Influenza t cell epitopes, megapools and uses thereof

Abstract

The present invention includes compositions, including epitope megapools, and methods for detecting the presence of: an influenza or an immune response relevant to an influenza infection including T cells responsive to one or more Influenza peptides or proteins comprising, consisting of, or consisting essentially of: one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof; a fusion protein; a pool of 2 or more peptides; or a polynucleotide that encodes one or more peptides or proteins, comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof, vaccines, diagnostics, therapies, and kits, comprising such proteins or peptides.

Description

INFLUENZA T CELL EPITOPES, MEGAPOOLS AND USES THEREOFCROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims priority to U.S. Provisional Application Serial No. 63 / 693,177, filed September 10, 2024, the entire contents of which is incorporated herein by reference.TECHNICAL FIELD

[0002] The present invention relates in general to the field of proteins and peptides that are T cell epitopes and / or antigens for Influenza, including epitopes and antigens from H5N1, and more particularly, to compositions and methods for the prevention, treatment, diagnosis, kits, and uses of such T cell epitopes and antigens, including megapools, for use in detecting and characterizing H5N1 specific responses in infection and following vaccination.STATEMENT OF GOVERNMENT SUPPORT

[0003] The inventions described in the present disclosure were made with government support under Contract No. 75N93019C00001, awarded by the National Institutes ofHealth. The government has certain rights in the invention.REFERENCE TO ELECTRONIC SEQUENCE LISTING

[0004] The application contains a Sequence Listing which has been submitted electronically in .XML format and is hereby incorporated by reference in its entirety. Said .XML copy, created on , 2025, is named “LJII2036WO.xml” and is bytes in size. The sequence listing contained in this .XML file is part of the specification and is hereby incorporated by reference herein in its entirety.BACKGROUND

[0005] Without limiting the scope of the invention, its background is described in connection with the Influenza.

[0006] A need remains for identifying antigens and T cell epitopes for use in diagnostics, treatments, vaccines, kits, etc., for Influenza related diseases and conditions, including the flu and / or H5N1. There is additionally a specific need in the art for optimized megapools for use in detecting and characterizing H5N 1 specific responses in infection and following vaccination.SUMMARY

[0007] As embodied and broadly described herein, an aspect of the present disclosure relates to a composition comprising: one or more peptides or proteins, comprising, consisting of, or consisting essentially of an amino acid sequence selected from any one of the sequences set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof; a fusion protein comprising one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to929 or Tables 1 to 5; a pool of 2 or more or more peptides comprising, consisting of, or consisting essentially of amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; or a polynucleotide that encodes one or more peptides or proteins, comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof. In one aspect, the one or more peptides or proteins comprises, or wherein the fusion protein comprises 2 or more or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof. In another aspect, the amino acid sequence is selected from an influenza T cell epitope selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5. In another aspect, the composition comprises one or more H5N 1 peptides amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof; a fusion protein comprising one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; or a pool of 2 or more peptides selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5. In another aspect, the peptide or protein comprises an influenza T cell epitope. In another aspect, the one or more peptides or proteins comprises an influenza CD8+ or CD4+ T cell epitope. In another aspect, the Influenza is H5N 1 and the H5N 1 T cell epitope is not conserved in another Influenza. In another aspect, the Influenza is H5N 1 and the H5N 1 T cell epitope is conserved in another Influenza. In another aspect, the one or more peptides or proteins has a length from about 9-15, 15-20, 20-25, 25-30, 30-40, 40-50, 50-75 or 75-100 amino acids. In another aspect, the one or more peptides or proteins elicits, stimulates, induces, promotes, increases or enhances a T cell response to an Influenza. In another aspect, the one or more peptides or proteins that elicits, stimulates, induces, promotes, increases or enhances the T cell response to the Influenza is an Influenza protein or peptide, or a variant, homologue, derivative or subsequence thereof. In another aspect, the composition further comprises formulating the one or more peptides or proteins into an immunogenic formulation with an adjuvant. In another aspect, the adjuvant is selected from the group consisting of adjuvant is selected from the group consisting of alum, aluminum hydroxide, aluminum phosphate, calcium phosphate hydroxide, cytosine-guanosine oligonucleotide (CpG-ODN) sequence, granulocyte macrophage colony stimulating factor (GM-CSF), monophosphoryl lipid A (MPL), poly(I:C), MF59, Quil A, N-acetyl muramyl-L-alanyl-D-isoglutamine (MDP), FIA, montanide, poly (DL-lactide- coglycolide), squalene, virosome, AS03, ASO4, IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-10, IL- 12, IL-15, IL-17, IL-18, STING, CD40L, pathogen-associated molecular patterns (PAMPs), damage- associated molecular pattern molecules (DAMPs), Freund’s complete adjuvant, Freund’s incomplete adjuvant, transforming growth factor (TGF)-beta antibody or antagonists, A2aR antagonists, lipopolysaccharides (LPS), Fas ligand, Trail, lymphotactin, Mannan (M-FP), APG-2, Hsp70 and Hsp90, pattern recognition receptor ligands, TLR3 ligands, TLR4 ligands, TLR5 ligands, TLR7 / 8 ligands, and TLR9 ligands. In another aspect, the composition further comprises a modulator of immune response. In another aspect, the modulator of immune response is a modulator of the innate immune response. In anotheraspect, the modulator is Interleukin-6 (IL-6), Interferon-gamma (IFN-y). Transforming growth factor beta (TGF-P), or Interleukin- 10 (IL- 10), or an agonist or antagonist thereof.

[0008] As embodied and broadly described herein, an aspect of the present disclosure relates to a composition comprising monomers or multimers of: peptides or proteins comprising, consisting of, or consisting essentially of: one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, concatemers, subsequences, portions, homologues, variants or derivatives thereof; a fusion protein comprising one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; or a polynucleotide that encodes one or more peptides or proteins, comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof.

[0009] As embodied and broadly described herein, an aspect of the present disclosure relates to a composition comprising one or more peptide-major histocompatibility complex (MHC) monomers or multimers, wherein the peptide-MHC monomer or multimer comprises a peptide comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, in a groove of the MHC monomer or multimer.

[0010] As embodied and broadly described herein, an aspect of the present disclosure relates to a composition comprising: one or more peptides or proteins comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof; a fusion protein comprising one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; a pool of 2 or more peptides selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; a polynucleotide that encodes one or more peptides or proteins, comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof. In one aspect, the one or more peptides or proteins comprises, or wherein the fusion protein comprises, 2 or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof. In another aspect, the protein or peptide comprises a H5N 1 T cell epitope. In another aspect, the one or more peptides or proteins comprises a H5N1 CD8+ or CD4+ T cell epitope. In another aspect, the H5N1 T cell epitope is not conserved in another Influenza. In another aspect, the H5N 1 T cell epitope is conserved in another Influenza. In another aspect, the one or more peptides or proteins has a length from about 9-15, 15-20, 20-25, 25-30, 30-40, 40- 50, 50-75 or 75-100 amino acids. In another aspect, the one or more peptides or proteins elicits, stimulates, induces, promotes, increases or enhances a T cell response to H5N1. In another aspect, the one or more peptides or proteins that elicits, stimulates, induces, promotes, increases or enhances the T cell response to H5N 1 is a H5N 1 protein or peptide, or a variant, homologue, derivative or subsequence thereof. In another aspect, the composition further comprises formulating the one or more peptides or proteins into animmunogenic formulation with an adjuvant. In another aspect, the adjuvant is selected from the group consisting of adjuvant is selected from the group consisting of alum, aluminum hydroxide, aluminum phosphate, calcium phosphate hydroxide, cytosine-guanosine oligonucleotide (CpG-ODN) sequence, granulocyte macrophage colony stimulating factor (GM-CSF), monophosphoryl lipid A (MPL), poly(I:C), MF59, Quil A, N-acetyl muramyl-L-alanyl-D-isoglutamine (MDP), FIA, montanide, poly (DL-lactide- coglycolide), squalene, virosome, AS03, ASO4, IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-10, IL- 12, IL-15, IL-17, IL-18, STING, CD40L, pathogen-associated molecular patterns (PAMPs), damage- associated molecular pattern molecules (DAMPs), Freund’s complete adjuvant, Freund’s incomplete adjuvant, transforming growth factor (TGF)-beta antibody or antagonists, A2aR antagonists, lipopolysaccharides (LPS), Fas ligand, Trail, lymphotactin, Mannan (M-FP), APG-2, Hsp70 and Hsp90, pattern recognition receptor ligands, TLR3 ligands, TLR4 ligands, TLR5 ligands, TLR7 / 8 ligands, and TLR9 ligands. In another aspect, the composition further comprises a modulator of immune response. In another aspect, the modulator of immune response is a modulator of the innate immune response. In another aspect, the modulator is Interleukin-6 (IL-6), Interferon-gamma (IFN-y). Transforming growth factor beta (TGF-P), or Interleukin- 10 (IL- 10), or an agonist or antagonist thereof.

[0011] As embodied and broadly described herein, an aspect of the present disclosure relates to a composition comprising monomers or multimers of: one or more peptides or proteins comprising, consisting of, or consisting essentially of: one or more H5N 1 amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, concatemers, subsequences, portions, homologues, variants or derivatives thereof; a fusion protein comprising one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; or a polynucleotide that encodes one or more peptides or proteins, comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof.

[0012] As embodied and broadly described herein, an aspect of the present disclosure relates to a composition comprising one or more peptide-major histocompatibility complex (MHC) monomers or multimers, wherein the peptide-MHC monomer or multimer comprises a peptide comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, in a groove of the (MHC) monomer or multimer.

[0013] As embodied and broadly described herein, an aspect of the present disclosure relates to a method for detecting the presence of: (i) an influenza or (ii) an immune response relevant to Influenza infections, vaccines ortherapies, including T cells responsive to one or more Influenza peptides, comprising: providing one or more proteins or peptides for detection of an amount or a relative amount of, and / or the activity of, and / or the state of antigen-specific T-cells; contacting a biological sample suspected of having Influenzaspecific T-cells to one or more proteins or peptides for detection; and detecting an amount or a relative amount of, and / or the activity of, and / or the state of antigen-specific T-cells in the biological sample, wherein the one or more proteins or peptides for detection comprise one or more amino acid sequences setforth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or comprise a pool of 2 or more or more amino acid sequences set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5. In one aspect, detecting the amount or a relative amount of, and / or activity of antigen-specific T-cells comprises one or more steps of identification or detection of the antigen-specific T-cells and measuring the amount of the antigen-specific T-cells. In another aspect, the one or more peptides or proteins comprises 2 or more amino acid sequences selected from SEQ ID NOS: 1 to 929 or Tables 1 to 5. In another aspect, the detecting the amount or a relative amount of, and / or activity of antigen-specific T-cells comprises indirect detection and / or direct detection. In another aspect, the method of detecting an immune response relevant to the Influenza comprises the following steps: providing an MHC monomer or an MHC multimer; contacting a population T-cells to the MHC monomer or MHC multimer; and measuring the number, activity or state of T-cells specific for the MHC monomer or MHC multimer. In one aspect, the MHC monomer or MHC multimer comprises a protein or peptide of the Influenza. In another aspect, the protein or peptide comprises a CD8+ or CD4+ T cell epitope. In another aspect, the T cell epitope is not conserved in another Influenza. In another aspect, the T cell epitope is conserved in another Influenza. In another aspect, the protein or peptide has a length from about 9-15, 15-20, 20-25, 25-30, 30-40, 40-50, 50-75 or 75-100 amino acids. In another aspect, the proteins or peptides comprise 2 or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof. In another aspect, the method further comprises detecting the presence or amount of the one or more peptides in a biological sample, or a response thereto, which is diagnostic of an influenza infection. In another aspect, the detecting an amount or a relative amount of, and / or the activity of, and / or the state of antigenspecific T-cells in the biological sample comprises measuring one or more of a cytokine or lymphokine secretion assay, T cell proliferation, immunoprecipitation, immunoassay, ELISA, radioimmunoassay, immunofluorescence assay, Western Blot, FACS analysis, a competitive immunoassay, a noncompetitive immunoassay, a homogeneous immunoassay a heterogeneous immunoassay, a bioassay, a reporter assay, a luciferase assay, a microarray, a surface plasmon resonance detector, a florescence resonance energy transfer, immunocytochemistry, or a cell mediated assay, or a cytokine proliferation assay. In another aspect, the method further comprises administering a treatment comprising the composition of one or more proteins, peptides or multimers to the subject from which the biological sample was drawn that increases the amount or relative amount of, and / or activity of the antigen-specific T-cells.

