicated regimens on day 35. Spiking responses were seen in CD4 and CD8 T cells. Spiking CD8 T cells exhibit greater cytokine secretion and degranulation than CD4 T cells. [Figure 67E] Figure 66 shows a co-culture spot formation assay from the animal study, showing the number of spots formed per 1x10^6 cells after treatment with the indicated regimens on day 35. Membrane responses were seen in CD4 and CD8 T cells and were strongest at the highest dose. IL2 secretion was seen in CD4 and CD8 T cells. [Figure 67F] Figure 66 shows a spot formation assay from the animal study, showing the number of spots formed per 1 x 10^6 cells after treatment with the indicated regimen on day 56. The spike response was not adversely affected by CorVac2.0. CorVac2.0 alone increased the spike response. Boosting with CorVac2.0 alone increased the spike response. The inclusion of CorVac2.0 did not result in a statistically significant change in spike response. The strongest membrane response was observed in the highest dose group. The strongest N response was observed with CorVac2.0 alone at the highest dose. The strongest Orf1ab response was observed with CorVac2.0 alone and at the separately formulated 3:1 dose. [Figure 67G] Figure 66 shows a co-culture spot formation assay from the animal study, showing the number of spots formed per 1x10^6 cells after treatment with the indicated regimens on day 56. Spike responses were seen in CD4 and CD8 T cells, some of which were enhanced by the inclusion of CorVac2.0. [Figure 67H] Figure 66 shows the co-culture spot formation assay from the animal study, showing the number of spots formed per 1x10^6 cells after treatment with the indicated regimen on day 56. Polyfunctional spike CD4 and CD8 T cells were slightly enhanced in the higher dose CorVac2.0 condition. [Figure 67I] Figure 66 shows a co-culture spot formation assay from the animal study, showing the number of spots formed per 1x10^6 cells after treatment with the indicated regimens on day 56. The membrane response is more pronounced in CD8 T cells. [Figure 67J] Figure 66 shows the co-culture spot formation assay from the animal study, showing the number of spots formed per 1 x 10^6 cells after treatment with the indicated regimen on day 56. Polyfunctional membrane CD4 and CD8 T cells were observed. [Figure 68A] Phenotypic data from an animal study shown in Figure 66 are presented, in which harvested lymph nodes were dissected and cell counts of the indicated cell populations as a percentage of CD45.2 cells were determined after 14 days of treatment with the indicated regimen. 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-. [Figure 68B] Phenotypic data from an animal study are shown in Figure 66. Harvested lymph nodes were dissected and cell counts of the indicated cell populations as a percentage of CD45.2 cells were determined after 35 days of 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-. The addition of CorVac2.0 to BNT162b2 slightly enhances class switching and GC B cells. CorVac2.0 results in a slight increase in Tfh cells. [Figure 68C]Phenotypic data from an animal study are shown in Figure 66. Harvested lymph nodes were dissected and cell counts of the indicated cell populations as a percentage of CD45.2 cells were determined after 56 days of 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 enhances B cell responses compared to no boost. CorVac2.0 in combination with BNT162b2 does not significantly affect B cell responses. [Figure 69] 1 shows an exemplary clinical study design for evaluating the safety of the CorVac2.0 vaccine in healthy human subjects. [Figure 70] 1 shows an exemplary clinical study design for evaluating the safety of the CorVac2.0 vaccine in immunocompromised human subjects. [Figure 71] 1 shows an exemplary clinical study design for evaluating the safety of the CorVac2.0 vaccine in immunocompromised human subjects. [Figure 72] Shown on the right are sequence variants and mutations across the spike protein in different SARS CoV-2 isolates. The data indicate that the spike protein is highly variable, presumably due to selective pressure. [Figure 73] As shown on the right, sequence variants and mutations across the nucleocapsid (N) and membrane (M) proteins in various SARS CoV-2 isolates and their respective mapping to the vaccine epitope sequences encoded by CorVac2.0 are shown. The data indicate that the CorVac2.0 vaccine sequence is rarely affected by N and M variant mutations. [Figure 74]As shown on the right, sequence variants and mutations across ORF1ab in various SARS CoV-2 isolates and their respective mapping to vaccine epitope sequences encoded by CorVac2.0 are shown. The data indicate that the CorVac2.0 vaccine sequence is rarely affected by variant mutations in ORF1ab. [Figure 75A] 1 shows a map representation of an exemplary CorVac2.0 RS-C7 string showing the linker, SEC domain, transmembrane (TM) domain, and viral epitopes contained within the string, including nucleocapsid epitopes, ORF1ab epitopes, and membrane epitopes. [Figure 75B] FIG. 1 shows a map representation of an exemplary CorVac2.0 RS-C7 string showing the observed viral epitopes contained within the string as revealed by mass spectrometry (MS), including nucleocapsid epitopes, ORF1ab epitopes, and membrane epitopes. [Figure 76] Shown is a representation of the MS-based HLA-I cleavage predictor used to optimize the order of candidate ORF1ab sequences for efficient epitope cleavage (top) and adding as few linkers as possible while retaining 18 ORF1ab epitopes optimized for the GSS linker context. [Figure 