[0014] As embodied and broadly described herein, an aspect of the present disclosure relates to a method for detecting the presence of: (i) H5N 1 or (ii) an immune response relevant to H5N 1 infections, vaccines or therapies, including T cells responsive to one or more H5N1 peptides, comprising: providing one or more proteins or peptides for detection of an amount or a relative amount of, and / or the activity of, and / or the state of antigen-specific T-cells; contacting a biological sample suspected of having H5Nl-specific T- cells to one or more proteins or peptides for detection; and detecting an amount or a relative amount of, and / or the activity of, and / or the state of antigen-specific T-cells in the biological sample, wherein the one or more proteins or peptides for detection comprise one or more amino acid sequences selected from thoseset forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or comprise a pool of 2 or more amino acid sequences selected from those set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5. In one aspect, detecting the amount or a relative amount of, and / or activity of antigen-specific T-cells comprises one or more steps of identification or detection of the antigen-specific T-cells and measuring the amount of the antigen-specific T-cells. In another aspect, the one or more peptides or proteins comprises 2 or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5. In another aspect, detecting the amount or a relative amount of, and / or activity of antigen-specific T-cells comprises indirect detection and / or direct detection. In another aspect, detecting an immune response relevant to H5N 1 comprises the following steps: providing an MHC monomer or an MHC multimer; contacting a population T-cells to the MHC monomer or MHC multimer; and measuring the number, activity or state of T-cells specific for the MHC monomer or MHC multimer. In another aspect, the MHC monomer or MHC multimer comprises a protein or peptide of H5N 1. In another aspect, the protein or peptide comprises a H5N 1 CD8+ or CD4+ T cell epitope. In another aspect, the H5N1 T cell epitope is not conserved in another Influenza. In another aspect, the H5N 1 T cell epitope is conserved in another Influenza. In another aspect, the protein or peptide has a length from about 9-15, 15-20, 20-25, 25-30, 30-40, 40-50, 50-75 or 75-100 amino acids. In another aspect, the proteins or peptides comprise 2 or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof. In another aspect, the method further comprises detecting the presence or amount of the one or more peptides in a biological sample, or a response thereto, which is diagnostic of a H5N1 infection. In another aspect, detecting an amount or a relative amount of, and / or the activity of, and / or the state of antigen-specific T-cells in the biological sample comprises measuring one or more of a cytokine or lymphokine secretion assay, T cell proliferation, immunoprecipitation, immunoassay, ELISA, radioimmunoassay, immunofluorescence assay, Western Blot, FACS analysis, a competitive immunoassay, a noncompetitive immunoassay, a homogeneous immunoassay a heterogeneous immunoassay, a bioassay, a reporter assay, a luciferase assay, a microarray, a surface plasmon resonance detector, a florescence resonance energy transfer, immunocytochemistry, or a cell mediated assay, or a cytokine proliferation assay. In another aspect, the method further comprises administering a treatment comprising the composition of one or more proteins, peptides or multimers to the subject from which the biological sample was drawn that increases the amount or relative amount of, and / or activity of the antigenspecific T-cells.

[0015] As embodied and broadly described herein, an aspect of the present disclosure relates to an influenza infection or exposure in a subject, the method comprising, consisting of, or consisting essentially of: contacting a biological sample from a subject with a composition of composition of one or more proteins, peptides or multimers; and determining if the composition elicits an immune response from the contacted cells, wherein the presence of an immune response indicates that the subject has been exposed to or infected with Influenza. In one aspect, the sample comprises T cells. In another aspect, the response comprises inducing, increasing, promoting or stimulating anti -Influenza activity of T cells. In another aspect, the Tcells are CD8+ or CD4+ T cells. In another aspect, the method comprises determining whether the subject has been infected by or exposed to the Influenza more than once by determining if the subject elicits a secondary T cell immune response profde that is different from a primary T cell immune response profde. In another aspect, the method further comprises diagnosing an influenza infection or exposure in a subject, the method comprising contacting a biological sample from a subject with a composition of composition of one or more proteins, peptides or multimers, and determining if the composition elicits a T cell immune response, wherein the T cell immune response identifies that the subject has been infected with or exposed to an influenza. In another aspect, the method is conducted three or more days following the date of suspected infection by or exposure to an influenza.

[0016] As embodied and broadly described herein, an aspect of the present disclosure relates to a method detecting H5N1 infection or exposure in a subject, the method comprising, consisting of, or consisting essentially of: contacting a biological sample from a subject with a composition of composition of one or more proteins, peptides or multimers; and determining if the composition elicits an immune response from the contacted cells, wherein the presence of an immune response indicates that the subject has been exposed to or infected with H5N1. In another aspect, the sample comprises T cells. In another aspect, the response comprises inducing, increasing, promoting or stimulating anti-H5Nl activity of T cells. In another aspect, the T cells are CD8+ or CD4+ T cells. In another aspect, the method comprises determining whether the subject has been infected by or exposed to H5N1 more than once by determining if the subject elicits a secondary T cell immune response profde that is different from a primary T cell immune response profde. In another aspect, the method further comprises diagnosing a H5N1 infection or exposure in a subject, the method comprising contacting a biological sample from a subject with a composition of one or more proteins, peptides or multimers; and determining if the composition elicits a T cell immune response, wherein the T cell immune response identifies that the subject has been infected with or exposed to H5N 1. In another aspect, the method is conducted three or more days following the date of suspected infection by or exposure to an influenza.

[0017] As embodied and broadly described herein, an aspect of the present disclosure relates to a kit for the detection of Influenza or an immune response to Influenza in a subject comprising, consisting of or consisting essentially of: one or more T cells that specifically detect the presence of: one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof; or a fusion protein comprising one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; or a pool of 2 or more or more peptides selected from the amino acid sequences set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5. In one aspect, the one or more amino acid sequences are selected from an influenza T cell epitope set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5. In another aspect, the composition comprises: one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof; a fusion protein comprising one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to929 or Tables 1 to 5; or a pool of 2 or more peptides selected from the amino acid sequences selected from those set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5. In another aspect, the amino acid sequence comprises an influenza CD8+ or CD4+ T cell epitope. In another aspect, the T cell epitope is not conserved in another Influenza. In another aspect, the T cell epitope is conserved in another Influenza. In another aspect, the fusion protein has a length from about 9-15, 15-20, 20-25, 25-30, 30-40, 40-50, 50-75 or 75- 100 amino acids. In another aspect, the kit includes instruction for a diagnostic method, a process, a composition, a product, a service or component part thereof for the detection of: (i) Influenza or (ii) an immune response relevant to Influenza infections, vaccines or therapies, including T cells responsive to Influenza. In another aspect, the kit includes reagents for detecting an amount or a relative amount of, and / or the activity of, and / or the state of antigen-specific T-cells in the biological sample comprises measuring one or more of a cytokine or lymphokine secretion assay, T cell proliferation, immunoprecipitation, immunoassay, ELISA, radioimmunoassay, immunofluorescence assay, Western Blot, FACS analysis, a competitive immunoassay, a noncompetitive immunoassay, a homogeneous immunoassay a heterogeneous immunoassay, a bioassay, a reporter assay, a luciferase assay, a microarray, a surface plasmon resonance detector, a florescence resonance energy transfer, immunocytochemistry, or a cell mediated assay, or a cytokine proliferation assay. In another aspect, the kit includes reagents for determining a Human Leukocyte Antigen (HLA) profile of a subject, and selecting peptides that are presented by the HLA profile of the subject for detecting an immune response to Influenza.

[0018] As embodied and broadly described herein, an aspect of the present disclosure relates to a kit for the detection of H5N 1 or an immune response to H5N 1 in a subject comprising, consisting of or consisting essentially of: one or more T cells that specifically detect the presence of: one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof; a fusion protein comprising one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; or a pool of 2 or more peptides selected from the amino acid sequences selected from those set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5. In another aspect, the amino acid sequence comprises a H5N 1 CD8+ or CD4+ T cell epitope . In another aspect, the H5N 1 T cell epitope is not conserved in another Influenza. In another aspect, the H5N 1 T cell epitope is conserved in another Influenza. In another aspect, the fusion protein has a length from about 9-15, 15-20, 20-25, 25-30, 30-40, 40-50, 50-75 or 75-100 amino acids. In another aspect, the kit includes instruction for a diagnostic method, a process, a composition, a product, a service or component part thereof for the detection of: (i) H5N1 or (ii) an immune response relevant to H5N1 infections, vaccines or therapies, including T cells responsive to H5N 1. In another aspect, the kit includes reagents for detecting an amount or a relative amount of, and / or the activity of, and / or the state of antigen-specific T-cells in the biological sample comprises measuring one or more of a cytokine or lymphokine secretion assay, T cell proliferation, immunoprecipitation, immunoassay, ELISA, radioimmunoassay, immunofluorescence assay, Western Blot, FACS analysis, a competitive immunoassay, a noncompetitive immunoassay, a homogeneous immunoassay a heterogeneous immunoassay, a bioassay, a reporter assay, a luciferase assay,a microarray, a surface plasmon resonance detector, a florescence resonance energy transfer, immunocytochemistry, or a cell mediated assay, or a cytokine proliferation assay. In another aspect, the kit includes reagents for determining a Human Leukocyte Antigen (HLA) profile of a subject, and selecting peptides that are presented by the HLA profile of the subject for detecting an immune response to H5N 1.

[0019] As embodied and broadly described herein, an aspect of the present disclosure relates to a method of stimulating, inducing, promoting, increasing, or enhancing an immune response against an influenza in a subject, comprising: administering a composition of one or more proteins, peptides, multimers or a polynucleotide that expresses the protein, peptide or multimers, in an amount sufficient to stimulate, induce, promote, increase, or enhance an immune response against the Influenza in the subject. In another aspect, the immune response provides the subject with protection against an influenza infection or pathology, or one or more physiological conditions, disorders, illnesses, diseases or symptoms caused by or associated with Influenza infection or pathology. In another aspect, the immune response is specific to: one or more H5N1 peptides selected from the amino acid sequences set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof.

[0020] As embodied and broadly described herein, an aspect of the present disclosure relates to a method of stimulating, inducing, promoting, increasing, or enhancing an immune response against H5N1 in a subject, comprising: administering a composition of proteins, peptides, multimers or a polynucleotide that expresses the protein, peptide or multimers, in an amount sufficient to stimulate, induce, promote, increase, or enhance an immune response against H5N 1 in the subject. In one aspect, the immune response provides the subject with protection against a H5N 1 infection or pathology, or one or more physiological conditions, disorders, illnesses, diseases or symptoms caused by or associated with H5N1 infection or pathology. In another aspect, the immune response is specific to: one or more H5N1 peptides selected from the amino acid sequences selected from those set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof.

[0021] As embodied and broadly described herein, an aspect of the present disclosure relates to a method of stimulating, inducing, promoting, increasing, or enhancing an immune response against H5N1 in a subject, comprising: administering to a subject an amount of a protein or peptide comprising, consisting of or consisting essentially of an amino acid sequence of a H5N 1 protein or peptide, or a variant, homologue, derivative or subsequence thereof, wherein the protein or peptide comprises at least two peptides selected from the amino acid sequences set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5 or a subsequence, portion, homologue, variant or derivative thereof, in an amount sufficient to prevent, stimulate, induce, promote, increase, immunize against, or enhance an immune response against H5N1 in the subject. In one aspect, the immune response provides the subject with protection against H5N1 infection or pathology, or one or more physiological conditions, disorders, illnesses, diseases or symptoms caused by or associated with H5N 1 infection or pathology.

[0022] As embodied and broadly described herein, an aspect of the present disclosure relates to a method of treating, preventing, or immunizing a subject against H5N1 infection, comprising administering to asubject an amount of a protein or peptide comprising, consisting of, or consisting essentially of an amino acid sequence of an influenza protein or peptide, or a variant, homologue, derivative or subsequence thereof, wherein the protein or peptide comprises at least two amino acid sequences selected from SEQ ID NOS: 1 to 929 or Tables 1 to 5 or a subsequence, portion, homologue, variant or derivative thereof, in an amount sufficient to treat, prevent, or immunize the subject for H5N1 infection, wherein the protein or peptide comprises or consists of an influenza T cell epitope that elicits, stimulates, induces, promotes, increases, or enhances an anti-H5Nl T cell immune response. In one aspect, the one or more amino acid sequences are selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof; a fusion protein comprising one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; or a pool of 2 or more peptides selected from the amino acid sequences selected from those set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5. In one aspect, the anti-H5Nl T cell response is a CD8+, a CD4+ T cell response, or both. In another aspect, the T cell epitope is conserved across two or more clinical isolates of H5N 1 or two or more circulating forms of H5N 1. In another aspect, the H5N 1 infection is an acute infection. In another aspect, the subject is a mammal or a human. In another aspect, the method reduces Influenza viral titer, increases or stimulates Influenza viral clearance, reduces or inhibits Influenza viral proliferation, reduces or inhibits increases in Influenza viral titer or Influenza viral proliferation, reduces the amount of an Influenza viral protein or the amount of a H5N1 nucleic acid, or reduces or inhibits synthesis of an influenza viral protein or an influenza viral nucleic acid. In another aspect, the method reduces one or more adverse physiological conditions, disorders, illness, diseases, symptoms or complications caused by or associated with H5N1 infection or pathology. In another aspect, the method improves one or more adverse physiological conditions, disorders, illness, diseases, symptoms or complications caused by or associated with H5N 1 infection or pathology. In another aspect, the symptom is fever or chills, joint pain, fatigue, muscle or body aches or pains, headache, nausea or vomiting, diarrhea, conjunctivitis or rash. In another aspect, the method reduces or inhibits susceptibility to H5N1 infection or pathology. In another aspect, the protein or peptide, or a subsequence, portion, homologue, variant or derivative thereof, is administered prior to, substantially contemporaneously with or following exposure to or infection of the subject with H5N1. In another aspect, a plurality of H5N1 T cell epitopes are administered prior to, substantially contemporaneously with or following exposure to or infection of the subject with H5N 1. In another aspect, the protein or peptide, or a subsequence, portion, homologue, variant or derivative thereof is administered within 2-72 hours, 2-48 hours, 4-24 hours, 4-18 hours, or 6-12 hours after a symptom of H5N1 infection or exposure develops. In another aspect, the protein or peptide, or a subsequence, portion, homologue, variant or derivative thereof is administered prior to exposure to or infection of the subject with H5N1. In another aspect, the method further comprises administering a modulator of immune response prior to, substantially contemporaneously with or following the administration to the subject of an amount of a protein or peptide. In another aspect, the modulator ofimmune response is a modulator of the innate immune response. In another aspect, the modulator is IL-6, IFN-y. TGF-P, or IL- 10, or an agonist or antagonist thereof.

[0023] As embodied and broadly described herein, an aspect of the present disclosure relates to a method of treating, preventing, or immunizing a subject against H5N1 infection, comprising administering to a subject the composition of one or more proteins, peptides or multimers in an amount sufficient to treat, prevent, or immunize the subject for H5N1 infection. In one aspect, the H5N1 infection is an acute infection. In another aspect, the method reduces Influenza viral titer, increases or stimulates Influenza viral clearance, reduces or inhibits Influenza viral proliferation, reduces or inhibits increases in Influenza viral titer or Influenza viral proliferation, reduces the amount of an influenza viral protein or the amount of an influenza viral nucleic acid, or reduces or inhibits synthesis of an influenza viral protein or an influenza viral nucleic acid. In another aspect, the method reduces one or more adverse physiological conditions, disorders, illness, diseases, symptoms or complications caused by or associated with H5N 1 infection or pathology. In another aspect, the method improves one or more adverse physiological conditions, disorders, illness, diseases, symptoms or complications caused by or associated with H5N 1 infection or pathology. In another aspect, the symptom is fever or chills, joint pain, fatigue, muscle or body aches, headache, nausea or vomiting, diarrhea, conjunctivitis or rash. In another aspect, the method reduces or inhibits susceptibility to H5N 1 infection or pathology. In another aspect, the composition is administered prior to, substantially contemporaneously with or following exposure to or infection of the subject with H5N 1. In another aspect, the composition is administered prior to, substantially contemporaneously with or following exposure to or infection of the subject with H5N 1. In another aspect, the composition is administered within 2-72 hours, 2-48 hours, 4-24 hours, 4-18 hours, or 6-12 hours after a symptom ofH5Nl infection or exposure develops. In another aspect, the composition is administered prior to exposure to or infection of the subject with H5N1.

[0024] As embodied and broadly described herein, an aspect of the present disclosure relates to a peptide or peptides that are immunoprevalent or immunodominant in a virus obtained by a method consisting of, or consisting essentially of: obtaining an amino acid sequence of the virus; determining one or more sets of overlapping peptides spanning one or more virus antigen using unbiased selection; synthesizing one or more pools of viral peptides comprising the one or more sets of overlapping peptides; combining the one or more pools of viral peptides with Class I major histocompatibility proteins (MHC), Class II MHC, or both Class I and Class II MHC to form peptide-MHC complexes; contacting the peptide-MHC complexes with T cells from subjects exposed to the virus; determining which pools triggered cytokine release by the T cells; and deconvoluting from the pool of peptides that elicited cytokine release by the T cells, which peptide or peptides are immunoprevalent or immunodominant in the pool. In one aspect, the virus is an influenza. In another aspect, the Influenza is H5N 1. In another aspect, the immunodominant peptides are selected from 1, 2 or more peptides selected from the amino acid sequences set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5. In another aspect, the immunodominant peptides are selected from 1, 2 or morepeptides selected from the amino acid sequences selected from those set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5.

[0025] As embodied and broadly described herein, an aspect of the present disclosure relates to a method of selecting an immunoprevalent or immunodominant peptide or protein of a viral comprising, consisting of, or consisting essentially of: obtaining an amino acid sequence of the virus; determining one or more sets of overlapping peptides spanning one or more virus antigen using unbiased selection; synthesizing one or more pools of virus peptides comprising the one or more sets of overlapping peptides; combining the one or more pools of viral peptides with Class I major histocompatibility proteins (MHC), Class II MHC, or both Class I and Class II MHC to form peptide-MHC complexes; contacting the peptide-MHC complexes with T cells from subjects exposed to the virus; determining which pools triggered cytokine release by the T cells; and deconvoluting from the pool of peptides that elicited cytokine release by the T cells, which peptide or peptides are immunoprevalent or immunodominant in the pool. In one aspect, the virus is an influenza. In another aspect, the Influenza is H5N 1. In another aspect, the immunodominant peptides are selected from 1, 2 or more peptides selected from the amino acid sequences set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5. In another aspect, the immunodominant peptides are selected from 1, 2 or more peptides selected from the amino acid sequences selected from those set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5.

[0026] As embodied and broadly described herein, an aspect of the present disclosure relates to a polynucleotide that expresses one or more peptides or proteins, comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof; a fusion protein comprising one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; or a pool of 2 or more or more peptides comprising, consisting of, or consisting essentially of amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5. In one aspect, the vector comprises the polynucleotide of claim that expresses one or more peptides or proteins, comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof; a fusion protein comprising one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; or a pool of 2 or more or more peptides comprising, consisting of, or consisting essentially of amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, a viral vector, or a host cell the comprises the same.

[0027] As embodied and broadly described herein, an aspect of the present disclosure relates to a polynucleotide that expresses one or more peptides or proteins comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof; a fusion protein comprising one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to929 or Tables 1 to 5; or a pool of 2 or more peptides selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5. In one aspect, the vector comprises the polynucleotide of claim that expresses one or more peptides or proteins comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof; a fusion protein comprising one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; or a pool of 2 or more peptides selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, a viral vector, or a host cell that comprises the same.BRIEF DESCRIPTION OF THE DRAWINGS

[0028] For a more complete understanding of the features and advantages of the present disclosure, reference is now made to the detailed description of the disclosure along with the accompanying figures and in which:

[0029] FIGS. 1A to ID show the percentage of H5N1 B cell (left), CD4 (middle), and CD8 (right) T cell epitopes per influenza virus antigen. No epitopes were reported for PA-X and other accessory proteins. FIG. 1B-1D, Conservation of H1N1, H2N2 and H3N2 epitopes in avian isolates. The percentages of epitopes are shown based on the level of conservation greater or equal to 100%, 80%, and 67%. B cells (gray, FIG. IB). CD4 T cells (gray, FIG. 1C). CD8 T cells (gray, FIG. ID). Conservation with prototype H5N 1 sequence (solid bars) is compared with the distribution of conservation for six recent isolates by one sample T-test. Fold change is calculated as the ratio of the average of the novel isolates Vs the prototype one. **p<0.01; ****P<0.000I.

[0030] FIGS. 2A and 2B show the antigen immunodominance comparison between avian (H5N1) and non- avian (influenza H1N1, H3N2 and H2N2) subtypes for CD4 (FIG. 2A) and CD8 T (FIG. 2B) cells. Spearman correlations were calculated, and two-tailed p-values shown in each panel.

[0031] FIGS. 3A to 3G show a comparison of T cell responses to non-avian (H1N1, H3N2, and H2N2) and avian (H5N1) antigens. T cell responses were assessed in PBMCs from the healthy donors. The comparison of T cell responses and the ratio between non-avian and avian MPs were shown at the left and right sides of each panel, respectively. FIG. 3A-3C, CD4+ T cell responses to non-avian and avian CD4 MPs. CD4+AIM+ (FIG. 3A), CD4+Granzyme B+ (FIG. 3B), and CD4+IFN-y+ (c) T cell responses. FIG. 3D-3E, CD8+ T cell responses to non-avian and avian CD8 MPs. CD8+Granzyme B+ (FIG. 3D) and CD8+IFN-y+ (FIG. 3E) T cell responses. FIG. 3F-3G, CD8+ T cell responses to non-avian and avian CD4 MPs. CD8+Granzyme B+ (FIG. 3F) and CD8+IFN-y+ (FIG. 3F) T cell responses. The comparisons are performed by paired Wilcoxon test and the significance of the ratio is analyzed by one-sample Wilcoxon test compared with a hypothetical median of 1. p values are listed at the top of each graph. The ratios between non-avian and avian MPs-specific responses are calculated if either value is above the LOS. Bars represent the geometric mean. The y-axis starts at the LOD, and the dotted lines indicate the LOS (bar graphs).DETAILED DESCRIPTION

[0032] While the making and using of various aspects of the present disclosure are discussed in detail below, it should be appreciated that the present disclosure provides many applicable inventive concepts that can be embodied in a wide variety of specific contexts. The specific aspects discussed herein are merely illustrative of specific ways to make and use the disclosure and do not delimit the scope of the disclosure.

[0033] To facilitate the understanding of this disclosure, a number of terms are defined below. Terms defined herein have meanings as commonly understood by a person of ordinary skill in the areas relevant to the present disclosure. Terms such as “a”, “an” and “the” are not intended to refer to only a singular entity, but include the general class of which a specific example may be used for illustration. The terminology herein is used to describe specific aspects of the disclosure, but their usage does not delimit the disclosure, except as outlined in the claims.