77A] 1 shows a map representation of an exemplary CorVac2.0 RS-C7 string. The antigen selected for CorVac2.0 mutates rarely. Across all WHO-designated variants, RS-C7 is affected by only three mutations, leaving the majority of the epitope unchanged. [Figure 77B]A map representation of an exemplary CorVac2.0 RS-C7 string is shown. The antigen selected for CorVac2.0 mutates rarely. Across all WHO-designated variants, RS-C7 is affected by only three mutations, leaving the majority of the epitope unchanged. As shown in Figures 77B-C, even in the highly mutated Omicron variant, only one mutation affects the CorVac2.0 string (as opposed to the approximately 39 amino acid changes in the spike protein). [Figure 77C] A map representation of an exemplary CorVac2.0 RS-C7 string is shown. The antigen selected for CorVac2.0 mutates rarely. Across all WHO-designated variants, RS-C7 is affected by only three mutations, leaving the majority of the epitope unchanged. As shown in Figures 77B-C, even in the highly mutated Omicron variant, only one mutation affects the CorVac2.0 string (as opposed to the approximately 39 amino acid changes in the spike protein). [Figure 78A] 1 shows the dynamics of antibody concentration against spike protein. [Figure 78B] 1 shows the dynamics of antibody concentration against spike protein. [Figure 79] 79 shows an exemplary structure of RS C7 and indicates specific factors considered in designing the CorVac2.0 string. "Count," as used in Figure 79, refers to the number of pMHC allele pairs that overlap with the indicated residues in the 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). "Entropy," as used in Figure 79, refers to Shannon entropy, which is a measure of the level of conservation (where lower entropy indicates higher conservation). [Figure 80A] 1 shows epitopes present in an exemplary CorVac2.0 string (e.g., RS C7 string) observed by mass spectrometry as processed and presented by the MHC complex. [Figure 80B]Data for one exemplary epitope observed by mass spectrometry is shown (epitope 23 in Table 19). [Figure 81] 1 shows the study design for testing the immunogenicity of various BNT162b2+CorVac2.0 string administration regimens in K18-hACE2 mice. [Figure 82A] Figure 82 shows the anti-spike protein, IgG, concentrations measured over time from serum samples collected from the experiment shown in Figure 81. IgG concentrations measured by ELISA. Error bars indicate the standard error of the mean. [Figure 82B] Figure 82 shows the anti-spike protein, IgG, concentrations measured over time from serum samples collected from the experiment shown in Figure 81. IgG concentrations measured by ELISA. Error bars indicate the standard error of the mean. [Figure 83A] Shown are the neutralization titers measured from serum samples collected from the experiment shown in Figure 81. Neutralization titers were measured using a pseudovirus neutralization assay using a pseudovirus containing the SARS-CoV-2 S protein from the Wuhan stain. [Figure 83B] Shown are the neutralization titers measured from serum samples collected from the experiment shown in Figure 81. Neutralization titers were measured using a pseudovirus neutralization assay using a pseudovirus containing the SARS-CoV-2 S protein from the Wuhan stain. [Figure 84] An experimental protocol is presented to measure the efficacy of CorVac2.0 string administered alone or in combination with RNA encoding the SARS-CoV-2 S protein in Syrian hamsters. [Figure 85] Results are shown from the study depicted in Figure 84. Specifically, Figure 85 shows the change in body weight of hamsters following challenge with SARS-CoV-2 (Wuhan strain). [Figure 86] 1 shows an exemplary protocol for Spike-specific B and T cell clonotype analysis. [Figure 87]Figure 1 summarizes the 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 the same clonotype, and clonotypes within the same "clonotype cluster" (i.e., clonotypes with similar sequences) are indicated by lines connecting the dots. As shown in the figure, administration of the CorVac2.0 construct increases the propensity for higher clonal expansion but does not adversely affect clonality. [Figure 88] An exemplary clinical study design for evaluating the safety of the CorVac2.0 vaccine in healthy human subjects is shown. "SpikeVac" refers to RNA encoding the SARS-CoV-2 S protein, which contains one or more mutations (e.g., one or more mutations disclosed herein or known in the art) that stabilize the prefusion conformation. In this exemplary clinical study design, a bivalent vaccine is administered containing RNA encoding a SARS-CoV-2 S polypeptide of the Wuhan strain and a SARS-CoV-2 S polypeptide containing one or more mutations characteristic of the BA.4 / 5 Omicron variant (e.g., one or more mutations disclosed herein). a If acceptable tolerability is demonstrated and stop / pause rules are not met, further dosing of the subject or initiation of a new cohort may proceed. b An exemplary SpikeVac bivalent is the BNT162b2 bivalent (Wuhan + OMI BA.4 / BA.5). Abbreviations: d = day, h = hour(s), FIH = first-in-human, IRC = internal review committee, N = number of subjects, OMI = omicron, WT = wild-type. Study population: Healthy volunteers aged 18-55 years who have received at least three previous vaccinations with any licensed COVID19 RNA vaccine (the last COVID19 RNA vaccine dose must have been administered at least 4 months prior to Visit 1). Subjects who had SARS-CoV-2 infection more than 60 days prior to randomization are not excluded from the study. DETAILED DESCRIPTION OF THE INVENTION