[0034] In the specification, reference may be made to the spatial relationships between various components and to the spatial orientation of various aspects of components as the devices are depicted in the attached drawings. However, as will be recognized by those skilled in the art after a complete reading of the present application, the devices, members, apparatuses, etc. described herein may be positioned in any desired orientation. Thus, the use of terms such as “above,” “below,” “upper,” “lower,” or other like terms to describe a spatial relationship between various components or to describe the spatial orientation of aspects of such components should be understood to describe a relative relationship between the components or a spatial orientation of aspects of such components, respectively, as the device described herein may be oriented in any desired direction.Definitions:

[0035] The term “gene” means the segment of DNA involved in producing a protein; it includes regions preceding and following the coding region (leader and trailer) as well as intervening sequences (introns) between individual coding segments (exons). The leader, the trailer as well as the introns include regulatory elements that are necessary during the transcription and the translation of a gene. Further, a “protein gene product” is a protein expressed from a particular gene.

[0036] The word “expression” or “expressed” as used herein in reference to a gene means the transcriptional and / or translational product of that gene. The level of expression of a DNA molecule in a cell may be determined on the basis of either the amount of corresponding mRNA that is present within the cell or the amount of protein encoded by that DNA produced by the cell. The level of expression of non-coding nucleic acid molecules (e.g., sgRNA) may be detected by standard PCR or Northern blot methods well known in the art. See, Sambrook et al., 1989 Molecular Cloning: A Laboratory Manual, 18.1- 18.88.

[0037] The term “amino acid” refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring aminoacids. Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, y-carboxyglutamate, and O-phosphoserine. Amino acid analogs refers to compounds that have the same basic chemical structure as a naturally occurring amino acid, i.e., an a carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs have modified R groups (e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid. Amino acid mimetics refers to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that functions in a manner similar to a naturally occurring amino acid. The terms “non-naturally occurring amino acid” and “unnatural amino acid” refer to amino acid analogs, synthetic amino acids, and amino acid mimetics which are not found in nature.

[0038] Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes.

[0039] The terms “polypeptide,” “peptide” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues, wherein the polymer may, in embodiments, be conjugated to a moiety that does not consist of amino acids. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers and non-naturally occurring amino acid polymers. A “fusion protein” refers to a chimeric protein encoding two or more separate protein sequences that are recombinantly expressed as a single moiety.

[0040] Proteins and peptides include isolated and purified forms. Proteins and peptides also include those immobilized on a substrate, as well as amino acid sequences, subsequences, portions, homologues, variants, and derivatives immobilized on a substrate.

[0041] Proteins and peptides can be included in compositions, for example, a pharmaceutical composition. In particular embodiments, a pharmaceutical composition is suitable for specific or non-specific immunotherapy, or is a vaccine composition.

[0042] Isolated nucleic acid (including isolated nucleic acid) encoding the proteins and peptides are also provided. Cells expressing a protein or peptide are further provided. Such cells include eukaryotic and prokaryotic cells, such as mammalian, insect, fungal and bacterial cells.

[0043] Methods and uses and medicaments of proteins and peptides of the invention are included. Such methods, uses and medicaments include modulating immune activity of a cell against a pathogen, for example, a virus or virion.

[0044] The term “peptide mimetic” or “peptidomimetic” refers to protein-like chain designed to mimic a peptide or protein. Peptide mimetics may be generated by modifying an existing peptide or by designing a compound that mimic peptides, including peptoids and [3-peptides.

[0045] “Conservatively modified variants” applies to both amino acid and nucleic acid sequences. With respect to particular nucleic acid sequences, “conservatively modified variants” refers to those nucleic acids that encode identical or essentially identical amino acid sequences. Because of the degeneracy of the genetic code, a number of nucleic acid sequences will encode any given protein. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine. Thus, at every position where an alanine is specified by a codon, the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are “silent variations,” which are one species of conservatively modified variations. Every nucleic acid sequence herein which encodes a polypeptide also describes every possible silent variation of the nucleic acid. One of skill will recognize that each codon in a nucleic acid (except AUG, which is ordinarily the only codon for methionine, and TGG, which is ordinarily the only codon for tryptophan) can be modified to yield a functionally identical molecule. Accordingly, each silent variation of a nucleic acid which encodes a polypeptide is implicit in each described sequence.

[0046] As to amino acid sequences, one of skill will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a “conservatively modified variant” where the alteration results in the substitution of an amino acid with a chemically similar amino acid. Conservative substitution table providing functionally similar amino acids are well known in the art. Such conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homologs, and alleles of the disclosure. The following eight groups each contain amino acids that are conservative substitutions for one another: (1) Alanine (A), Glycine (G); (2) Aspartic acid (D), Glutamic acid (E); (3) Asparagine (N), Glutamine (Q); (4) Arginine (R), Lysine (K); (5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); (6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W); (7) Serine (S), Threonine (T); and (8) Cysteine (C), Methionine (M) (see, e.g.. Creighton, Proteins (1984)).

[0047] A “percentage of sequence identity” is determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide or polypeptide sequence in the comparison window may comprise additions or deletions (i. e. , gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity.

[0048] The terms “identical” or percent “identity,” in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same (i.e., about 60% identity, preferably 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or higher identity over a specified region, when compared and aligned for maximum correspondence over a comparisonwindow or designated region) as measured using a BLAST or BLAST 2.0 sequence comparison algorithms with default parameters described below, or by manual alignment and visual inspection (see, e.g., NCBI web site ncbi.nlm.nih.gov / BLAST / or the like). Such sequences are then said to be “substantially identical.” This definition also refers to, or may be applied to, the compliment of a test sequence. The definition also includes sequences that have deletions and / or additions, as well as those that have substitutions. As described below, the preferred algorithms can account for gaps and the like. Preferably, identity exists over a region that is at least about 25 amino acids or nucleotides in length, or more preferably over a region that is 50-100 amino acids or nucleotides in length.

[0049] An amino acid or nucleotide base “position” is denoted by a number that sequentially identifies each amino acid (or nucleotide base) in the reference sequence based on its position relative to the N- terminus (or 5 ’-end). Due to deletions, insertions, truncations, fusions, and the like that must be taken into account when determining an optimal alignment, in general the amino acid residue number in a test sequence determined by simply counting from the N-terminus will not necessarily be the same as the number of its corresponding position in the reference sequence. For example, in a case where a variant has a deletion relative to an aligned reference sequence, there will be no amino acid in the variant that corresponds to a position in the reference sequence at the site of deletion. Where there is an insertion in an aligned reference sequence, that insertion will not correspond to a numbered amino acid position in the reference sequence. In the case of truncations or fusions there can be stretches of amino acids in either the reference or aligned sequence that do not correspond to any amino acid in the corresponding sequence.

[0050] The terms “numbered with reference to” or “corresponding to,” when used in the context of the numbering of a given amino acid or polynucleotide sequence, refers to the numbering of the residues of a specified reference sequence when the given amino acid or polynucleotide sequence is compared to the reference sequence.

[0051] The term “multimer” refers to a complex comprising multiple monomers (e.g., a protein complex) associated by noncovalent bonds. The monomers be substantially identical monomers, or the monomers may be different. In embodiments, the multimer is a dimer, a trimer, a tetramer, or a pentamer.

[0052] As used herein, the term “Major Histocompatibility Complex” (MHC) is a generic designation meant to encompass the histocompatibility antigen systems described in different species including the human leucocyte antigens (HLA). Typically, MHC Class I or Class II multimers are well known in the art and include but are not limited to dimers, tetramers, pentamers, hexamers, heptamers and octamers.

[0053] As used herein, the term “MHC / peptide multimer” refers to a stable multimeric complex composed of MHC protein(s) subunits loaded with a peptide of the present invention. For example, an MHC / peptide multimer (also called herein MHC / peptide complex) include, but are not limited to, an MHC / peptide dimer, trimer, tetramer, pentamer or higher valency multimer. In humans there are three major different genetic loci that encode MHC class I molecules (the MHC molecules of the human are also designated human leukocyte antigens (HLA)): HLA-A, HLA-B, HLA-C, e.g., HLA-A*01, HLA- A*02, and HLA-A* 11 are examples of different MHC class I alleles that can be expressed from theseloci. Non-classical human MHC class I molecules such as HLA-E (homolog of mice Qa-lb) and MICA / B molecules are also encompassed by the present invention. In some embodiments, the MHC / peptide multimer is an HLA / peptide multimer selected from the group consisting of HLA- A / peptide multimer, HLA-B / peptide multimer, HLA-C / peptide multimer, HLA-E / peptide multimer, MICA / peptide multimer and MICB / peptide multimer.

[0054] In humans there are three major different genetic loci that encode MHC class II molecules: HLA- DR, HLA-DP, and HLA-DQ, each formed of two polypeptides, alpha and beta chains (A and B genes). For example, HLA-DQAl*01, HLA-DRBl*01, and HLA-DRBl*03 are different MHC class II alleles that can be expressed from these loci. It should be further noted that non-classical human MHC class II molecules such as HLA-DM and HL-DOA (homolog in mice is H2-DM and H2-O) are also encompassed by the present invention. In some embodiments, the MHC / peptide multimer is an HLA / peptide multimer selected from the group consisting of HLA-DP / peptide multimer, HLA- DQ / peptide multimer, HLA-DR / peptide multimer, HLA-DM / peptide multimer and HLA-DO / peptide multimer.

[0055] An MHC / peptide multimer may be a multimer where the heavy chain of the MHC is biotinylated, which allows combination as a tetramer with streptavidin. MHC -peptide tetramers have increased avidity for the appropriate T cell receptor (TCR) on T lymphocytes. The multimers can also be attached to paramagnetic particles or magnetic beads to facilitate removal of non-specifically bound reporter and cell sorting. Multimer staining does not kill the labelled cells, thus, cell integrity is maintained for further analysis. In some embodiments, the MHC / peptide multimer of the present invention is particularly suitable for isolating and / or identifying a population of CD8+ T cells having specificity for the peptide of the present invention (in a flow cytometry assay).

[0056] The peptides or MHC class I or class II multimer as described herein is particularly suitable for detecting T cells specific for one or more peptides of the present invention. The peptide(s) and / or the MHC / multimer complex of the present invention is particularly suitable for diagnosing Influenza infection in a subject. For example, the method comprises obtaining a blood or PBMC sample obtained from the subject with an amount of a least peptide of the present invention and detecting at least one T cell displaying a specificity for the peptide. Another diagnostic method of the present invention involves the use of a peptide of the present invention that is loaded on multimers as described above, so that the isolated CD8+ or CD4+ T cells from the subject are brought into contact with the multimers, at which the binding, activation and / or expansion of the T cells is measured. For example, following the binding to antigen presenting cells, e.g., those having the MHC class I or class II multimer, the number of CD8+ and / or CD4+ cells binding specifically to the HLA-peptide multimer may be quantified by measuring the secretion of lymphokines / cytokines, division of the T cells, or standard flow cytometry methods, such as, for example, using fluorescence activated cell sorting (FACS). The multimers can also be attached to paramagnetic ferrous or magnetic beads to facilitate removal of non-specifically bound reporter and cell sorting.

[0057] The MHC class I or class II peptide multimers as described herein can also be used as therapeutic agents. The peptide and / or the MHC class I or class II peptide multimers of the present invention are suitable for treating or preventing an influenza infection in a subject. The MHC Class I or Class II multimers can be administered in soluble form or loaded on nanoparticles.

[0058] The term “antibody” refers to a polypeptide encoded by an immunoglobulin gene or functional fragments thereof that specifically binds and recognizes an antigen. The recognized immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon, and mu constant region genes, as well as the myriad immunoglobulin variable region genes. Light chains are classified as either kappa or lambda. Heavy chains are classified as gamma, mu, alpha, delta, or epsilon, which in turn define the immunoglobulin classes, IgG, IgM, IgA, IgD and IgE, respectively.

[0059] The phrase “specifically (or selectively) binds” to an antibody or “specifically (or selectively) immunoreactive with,” when referring to a protein or peptide, refers to a binding reaction that is determinative of the presence of the protein or peptide, often in a heterogeneous population of proteins and other biologies. Thus, under designated immunoassay conditions, the specified antibodies bind to a particular protein at least two times the background and more typically more than 10 to 100 times background. Specific binding to an antibody under such conditions requires an antibody that is selected for its specificity for a particular protein. For example, polyclonal antibodies can be selected to obtain only a subset of antibodies that are specifically immunoreactive with the selected antigen and not with other proteins. This selection may be achieved by subtracting out antibodies that cross-react with other molecules . A variety of immunoassay formats may be used to select antibodies specifically immunoreactive with a particular protein. For example, solid-phase ELISA immunoassays are routinely used to select antibodies specifically immunoreactive with a protein (see, e.g., Harlow & Lane, Using Antibodies, A Laboratory Manual (1998) for a description of immunoassay formats and conditions that can be used to determine specific immunoreactivity).

[0060] Antibodies are large, complex molecules (molecular weight of -150,000 or about 1320 amino acids) with intricate internal structure. A natural antibody molecule contains two identical pairs of polypeptide chains, each pair having one light chain and one heavy chain. Each light chain and heavy chain in turn consists of two regions: a variable (“V”) region involved in binding the target antigen, and a constant (“C”) region that interacts with other components of the immune system. The light and heavy chain variable regions come together in 3 -dimensional space to form a variable region that binds the antigen (for example, a receptor on the surface of a cell). Within each light or heavy chain variable region, there are three short segments (averaging 10 amino acids in length) called the complementarity determining regions (“CDRs”). The six CDRs in an antibody variable domain (three from the light chain and three from the heavy chain) fold up together in 3 -dimensional space to form the actual antibody binding site which docks onto the target antigen. The position and length of the CDRs have been precisely defined by Kabat, E. et al., Sequences of Proteins of Immunological Interest, U.S. Department of Health and Human Services, 1983, 1987. Thepart of a variable region not contained in the CDRs is called the framework (“FR”), which forms the environment for the CDRs.

[0061] The term “antibody” is used according to its commonly known meaning in the art. Antibodies exist, e.g., as intact immunoglobulins or as a number of well-characterized fragments produced by digestion with various peptidases. Thus, for example, pepsin digests an antibody below the disulfide linkages in the hinge region to produce F(ab)’2, a dimer of Fab which itself is a light chain joined to VH-CHI by a disulfide bond. The F(ab)’2 may be reduced under mild conditions to break the disulfide linkage in the hinge region, thereby converting the F(ab)’2 dimer into a Fab’ monomer. The Fab’ monomer is essentially Fab with part of the hinge region (see Fundamental Immunology (Paul ed., 3d ed. 1993). While various antibody fragments are defined in terms of the digestion of an intact antibody, one of skill will appreciate that such fragments may be synthesized de novo either chemically or by using recombinant DNA methodology. Thus, the term antibody, as used herein, also includes antibody fragments either produced by the modification of whole antibodies, orthose synthesized de novo using recombinant DNA methodologies (e.g., single chain Fv) or those identified using phage display libraries (see, e.g., McCafferty et al., Nature 348:552-554 (1990)).

[0062] An exemplary immunoglobulin (antibody) structural unit comprises a tetramer. Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one “light” (about 25 kD) and one “heavy” chain (about 50-70 kD). The N-terminus of each chain defines a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition. The terms variable light chain (VL) and variable heavy chain (VH) refer to these light and heavy chains respectively. The Fc (i.e., fragment crystallizable region) is the “base” or “tail” of an immunoglobulin and is typically composed of two heavy chains that contribute two or three constant domains depending on the class of the antibody. By binding to specific proteins, the Fc region ensures that each antibody generates an appropriate immune response for a given antigen. The Fc region also binds to various cell receptors, such as Fc receptors, and other immune molecules, such as complement proteins.

[0063] As used herein, the term “antigen” and the term “epitope” refers to a molecule or substance capable of stimulating an immune response. In one example, epitopes include but are not limited to a polypeptide and a nucleic acid encoding a polypeptide, wherein expression of the nucleic acid into a polypeptide is capable of stimulating an immune response when the polypeptide is processed and presented on a Major Histocompatibility Complex (MHC) molecule. Generally, epitopes include peptides presented on the surface of cells non-covalently bound to the binding groove of Class I or Class II MHC, such that they can interact with T cell receptors and the respective T cell accessory molecules. However, antigens and epitopes also apply when discussing the antigen binding portion of an antibody, wherein the antibody binds to a specific structure of the antigen.

[0064] Proteolytic Processing of Antigens. Epitopes that are displayed by MHC on antigen presenting cells are cleavage peptides or products of larger peptide or protein antigen precursors. For MHC I epitopes, protein antigens are often digested by proteasomes resident in the cell. Intracellular proteasomal digestion produces peptide fragments of about 3 to 23 amino acids in length that are then loaded onto the MHCprotein. Additional proteolytic activities within the cell, or in the extracellular milieu, can trim and process these fragments further. Processing of MHC Class II epitopes generally occurs via intracellular proteases from the lysosomal / endosomal compartment. The present invention includes, in one embodiment, pre- processed peptides that are attached to the anti-CD40 antibody (or fragment thereof) that directs the peptides against which an enhanced immune response is sought directly to antigen presenting cells.

[0065] The present invention includes methods for specifically identifying the epitopes within antigens most likely to lead to the immune response sought for the specific sources of antigen presenting cells and responder T cells.

[0066] As used herein, the term “T cell epitope” refers to a specific amino acid that when present in the context of a Major or Minor Histocompatibility Complex provides a reactive site for a T cell receptor. The T-cell epitopes or peptides that stimulate the cellular arm of a subject’s immune system are short peptides of about 8-25 amino acids. T-cell epitopes are recognized by T cells from animals that are immune to the antigen of interest. These T-cell epitopes or peptides can be used in assays such as the stimulation of cytokine release or secretion or evaluated by constructing major histocompatibility (MHC) proteins containing or “presenting” the peptide. Such immunogenically active fragments are often identified based on their ability to stimulate lymphocyte proliferation in response to stimulation by various fragments from the antigen of interest.

[0067] As used herein, the term “immunological response” refers to an antigen or composition is the development in a subject of a humoral and / or a cellular immune response to an antigen present in the composition of interest. For purposes of the present disclosure, a “humoral immune response” refers to an immune response mediated by antibody molecules, while a “cellular immune response” is one mediated by T-lymphocytes and / or other white blood cells. One important aspect of cellular immunity involves an antigen-specific response by cytolytic T-cells (“CTL”s). CTLs have specificity for peptide antigens that are presented in association with proteins encoded by the major histocompatibility complex (MHC) and expressed on the surfaces of cells. CTLs help induce and promote the destruction of intracellular microbes, or the lysis of cells infected with such microbes. Another aspect of cellular immunity involves an antigenspecific response by helper T-cells. Helper T-cells act to help stimulate the function, and focus the activity of, nonspecific effector cells against cells displaying peptide antigens in association with MHC molecules on their surface. A “cellular immune response” also refers to the production of cytokines, chemokines and other such molecules produced by activated T-cells and / or other white blood cells, including those derived from CD4+ and CD8+ T-cells. Hence, an immunological response may include one or more of the following effects: the production of antibodies by B-cells; and / or the activation of effector and / or suppressor T-cells and / or gamma-delta T-cells directed specifically to an antigen or antigens present in the composition or vaccine of interest. These responses may serve to neutralize infectivity, and / or mediate antibody-complement, or antibody dependent cell cytotoxicity (ADCC) to provide protection to an immunized host. Such responses can be determined using standard immunoassays and neutralization assays, well known in the art.

[0068] As used herein, the term an “immunogenic composition” and “vaccine” refer to a composition that comprises an antigenic molecule where administration of the composition to a subject or patient results in the development in the subject of a humoral and / or a cellular immune response to the antigenic molecule of interest. “Vaccine” refers to a composition that can provide active acquired immunity to and / or therapeutic effect (e.g., treatment) of a particular disease or a pathogen. A vaccine typically contains one or more agents that can induce an immune response in a subject against a pathogen or disease, i.e., a target pathogen or disease. The immunogenic agent stimulates the body’s immune system to recognize the agent as a threat or indication of the presence of the target pathogen or disease, thereby inducing immunological memory so that the immune system can more easily recognize and destroy any of the pathogen on subsequent exposure. Vaccines can be prophylactic (e.g., preventing or ameliorating the effects of a future infection by any natural or pathogen) or therapeutic (e.g., reducing symptoms or aberrant conditions associated with infection). The administration of vaccines is referred to vaccination.

[0069] In some examples, a vaccine composition can provide nucleic acid, e.g., mRNA that encodes antigenic molecules (e.g., peptides) to a subject. The nucleic acid that is delivered via the vaccine composition in the subject can be expressed into antigenic molecules and allow the subject to acquire immunity against the antigenic molecules. In the context of the vaccination against infectious disease, the vaccine composition can provide mRNA encoding antigenic molecules that are associated with a certain pathogen, e.g., one or more peptides that are known to be expressed in the pathogen (e.g., pathogenic virus).

[0070] The present invention provides nucleic acid molecules, specifically polynucleotides, primary constructs and / or mRNA that encode one or more polynucleotides that express one or more peptides or proteins, comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof for use in immune modulation. The term “nucleic acid” refers to any compound and / or substance that comprise a polymer of nucleotides, referred to herein as polynucleotides. Exemplary nucleic acids or polynucleotides of the invention include, but are not limited to, ribonucleic acids (RNAs), deoxyribonucleic acids (DNAs), threose nucleic acids (TNAs), glycol nucleic acids (GNAs), peptide nucleic acids (PNAs), locked nucleic acids (LNAs), including diastereomers of LNAs, functionalized LNAs, or hybrids thereof.

[0071] One method of immune modulation of the present invention includes direct or indirect gene transfer, i.e., local application of a preparation containing the one or more polynucleotides (DNA, RNA, mRNA, etc.) that expresses the one or more peptides or proteins, comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof. A variety of well-known vectors can be used to deliver to cells the one or more polynucleotides or the peptides or proteins expressed by the polynucleotides, including but not limited to adenobacterial vectors and adeno-associated vectors. In addition, naked DNA, liposome delivery methods, or other novel vectors developed to deliver the polynucleotides to cells can also be beneficial. Any of a variety of promoters can be used to drive peptideor protein expression, including but not limited to endogenous promoters, constitutive promoters (e.g., cytomegalobacteria, adenobacteria, or SV40), inducible promoters (e.g., a cytokine promoter such as the interleukin- 1, tumor necrosis factor-alpha, or interleukin-6 promoter), and tissue specific promoters to express the immunogenic peptides or proteins of the present invention.

[0072] The immunization may include adenobacteria, adeno-associated bacteria, herpes bacteria, vaccinia bacteria, retrobacteriaes, or other bacterial vectors with the appropriate tropism for cells likely to present the antigenic peptide(s) or protein(s) may be used as a gene transfer delivery system for a therapeutic peptide(s) or protein(s), comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof, gene expression construct. Bacterial vectors which do not require that the target cell be actively dividing, such as adenobacterial and adeno-associated vectors, are particularly useful when the cells are accumulating, but not proliferative. Numerous vectors useful for this purpose are generally known (Miller, Human Gene Therapy 15-14, 1990; Friedman, Science 244: 1275- 1281, 1989; Eglitis and Anderson, BioTechniques 6:608-614, 1988; Tolstoshev and Anderson, Current Opinion in Biotechnology 1:55-61, 1990; Sharp, The Lancet 337: 1277-1278, 1991; Cometta et al., Nucleic Acid Research and Molecular Biology 36:311-322, 1987; Anderson, Science 226:401-409, 1984; Moen, Blood Cells 17:407-416, 1991; and Miller and Rosman, Bio Techniques 7:980-990, 1989; Le Gal La Salle et al., Science 259:988-990, 1993; and Johnson, Chest 107:77S-83S, 1995). Retrobacterial vectors are particularly well developed and have been used in clinical settings (Rosenberg et al., N. Engl. J. Med 323:370, 1990; Anderson et al., U.S. Pat. No. 5,399,346).

[0073] The immunization may also include inserting the one or more polynucleotides (DNA, RNA, mRNA, etc.) that express the one or more peptides or proteins, comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof into the viral vector, along with another gene which encodes the ligand for a receptor on a specific target cell, for example, such that the vector is now target specific. Bacterial vectors can be made target specific by attaching, for example, a sugar, a glycolipid, or a protein. Targeting can also be accomplished by using an antibody to target the bacterial vector. Those of skill in the art will know of, or can readily ascertain without undue experimentation, specific polynucleotide sequences which can be inserted into the bacterial genome or attached to a bacterial envelope to allow target specific delivery of the bacterial vector containing the gene.