[0603] Described herein are novel therapeutics and vaccines based on viral epitopes. Accordingly, the disclosure described herein provides peptides, polynucleotides encoding the peptides, and peptide-binding agents that can be used to generate immunogenic compositions or vaccines for use in treating or preventing viral infections, for example, to stimulate an immune response to viral antigens.

[0604] definition To facilitate understanding of this disclosure, several terms and phrases are defined below.

[0605] "Viral antigen" refers to an antigen encoded by a virus, including, but not limited to, an antigen of a coronavirus such as COVID-19.

[0606] Throughout this disclosure, "binding data" results can be expressed as "IC50." IC50 is the concentration of test peptide in a binding assay at which 50% inhibition of binding of a labeled reference peptide is observed. Given the conditions under which the assay is performed (i.e., limiting concentrations of HLA protein and labeled reference peptide), these values ​​approximate KD values. Assays for determining binding are well known in the art and are described in detail in, for example, PCT Publications WO94 / 20127 and WO94 / 03205, as well as other publications such as, for example, Sidney, et al., Current Protocols in Immunology, 18.3.1 (1998); Sidney, et al., J. Immunol. 154:247 (1995); and Sette, et al., Mol. Immunol. 31:813 (1994). Alternatively, binding can be expressed relative to binding by a reference standard peptide. For example, binding can be based on its IC50 relative to the IC50 of the reference standard peptide.Binding can be achieved using live cells (e.g., Ceppellini et al., Nature, 339:392 (1989); Christnick et al., Nature, 352:67 (1991); Busch et al., Int. Immunol. 2:443 (1990); Hill et al., J. Immunol. 147:189 (1991); del Guercio et al., J. Immunol. 154:685 (1995)), cell-free systems using detergent lysates (e.g., Cerundolo et al., J. Immunol. 21:2069 (1991)), immobilized purified MHC (e.g., Hill et al., J. Immunol. 152:2890 (1994); Marshall et al. 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-flow soluble phase assays (Hammer, et al., J. Exp. Med. 180:2353 (1994)), and measurements of class I MHC stabilization or association (e.g., Ljunggren, et al., Nature 346:476 (1990); Schumacher, et al., Cell 62:563 (1990); Townsend, et al., Cell 62:285 (1990); Parker, et al. Other assay systems may also be used to determine the level of IL-1 expression, including those using IL-1 (e.g., IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12, IL-13, IL-14, IL-15, IL-16, IL-17, IL-

[0607] The term "derived" when used to discuss epitopes is synonymous with "prepared." Derived epitopes can be derived from natural sources or synthesized according to standard protocols in the art. Synthetic epitopes can include artificial amino acid residues, "amino acid mimetics," such as D-isomers of naturally occurring L-amino acid residues, or non-natural amino acid residues, such as cyclohexylalanine. Derived or prepared epitopes can be analogs of natural epitopes.

[0608] "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 employed as diluents, for example, in injectable solutions.