[0074] Since recombinant bacteria are defective, they require assistance in order to produce infectious vector particles. This assistance can be provided, for example, by using helper cell lines that contain plasmids encoding all of the structural genes of the bacteria under the control of regulatory sequences within the bacterial genome. These plasmids are missing a nucleotide sequence which enables the packaging mechanism to recognize a polynucleotide transcript for encapsidation. These cell lines produce empty virions, since no genome is packaged. If a bacterial vector is introduced into such cells in which thepackaging signal is intact, but the structural genes are replaced by other genes of interest, the vector can be packaged and vector virion produced.

[0075] Bacterial or non-bacterial approaches may also be employed for the introduction of one or more therapeutic polynucleotides that express the one or more peptides or proteins, comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof, into polynucleotide-encoding polynucleotide into antigen presenting cells. The polynucleotides may be DNA, RNA, mRNA that directly encode the one or more peptides or proteins of the present invention, or may be introduced as part of an expression vector.

[0076] Another example of an immunization includes colloidal dispersion systems that include macromolecule complexes, nanocapsules, microspheres, beads, and lipid-based systems including oil-in- water emulsions, micelles, mixed micelles, and liposomes and the one or more polynucleotides that express the one or more peptides or proteins, comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof. One non-limiting example of a colloidal system for use with the present invention is a liposome. Liposomes are artificial membrane vesicles which are useful as delivery vehicles in vitro and in vivo. It has been shown that large unilamellar vesicles (LUV), which range in size from 0.2-4.0 micrometers that can encapsulate a substantial percentage of an aqueous buffer containing large macromolecules. RNA, DNA and intact virions can be encapsulated within the aqueous interior and be delivered to cells in a biologically active form (Fraley, et al., Trends Biochem. Sci., 6:77, 1981). In addition to mammalian cells, liposomes have been used for delivery of polynucleotides in plant, yeast and bacterial cells. In order for a liposome to be an efficient gene transfer vehicle, the following characteristics should be present: (Zakut and Givol, supra) encapsulation of the genes of interest at high efficiency while not compromising their biological activity; (Feamhead, et al., supra) preferential and substantial binding to a target cell in comparison to non-target cells; (Korsmeyer, S. J., supra) delivery of the aqueous contents of the vesicle to the target cell cytoplasm at high efficiency; and (Kinoshita, et al., supra) accurate and effective expression of genetic information (Mannino, et al., Bio Techniques, 6:682, 1988).

[0077] The composition for immunizing the subject or patient may, in certain embodiments comprise a combination of phospholipid, particularly high-phase-transition-temperature phospholipids, usually in combination with steroids, especially cholesterol. Other phospholipids or other lipids may also be used. The physical characteristics of liposomes depend on pH, ionic strength, and the presence of divalent cations. The targeting of liposomes can be classified based on anatomical and mechanistic factors. Anatomical classification is based on the level of selectivity, for example, organ-specific, cell-specific, and organelle-specific. Mechanistic targeting can be distinguished based upon whether it is passive or active. Passive targeting utilizes the natural tendency of liposomes to distribute to cells of the reticuloendothelial system (RES) in organs which contain sinusoidal capillaries. Active targeting, on the other hand, involvesalteration of the liposome by coupling the liposome to a specific ligand such as a monoclonal antibody, sugar, glycolipid, or protein, or by changing the composition or size of the liposome in order to achieve targeting to organs and cell types other than the naturally occurring sites of localization, specifically, cells that can become infected with an influenza or interact with the proteins, peptides, and / or gene products of an influenza, e.g., immune cells.

[0078] For any of the above approaches, the immune modulating polynucleotide construct, composition, or formulation is preferably applied to a site that will enhance the immune response. For example, the immunization may be intramuscular, intraperitoneal, enteral, parenteral, intranasal, intrapulmonary, or subcutaneous. In the gene delivery constructs of the instant invention, polynucleotide expression is directed from any suitable promoter (e.g., the human cytomegalobacteria, simian bacteria 40, actin or adenobacteria constitutive promoters; or the cytokine or metalloprotease promoters for activated synoviocyte specific expression).

[0079] In one example of the immune modifying peptide(s) or protein(s) include polynucleotides, constructs and / or mRNAs that express the one or more polynucleotides that express the one or more peptides or proteins, comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof, that are designed to improve one or more of the stability and / or clearance in tissues, uptake and / or kinetics, cellular access by the peptide(s) or protein(s), translational, mRNA half-life, translation efficiency, immune evasion, protein production capacity, accessibility to circulation, peptide(s) or protein(s) half-life and / or presentation in the context of MHC on antigen presenting cells.

[0080] The present invention contemplates immunization for use in both active and passive immunization embodiments. Immunogenic compositions, proposed to be suitable for use as a vaccine, may be prepared most readily directly from immunogenic peptides, proteins, monomers, multimers and / or peptide-MHC complexes prepared in a manner disclosed herein. The antigenic material is generally processed to remove undesired contaminants, such as, small molecular weight molecules, incomplete proteins, or when manufactured in plant cells, plant components such as cell walls, plant proteins, and the like. Often, these immunizations are lyophilized for ease of transport and / or to increase shelf-life and can then be more readily dissolved in a desired vehicle, such as saline.

[0081] The preparation of immunizations (also referred to as vaccines) that contain the immunogenic proteins of the present invention as active ingredients is generally well understood in the art, as exemplified by United States Letters Patents 4,608,251; 4,601,903; 4,599,231; 4,599,230; 4,596,792; and 4.578,770, all incorporated herein by reference. Typically, such immunizations are prepared as injectable. The immunizations can be a liquid solution or suspension but may also be provided in a solid form suitable for solution in, or suspension in, liquid prior to injection may also be prepared. The preparation may also be emulsified. The active immunogenic ingredient is often mixed with excipients that are pharmaceutically acceptable and compatible with the active ingredient. Suitable excipients are, for example, water, saline,dextrose, glycerol, ethanol, buffers, or the like and combinations thereof. In addition, if desired, the immunization may contain minor amounts of auxiliary substances such as wetting or emulsifying agents, pH buffering agents, or adjuvants which enhance the effectiveness of the vaccines.

[0082] The immunization is / are administered in a manner compatible with the dosage formulation, and in such amount as will be therapeutically effective and immunogenic. The quantity to be administered depends on the subject to be treated, including, e.g., the capacity of the individual’s immune system to synthesize antibodies, and the degree of protection desired. Precise amounts of active ingredient required to be administered depend on the judgment of the practitioner. However, suitable dosage ranges are of the order of several hundred micrograms active ingredient per vaccination. Suitable regimes for initial administration and booster shots are also variable but are typified by an initial administration followed by subsequent inoculations or other administrations.

[0083] The manner of application of the immunization may be varied widely. Any of the conventional methods for administration of a vaccine are applicable. These are believed to also include oral application on a solid physiologically acceptable base or in a physiologically acceptable dispersion, parenterally, by injection or the like. The dosage of the vaccine will depend on the route of administration and will vary according to the size of the host.

[0084] Various methods of achieving adjuvant effect for the vaccine includes use of agents such as aluminum hydroxide or phosphate (alum), commonly used as 0.05 to 0.1 percent solution in phosphate buffered saline, admixture with synthetic polymers of sugars (Carbopol) used as 0.25 percent solution, aggregation of the protein in the vaccine by heat treatment with temperatures ranging between 70° to 101°C for 30 second to 2-minute periods respectively. Aggregation by reactivating with pepsin treated (Fab) antibodies to albumin, mixture with bacterial cells such as C. parvum or endotoxins or lipopolysaccharide components of gram-negative bacteria, emulsion in physiologically acceptable oil vehicles such as mannide mono-oleate (Aracel A) or emulsion with 20 percent solution of a perfluorocarbon (Fluosol-DA) used as a block substitute may also be employed.

[0085] In many instances, it will be desirable to have multiple administrations of the vaccine, usually not exceeding six to ten immunizations, more usually not exceeding four immunizations and preferably one or more, usually at least about three immunizations. The immunizations will normally be at from two to twelve-week intervals, more usually from three to five-week intervals. Periodic boosters at intervals of 1- 5 years, usually three years, will be desirable to maintain protective levels of the antibodies. The course of the immunization may be followed by assays for antibodies for the supernatant antigens. The assays may be performed by labeling with conventional labels, such as radionuclides, enzymes, fluorescent agents, and the like. These techniques are well known and may be found in a wide variety of patents, such as Hudson and Cranage, Vaccine Protocols, 2003 Humana Press, relevant portions incorporated herein by reference.

[0086] Techniques and compositions for making useful dosage forms using the present invention are described in one or more of the following references: Anderson, Philip O.; Knoben, James E.; Troutman, William G, eds., Handbook of Clinical Drug Data, Tenth Edition, McGraw-Hill, 2002; Pratt and Taylor,eds., Principles of Drug Action, Third Edition, Churchill Livingston, New York, 1990; Katzung, ed., Basic and Clinical Pharmacology, Ninth Edition, McGraw Hill, 2007; Goodman and Gilman, eds., The Pharmacological Basis of Therapeutics, Tenth Edition, McGraw Hill, 2001; Remington’s Pharmaceutical Sciences, 20th Ed., Lippincott Williams & Wilkins., 2000, and updates thereto; Martindale, The Extra Pharmacopoeia, Thirty-Second Edition (The Pharmaceutical Press, London, 1999); all of which are incorporated by reference, and the like, relevant portions incorporated herein by reference.

[0087] Many suitable expression systems are commercially available, including, for example, the following: baculoviral expression (Reilly, P. R., et al., BACULOVIRUS EXPRESSION VECTORS: A LABORATORY MANUAL (1992); Beames, et al., Biotechniques 11:378 (1991); Pharmingen; Clontech, Palo Alto, Calif.)), vaccinia expression systems (Earl, P. L., et al., “Expression of proteins in mammalian cells using vaccinia” In Current Protocols in Molecular Biology (F. M. Ausubel, et al. Eds.), Greene Publishing Associates & Wiley Interscience, New York (1991); Moss, B., et al., U.S. Pat. No. 5,135,855, issued Aug. 4, 1992), expression in bacteria (Ausubel, F. M., et al., CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley and Sons, Inc., Media Pa.; Clontech), expression in yeast (Rosenberg, S. and Tekamp-Olson, P., U.S. Pat. No. RE35,749, issued, Mar. 17, 1998, herein incorporated by reference; Shuster, J. R., U.S. Pat. No. 5,629,203, issued May 13, 1997, herein incorporated by reference; Gellissen, G., et al., Antonie Van Leeuwenhoek, 62(l-2):79-93 (1992); Romanos, M. A., et al., Yeast 8(6):423-488 (1992); Goeddel, D. V., Methods in Enzymology 185 (1990); Guthrie, C., and G. R. Fink, Methods in Enzymology 194 (1991)), expression in mammalian cells (Clontech; Gibco-BRL, Ground Island, N.Y.; e.g., Chinese hamster ovary (CHO) cell lines (Haynes, J., et al., Nuc. Acid. Res. 11:687-706 (1983); 1983, Lau, Y. F„ et al., Mol. Cell. Biol. 4: 1469-1475 (1984); Kaufinan, R. J., “Selection and coamplification of heterologous genes in mammalian cells,” in Methods in Enzymology, vol. 185, pp 537- 566. Academic Press, Inc., San Diego Calif. (1991)), and expression in plant cells (plant cloning vectors, Clontech Laboratories, Inc., Palo-Alto, Calif., and Pharmacia LKB Biotechnology, Inc., Piscataway, N.J.; Hood, E„ et al., J. Bacteriol. 168: 1291-1301 (1986); Nagel, R„ et al., FEMS Microbiol. Lett. 67:325 (1990); An, et al., “Binary Vectors”, and others in Plant Molecular Biology Manual A3: 1-20 (1988); Miki, B. L. A., et al., pp. 249-265, and others in Plant DNA Infectious Agents (Hohn, T., et al., eds.) Springer-Verlag, Wien, Austria, (1987); Plant Molecular Biology: Essential Techniques, P. G. Jones and J. M. Sutton, New York, J. Wiley, 1997; Miglani, Gurbachan Dictionary of Plant Genetics and Molecular Biology, New York, Food Products Press, 1998; Henry, R. J., Practical Applications of Plant Molecular Biology, New York, Chapman & Hall, 1997), relevant portion incorporated herein by reference.

[0088] As used herein, the term “effective amount” or “effective dose” refers to that amount of the peptide or protein T cell epitopes of the invention sufficient to induce immunity, to prevent and / or ameliorate an infection or to reduce at least one symptom of an infection and / or to enhance the efficacy of another dose of peptide or protein T cell epitopes. An effective dose may refer to the amount of peptide or protein T cell epitopes sufficient to delay or minimize the onset of an infection. An effective dose may also refer to the amount of peptide or protein T cell epitopes that provides a therapeutic benefit in the treatment ormanagement of an infection. Further, an effective dose is the amount with respect to peptide or protein T cell epitopes of the invention alone, or in combination with other therapies, that provides a therapeutic benefit in the treatment or management of an infection. An effective dose may also be the amount sufficient to enhance a subject’s (e.g., a human’s) own immune response against a subsequent exposure to an infectious agent. Levels of immunity can be monitored, e.g., by measuring amounts of neutralizing secretory and / or serum antibodies, e.g., by plaque neutralization, complement fixation, enzyme-linked immunosorbent, or microneutralization assay. In the case of a vaccine, an “effective dose” is one that prevents disease and / or reduces the severity of symptoms. A “reduction” of a symptom or symptoms (and grammatical equivalents of this phrase) means decreasing of the severity or frequency of the symptom(s), or elimination of the symptom(s). A “prophylactically effective amount” of a drug is an amount of a drug that, when administered to a subject, will have the intended prophylactic effect, e.g., preventing or delaying the onset (or reoccurrence) of an injury, disease, pathology or condition, or reducing the likelihood of the onset (or reoccurrence) of an injury, disease, pathology, or condition, or their symptoms, in this case, an infectious disease, and more particularly, an influenza infection. The full prophylactic effect does not necessarily occur by administration of one dose, and may occur only after administration of a series of doses. Thus, a prophylactically effective amount may be administered in one or more administrations. Guidance can be found in the literature for appropriate dosages for given classes of pharmaceutical products. For example, for the given parameter, an effective amount will show an increase or decrease of at least 5%, 10%, 15%, 20%, 25%, 40%, 50%, 60%, 75%, 80%, 90%, or at least 100%. Efficacy can also be expressed as “-fold” increase or decrease. For example, a therapeutically effective amount can have at least a 1.2-fold, 1.5-fold, 2-fold, 5-fold, or more effect over a control. The exact amounts will depend on the purpose of the treatment, and will be ascertainable by one skilled in the art using known techniques (see, e.g., Lieberman, Pharmaceutical Dosage Forms (vols. 1-3, 1992); Lloyd, The Art, Science and Technology of Pharmaceutical Compounding (1999); Pickar, Dosage Calculations (1999); and Remington: The Science and Practice of Pharmacy, 20th Edition, 2003, Gennaro, Ed., Lippincott, Williams & Wilkins), relevant portions incorporated herein by reference.

[0089] As used herein, the term “immune stimulator” refers to a compound that enhances an immune response via the body’s own chemical messengers (cytokines). These molecules comprise various cytokines, lymphokines and chemokines with immunostimulatory, immunopotentiating, and pro- inflammatory activities, such as interferons, interleukins (e.g., IL-1, IL-2, IL-3, IL-4, IL-12, IL-13); growth factors (e.g., granulocyte-macrophage (GM)-colony stimulating factor (CSF)); and other immunostimulatory molecules, such as macrophage inflammatory factor, Flt3 ligand, B7.1; B7.2, etc. The immune stimulator molecules can be administered in the same formulation as peptide or protein T cell epitopes s of the invention, or can be administered separately. Either the protein or an expression vector encoding the protein can be administered to produce an immunostimulatory effect.

[0090] As used herein, in certain embodiments, the term “protective immune response” or “protective response” refers to an immune response mediated by antibodies against an infectious agent, which isexhibited by a vertebrate (e.g., a human), which prevents or ameliorates an infection or reduces at least one symptom thereof. Peptide and protein T cell epitopes of the invention can stimulate the production of antibodies that, for example, neutralize infectious agents, blocks infectious agents from entering cells, blocks replication of said infectious agents, and / or protect host cells from infection and destruction. In other embodiments, the term can also refer to an immune response that is mediated by T-lymphocytes and / or other white blood cells against an infectious agent, exhibited by a vertebrate (e.g., a human), that prevents or ameliorates Influenza infection or reduces at least one symptom thereof. Peptide and protein T cell epitopes of the invention can stimulate the T cell responses that, for example, neutralize infectious agents, kill virus infected cells, blocks infectious agents from entering cells, blocks replication of said infectious agents, and / or protect host cells from infection and destruction.

[0091] The terms “biological sample” or “sample” refer to materials obtained from or derived from a subject or patient. A biological sample includes sections of tissues such as biopsy and autopsy samples, and frozen sections taken for histological purposes. Such samples include bodily fluids such as blood and blood fractions or products (e.g., serum, plasma, platelets, red blood cells, and the like), sputum, tissue, cultured cells (e.g., primary cultures, explants, and transformed cells) stool, urine, synovial fluid, joint tissue, synovial tissue, synoviocytes, fibroblast-like synoviocytes, macrophage-like synoviocytes, immune cells, hematopoietic cells, fibroblasts, macrophages, T cells, etc. A biological sample is typically obtained from a eukaryotic organism, such as a mammal such as a primate e.g., chimpanzee or human; cow; dog; cat; a rodent, e.g., guinea pig, rat, mouse; rabbit; or a bird; reptile; or fish.

[0092] As used herein, a “cell” refers to a cell carrying out metabolic or other function sufficient to preserve or replicate its genomic DNA. A cell can be identified by well-known methods in the art including, for example, presence of an intact membrane, staining by a particular dye, ability to produce progeny or, in the case of a gamete, ability to combine with a second gamete to produce a viable offspring. Cells may include prokaryotic and eukaryotic cells. Prokaryotic cells include but are not limited to bacteria. Eukaryotic cells include but are not limited to yeast cells and cells derived from plants and animals, for example mammalian, insect (e.g., spodoptera) and human cells. Cells may be useful when they are naturally nonadherent or have been treated not to adhere to surfaces, for example by trypsinization.

[0093] As used herein, the term “contacting” is used in accordance with its plain ordinary meaning and refers to the process of allowing at least two distinct species to become sufficiently proximal to react, interact or physically touch. It should be appreciated, however, the resulting reaction product can be produced directly from a reaction between the added reagents or from an intermediate from one or more of the added reagents which can be produced in the reaction mixture. The term “contacting” may include allowing two species to react, interact, or physically touch, wherein the two species may be, for example, an amino acid sequence, protein, or peptide as provided herein and an immune cell, such as a T cell.

[0094] As used herein, a “control” sample or value refers to a sample that serves as a reference, usually a known reference, for comparison to a test sample. For example, a test sample can be taken from a test condition, e.g., in the presence of a test compound, and compared to samples from known conditions, e.g.,in the absence of the test compound (negative control), or in the presence of a known compound (positive control). A control can also represent an average value gathered from a number of tests or results. One of skill in the art will recognize that controls can be designed for assessment of any number of parameters. For example, a control can be devised to compare therapeutic benefit based on pharmacological data (e.g., half-life) or therapeutic measures (e.g., comparison of side effects). One of skill in the art will understand which controls are valuable in a given situation and be able to analyze data based on comparisons to control values. Controls are also valuable for determining the significance of data. For example, if values for a given parameter are widely variant in controls, variation in test samples will not be considered as significant.

[0095] The term “modulator” refers to a composition that increases or decreases the level of a target molecule or the function of a target molecule or the physical state of the target of the molecule relative to the absence of the modulator.

[0096] The term “modulate” is used in accordance with its plain ordinary meaning and refers to the act of changing or varying one or more properties. “Modulation” refers to the process of changing or varying one or more properties. For example, as applied to the effects of a modulator on a target protein, to modulate means to change by increasing or decreasing a property or function of the target molecule or the amount of the target molecule.

[0097] The terms “associated” or “associated with” in the context of a substance or substance activity or function associated with a disease (e.g. a protein associated disease, a cancer (e.g., cancer, inflammatory disease, autoimmune disease, or infectious disease)) means that the disease (e.g. cancer, inflammatory disease, autoimmune disease, or infectious disease) is caused by (in whole or in part), or a symptom of the disease is caused by (in whole or in part) the substance or substance activity or function. As used herein, what is described as being associated with a disease, if a causative agent, could be a target for treatment of the disease.

[0098] The term “aberrant” as used herein refers to different from normal. When used to describe enzymatic activity or protein function, aberrant refers to activity or function that is greater or less than a normal control or the average of normal non-diseased control samples. Aberrant activity may refer to an amount of activity that results in a disease, wherein returning the aberrant activity to a normal or nondisease-associated amount (e.g., by administering a compound or using a method as described herein), results in reduction of the disease or one or more disease symptoms.

[0099] The terms “subject” or “subject in need thereof’ refers to a living organism who is at risk of or prone to having a disease or condition, or who is suffering from a disease or condition that can be treated by administration of a composition or pharmaceutical composition as provided herein. Non-limiting examples include humans and other primates, but also includes non-human primates such as chimpanzees and other apes and monkey species; farm animals such as cattle, sheep, pigs, goats and horses; domestic mammals such as dogs and cats; laboratory animals including rodents such as mice, rats and guinea pigs; birds, including domestic, wild and game birds such as chickens, turkeys and other gallinaceous birds,ducks, geese, and the like. The term does not denote a particular age. Thus, both adult and newborn individuals are intended to be covered. The system described above is intended for use in any of the above vertebrate species, since the immune systems of all of these vertebrates operate similarly.

[0100] The terms “disease” or “condition” refer to a state of being or health status of a patient or subject capable of being treated with a compound, pharmaceutical composition, or method provided herein. In embodiments, a patient or subject is human. In embodiments, the disease is Influenza infection. In certain alternative embodiments, the disease is H5N1 infection. In still other embodiments, the disease is Chikungunya.

[0101] As used herein, “treatment” or “treating,” or “palliating” or “ameliorating” are used interchangeably herein. These terms refer to an approach for obtaining beneficial or desired results including but not limited to therapeutic benefit and / or a prophylactic benefit. By therapeutic benefit is meant eradication or amelioration of the underlying disorder being treated or the disorder resulting from viral infection. Also, a therapeutic benefit is achieved with the eradication or amelioration of one or more of the physiological symptoms associated with viral infection or the underlying disorder such that an improvement is observed in the patient, notwithstanding that the patient may still be afflicted with the underlying disorder or may still be infected. For prophylactic benefit, the compositions may be administered to a patient at risk of viral infection, of developing a particular disease, or to a patient reporting one or more of the physiological symptoms of a disease, even though a diagnosis of this disease may not have been made. Treatment includes preventing the infection or disease, that is, causing the clinical symptoms of the disease not to develop by administration of a protective composition prior to infection or the induction of the disease; suppressing the disease, that is, causing the clinical symptoms of the disease or infection not to develop by administration of a protective composition after the inductive event or infection but prior to the clinical appearance or reappearance of the disease; inhibiting the disease, that is, arresting the development of clinical symptoms by administration of a protective composition after their initial appearance; preventing re-occurring of the disease and / or relieving the disease, that is, causing the regression of clinical symptoms by administration of a protective composition after their initial appearance. “Treatment” can also refer to any of (i) the prevention of infection or reinfection, as in a traditional vaccine, (ii) the reduction or elimination of symptoms, and (iii) the substantial or complete elimination of the pathogen in question. Treatment may be affected prophylactically (prior to infection) or therapeutically (following infection).