[0609] An "epitope" is a collective molecular feature, such as primary, secondary, and tertiary peptide structure and charge, that together form the 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 set of amino acid residues involved in recognition by a particular immunoglobulin or in the context of a T cell, where those residues are necessary for recognition by a T cell receptor protein, a chimeric antigen receptor, and / or a major histocompatibility complex (MHC) receptor. Epitopes can be prepared by isolation from natural sources or synthesized according to standard protocols in the art. Synthetic epitopes can include artificial amino acid residues, such as D-isomers of naturally occurring L-amino acid residues, "amino acid mimetics," or non-natural amino acid residues, such as cyclohexylalanine. Throughout this disclosure, epitopes may sometimes be referred to as peptides or peptide epitopes.

[0610] It should be understood that proteins or peptides comprising the epitopes or analogs described herein and additional amino acid(s) remain within the scope of this disclosure. In certain embodiments, the peptide comprises a fragment of the antigen.

[0611] In certain embodiments, the peptides of the present disclosure are limited in length. Limited-length embodiments occur when a protein or peptide containing an epitope described herein contains a region (i.e., a contiguous stretch of amino acid residues) that shares 100% identity with a native sequence. For example, to avoid interpreting the definition of an epitope to the entire native molecule, there is a length limit for any region that shares 100% identity with a native peptide sequence. Thus, for peptides containing an epitope described herein and a region that shares 100% identity with a native peptide sequence, the region that shares 100% identity with the native sequence generally has a length of 600 or fewer amino acid residues, 500 or fewer amino acid residues, 400 or fewer amino acid residues, 250 or fewer amino acid residues, 100 or fewer amino acid residues, 85 or fewer amino acid residues, 75 or fewer amino acid residues, 65 or fewer amino acid residues, and 50 or fewer amino acid residues. In certain embodiments, an "epitope" as described herein is comprised of a peptide having a region with fewer than 51 amino acid residues that has 100% identity to a naturally occurring peptide sequence at any increment of up to 5 amino acid residues, e.g., 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.

[0612] "Human leukocyte antigen" or "HLA" is a human class I or class II major histocompatibility complex (MITC) protein (see, e.g., Stites, et al., IMMUNOLOGY, 8TH ED., Lange Publishing, Los Altos, Calif. (1994)). As used herein, "HLA supertype or HLA family" describes a set of HLA molecules classified based on shared peptide binding specificity. HLA class I molecules that share somewhat similar binding affinities for peptides with a particular amino acid motif are grouped into such HLA supertypes. The terms HLA superfamily, HLA supertype family, HLA family, and HLA xx-like molecule (where "xx" indicates a particular HLA type) are synonymous.

[0613] The terms "identical" or "percent identity" in the context of two or more peptide sequences or antigen fragments refer to two or more sequences or subsequences that are identical, or have a specified percentage of amino acid residues that are identical, 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.

[0614] An "immunogenic" peptide or "immunogenic" epitope or "peptide epitope" is a peptide that contains an allele-specific motif such that the peptide binds an HLA molecule and induces a cell-mediated or humoral response, e.g., 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 the appropriate HLA molecule and subsequently inducing a CTL (cytotoxic) response or an HTL (and humoral) response against the peptide.

[0615] As used herein, "chimeric antigen receptor" or "CAR" refers to an antigen-binding protein comprising an immunoglobulin antigen-binding domain (e.g., an immunoglobulin variable domain) and a T cell receptor (TCR) constant domain. As used herein, the "constant domain" of a TCR polypeptide comprises the membrane-proximal TCR constant domain and may also comprise the TCR transmembrane domain and / or the TCR cytoplasmic tail. For example, in some embodiments, a CAR is a dimer comprising a first polypeptide comprising an immunoglobulin heavy chain variable domain linked to a TCR-beta constant domain and a second polypeptide comprising an immunoglobulin light chain variable domain (e.g., an lc or 2\., variable domain) linked to a TCR alpha constant domain. In some embodiments, a CAR is a dimer comprising a first polypeptide comprising an immunoglobulin heavy chain variable domain linked to a TCR alpha constant domain and a second polypeptide comprising an immunoglobulin light chain variable domain linked to a TCR beta constant domain.

[0616] The phrases "isolated" or "biologically pure" refer to material that is substantially or essentially free from components normally associated with the material as found in its native state. Thus, the peptides described herein do not contain some or all of the substances normally associated with the peptide in its in situ environment. An "isolated" epitope refers to an epitope that does not contain the entire sequence of the antigen from which it is derived. Typically, an "isolated" epitope is free of additional amino acid residues that result in a sequence with 100% identity over the entire length of the native sequence. The native sequence can be a sequence such as a viral antigen from which the epitope is derived. Thus, the term "isolated" means that the material has been removed from its original environment (e.g., the natural environment if it occurs in nature). For example, a naturally occurring polynucleotide or peptide present in a living animal is not isolated, but the same polynucleotide or peptide separated from some or all of the coexisting materials 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" in that 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 further include synthetically produced such molecules.

[0617] The "major histocompatibility complex" or "MHC" is a cluster of genes that plays a role in regulating cellular interactions involved in 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 complex and the HLA complex, see Paul, FUNDAMENTAL IMMUNOLOGY, 3rd ed., Raven Press, New York (1993).

[0618] A "native" or "wild-type" sequence refers to a sequence found in nature. Such sequences can inherently include longer sequences.

[0619] "T cell epitope" should be understood to mean a peptide sequence which can be bound by class I or II MHC molecules in the form of a peptide-presenting MHC molecule or MHC complex and which can then be recognized and bound in this form by cytotoxic T lymphocytes or T helper cells, respectively.

[0620] "Receptor" should be understood to mean a biological molecule or series of molecules that can bind a ligand. Receptors can serve to transmit information in cells, cell formations, or organisms. A receptor comprises at least one receptor unit, where each receptor unit may be, for example, a protein molecule. A receptor has a structure complementary to that of a ligand and may complex with the ligand as a binding partner. The information is transmitted, in particular, by a conformational change in the receptor following ligand complex formation on the cell surface. In some embodiments, receptors should be understood to particularly mean proteins of MHC class I and II that can form receptor / ligand complexes with ligands, in particular peptides or peptide fragments of a suitable length.

[0621] A "ligand" should be understood to mean a molecule that has a structure complementary to that of a receptor and is capable of forming a complex with this receptor. In some embodiments, a ligand should be understood to mean a peptide or peptide fragment that has a suitable length and a suitable binding motif in its amino acid sequence, such that the peptide or peptide fragment is capable of forming a complex with an MHC class I or MHC class II protein.

[0622] In some embodiments, "receptor / ligand complex" should also be understood to mean a "receptor / peptide complex" or "receptor / peptide fragment complex" comprising a class I or class II MHC molecule that presents a peptide or peptide fragment.

[0623] "Major histocompatibility complex (MHC) protein or molecule," "MHC molecule," "MHC protein," or "HLA protein" should be understood to mean a protein that results from the proteolytic cleavage of a protein antigen and is capable of binding peptides representing potential lymphocyte epitopes (e.g., T-cell epitopes and B-cell epitopes) and transporting them to the cell surface, where they are presented to specific cells, particularly cytotoxic T lymphocytes, T-helper cells, or B-cells. The major histocompatibility complex in the genome contains gene regions whose gene products, expressed on the cell surface, are important for binding and presenting endogenous and / or foreign antigens and thus for regulating immunological processes. The major histocompatibility complex is divided into two groups of genes encoding different proteins: MHC class I molecules and MHC class II molecules. The cellular biology and expression patterns of the two MHC classes are adapted to these different roles.

[0624] The terms "peptide" and "peptide epitope" are used interchangeably herein with "oligopeptide" and refer to a series of residues that are typically connected to one another by peptide bonds between the α-amino and carboxyl groups of adjacent amino acid residues.

[0625] "Synthetic peptide" refers to a peptide that is obtained from a non-natural source, e.g., is man-made. Such peptides can be produced using methods such as chemical synthesis or recombinant DNA technology. "Synthetic peptide" includes "fusion proteins."

[0626] A "PanDR-binding" peptide or "PanDR-binding epitope" is a member of a family of molecules that bind more than one HLA class II DR molecule.

[0627] "Pharmaceutically acceptable" generally refers to a composition or component of a composition that is non-toxic, inert, and / or physiologically compatible.

[0628] "Pharmaceutical excipients" or "excipients" include, for example, substances such as adjuvants, carriers, pH adjusting and buffering agents, tonicity agents, humectants, preservatives, etc. 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, e.g., less than about 15 amino acid residues in length, or less than about 13 amino acid residues in length, e.g., about 8 to about 13 (e.g., 8, 9, 10, 11, 12, or 13) amino acid residues for class I HLA motifs and about 6 to about 25 (e.g., 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25) amino acid residues for class II HLA motifs, that are recognized by a specific HLA molecule. Motifs typically vary for each HLA protein encoded by a given human H...

Claims

[Claim 1] The invention described in the specification or drawings of this application.