[0102] In addition, in certain embodiments, “treatment,” “treat,” or “treating” refers to a method of reducing the effects of one or more symptoms of infection with an Influenza. Thus, in the disclosed method, treatment can refer to a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% reduction in the severity of an established infection, disease, condition, or symptom of the infection, disease or condition. For example, a method for treating a disease is considered to be a treatment if there is a 10% reduction in one or more symptoms of the disease in a subject as compared to a control. Thus, the reduction can be a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any percent reduction in between 10% and 100% as compared to native or control levels. It is understood that treatment does not necessarily refer toa cure or complete ablation of the disease, condition, or symptoms of the disease or condition and / or complete prevention of infection. Further, as used herein, references to decreasing, reducing, or inhibiting include a change of 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or greater as compared to a control level and such terms can include but do not necessarily include complete elimination.

[0103] As used herein the terms “diagnose” or “diagnosing” refers to recognition of an infection, disease or condition by signs and symptoms. Diagnosing can refer to determination of whether a subject has an infection or disease. Diagnosis may refer to determination of the type of disease or condition a subject has or the type of virus the subject is infected with.

[0104] Diagnostic agents provided herein include any such agent, which are well-known in the relevant art. Among imaging agents are fluorescent and luminescent substances, including, but not limited to, a variety of organic or inorganic small molecules commonly referred to as “dyes,” “labels,” or “indicators.” Examples include fluorescein, rhodamine, acridine dyes, Alexa dyes, and cyanine dyes. Enzymes that may be used as imaging agents in accordance with the embodiments of the disclosure include, but are not limited to, horseradish peroxidase, alkaline phosphatase, acid phosphatase, glucose oxidase, [3-galactosidase, [3- glucoronidase or [3-lactamase. Such enzymes may be used in combination with a chromogen, a Anorogenic compound or a luminogenic compound to generate a detectable signal.

[0105] The peptide(s) or protein(s) of the present invention can also be used in binding assays including, but are not limited to, immunoassays such as competitive and non-competitive assay systems using techniques such as western blots, radioimmunoassays, ELISA (enzyme linked immunosorbent assay), “sandwich” immunoassays, Meso Scale Discovery (MSD, Gaithersburg, Md.), immunoprecipitation assays, ELISPOT, precipitin reactions, gel diffusion precipitin reactions, immunodiffusion assays, agglutination assays, complement-fixation assays, immunoradiometric assays, Auorescent immunoassays, and protein A immunoassays. Such assays are routine and well known in the art (see, e.g., Ausubel et al., eds, 1994, Current Protocols in Molecular Biology, Vol. 1, John Wiley & Sons, Inc., New York, relevant portions incorporated herein by reference).

[0106] Radioactive substances that may be used as imaging agents in accordance with the embodiments of the disclosure include, but are not limited to,18F,32P,33P,45Ti,47Sc,52Fe,59Fe,62Cu,64Cu,67Cu,67Ga,68Ga,77As,86Y,90Y,89Sr,89Zr,94Tc,94Tc,99mTc, "Mo,105Pd,105Rh,i nAg,i nIn,123I,124I,125I,131I,142Pr,143Pr,149Pm,153Sm,154-1581Gd,161Tb,166Dy,166Ho,169Er,175Lu,177Lu,186Re,188Re,189Re,194Ir,198Au,199Au,211At,211Pb,212Bi,212Pb,213Bi,223Ra, and225Ac. Paramagnetic ions that may be used as additional imaging agents in accordance with the embodiments of the disclosure include, but are not limited to, ions of transition and lanthanide metals (e.g., metals having atomic numbers of 21-29, 42, 43, 44, or 57-71). These metals include ions of Cr, V, Mn, Fe, Co, Ni, Cu, La, Ce, Pr, Nd, Pm, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb and Lu.

[0107] When the imaging agent is a radioactive metal or paramagnetic ion, the agent may be reacted with another long-tailed reagent having a long tail with one or more chelating groups attached to the long tail for binding to these ions. The long tail may be a polymer such as a polylysine, polysaccharide, or other derivatized or derivatizable chain having pendant groups to which the metals or ions may be added forbinding. Examples of chelating groups that may be used according to the disclosure include, but are not limited to, ethylenediaminetetraacetic acid (EDTA), diethylenetriaminepentaacetic acid (DTP A), DOTA, NOTA, NETA, TETA, porphyrins, polyamines, crown ethers, bis-thiosemicarbazones, polyoximes, and like groups.

[0108] The terms “dose” and “dosage” are used interchangeably herein. A dose refers to the amount of active ingredient given to an individual at each administration. The dose will vary depending on a number of factors, including the range of normal doses for a given therapy, frequency of administration; size and tolerance of the individual; severity of the condition; risk of side effects; and the route of administration. One of skill will recognize that the dose can be modified depending on the above factors or based on therapeutic progress. The term “dosage form” refers to the particular format of the pharmaceutical or pharmaceutical composition, and depends on the route of administration. For example, a dosage form can be in a liquid form for nebulization, e.g., for inhalants, in a tablet or liquid, e.g., for oral delivery, or a saline solution, e.g., for injection.

[0109] As used herein, the term “administering” means oral administration, administration as a suppository, topical contact, intravenous, intraperitoneal, intramuscular, intralesional, intrathecal, intranasal or subcutaneous administration, or the implantation of a slow-re lease device, e.g., a mini -osmotic pump, to a subject. Administration is by any route, including parenteral and transmucosal (e.g., buccal, sublingual, palatal, gingival, nasal, vaginal, rectal, or transdermal). Parenteral administration includes, e.g., intravenous, intramuscular, intra-arteriole, intradermal, subcutaneous, intraperitoneal, intraventricular, and intracranial. Other modes of delivery include, but are not limited to, the use of liposomal formulations, intravenous infusion, transdermal patches, etc. By “co-administer” it is meant that a composition described herein is administered at the same time, just prior to, or just after the administration of one or more additional therapies, for example cancer therapies such as chemotherapy, hormonal therapy, radiotherapy, or immunotherapy. The compounds of the invention can be administered alone or can be co-administered to the patient. Co-administration is meant to include simultaneous or sequential administration of the compounds individually or in combination (more than one compound). Thus, the preparations can also be combined, when desired, with other active substances (e.g., to reduce metabolic degradation). The compositions of the present invention can be delivered by transdermally, by a topical route, formulated as applicator sticks, solutions, suspensions, emulsions, gels, creams, ointments, pastes, jellies, paints, powders, and aerosols.

[0110] Formulations suitable for oral administration can consist of (a) liquid solutions, such as an effective amount of the antibodies provided herein suspended in diluents, such as water, saline or PEG 400; (b) capsules, sachets or tablets, each containing a predetermined amount of the active ingredient, as liquids, solids, granules or gelatin; (c) suspensions in an appropriate liquid; and (d) suitable emulsions. Tablet forms can include one or more of lactose, sucrose, mannitol, sorbitol, calcium phosphates, com starch, potato starch, microcrystalline cellulose, gelatin, colloidal silicon dioxide, talc, magnesium stearate, stearic acid, and other excipients, colorants, fillers, binders, diluents, buffering agents, moistening agents, preservatives,flavoring agents, dyes, disintegrating agents, and pharmaceutically compatible carriers. Lozenge forms can comprise the active ingredient in a flavor, e.g., sucrose, as well as pastilles comprising the active ingredient in an inert base, such as gelatin and glycerin or sucrose and acacia emulsions, gels, and the like containing, in addition to the active ingredient, carriers known in the art.

[0111] Pharmaceutical compositions can also include large, slowly metabolized macromolecules such as proteins, polysaccharides such as chitosan, polylactic acids, polyglycolic acids and copolymers (such as latex functionalized sepharose (TM), agarose, cellulose, and the like), polymeric amino acids, amino acid copolymers, and lipid aggregates (such as oil droplets or liposomes). Additionally, these carriers can function as immunostimulating agents (z.e., adjuvants).

[0112] The term “adjuvant” refers to a compound that when administered in conjunction with the compositions provided herein including embodiments thereof, augments the composition’s immune response. Generally, adjuvants are non-toxic, have high-purity, are degradable, and are stable.

[0113] Adjuvants can augment an immune response by several mechanisms including lymphocyte recruitment, stimulation of B and / or T cells, and stimulation of macrophages. The adjuvant increases the titer of induced antibodies and / or the binding affinity of induced antibodies relative to the situation if the immunogen were used alone. A variety of adjuvants can be used in combination with the agents provided herein including embodiments thereof, to elicit an immune response. Preferred adjuvants augment the intrinsic response to an immunogen without causing conformational changes in the immunogen that affect the qualitative form of the response. Preferred adjuvants include aluminum hydroxide and aluminum phosphate, 3 De-O-acylated monophosphoryl lipid A (MPL™) see GB 2220211 (RIBI ImmunoChem Research Inc., Hamilton, Montana, now part of Corixa). Stimulon™ QS-21 is a triterpene glycoside or saponin isolated from the bark of the Quillaja Saponaria Molina tree found in South America (see Kensil el al., in Vaccine Design: The Subunit and Adjuvant Approach (eds. Powell & Newman, Plenum Press, NY, 1995); US Patent No. 5,057,540), (Aquila BioPharmaceuticals, Framingham, MA). Other adjuvants are oil in water emulsions (such as squalene or peanut oil), optionally in combination with immune stimulants, such as monophosphoryl lipid A (see Stoute etal., N. Engl. J. Med. 336, 86-91 (1997)), pluronic polymers, and killed mycobacteria. Another adjuvant is CpG (WO 98 / 40100). Adjuvants can be administered as a component of a therapeutic composition with an active agent or can be administered separately, before, concurrently with, or after administration of the therapeutic agent.

[0114] Other adjuvants contemplated for the invention are saponin adjuvants, such as Stimulon™ (QS-21, Aquila, Framingham, MA) or particles generated therefrom such as ISCOMs (immunostimulating complexes) and ISCOMATRIX. Other adjuvants include RC-529, GM-CSF and Complete Freund’s Adjuvant (CFA) and Incomplete Freund’s Adjuvant (IF A). Other adjuvants include cytokines, such as interleukins (e.g., IL-1 a and [3 peptides, IL-2, IL-4, IL-6, IL-12, IL-13, and IL-15), macrophage colony stimulating factor (M-CSF), granulocyte -macrophage colony stimulating factor (GM-CSF), tumor necrosis factor (TNF), chemokines, such as MIPloc and [3 and RANTES. Another class of adjuvants is glycolipidanalogues including N-glycosylamides, N-glycosylureas and N-glycosylcarbamates, each of which is substituted in the sugar residue by an amino acid, as immuno-modulators or adjuvants (see US Pat. No. 4,855,283). Heat shock proteins, e.g., HSP70 and HSP90, may also be used as adjuvants.

[0115] Suitable formulations for rectal administration include, for example, suppositories, which consist of the packaged nucleic acid with a suppository base. Suitable suppository bases include natural or synthetic triglycerides or paraffin hydrocarbons. In addition, it is also possible to use gelatin rectal capsules which consist of a combination of the compound of choice with a base, including, for example, liquid triglycerides, polyethylene glycols, and paraffin hydrocarbons.

[0116] Formulations suitable for parenteral administration, such as, for example, by intraarticular (in the joints), intravenous, intramuscular, intratumoral, intradermal, intraperitoneal, and subcutaneous routes, include aqueous and non-aqueous, isotonic sterile injection solutions, which can contain antioxidants, buffers, bacteriostats, and solutes that render the formulation isotonic with the blood of the intended recipient, and aqueous and non-aqueous sterile suspensions that can include suspending agents, solubilizers, thickening agents, stabilizers, and preservatives. In the practice of this invention, compositions can be administered, for example, by intravenous infusion, orally, topically, intraperitoneally, intravesically or intrathecally. Parenteral administration, oral administration, and intravenous administration are the preferred methods of administration. The formulations of compounds can be presented in unit-dose or multi-dose sealed containers, such as ampules and vials.

[0117] Injection solutions and suspensions can be prepared from sterile powders, granules, and tablets of the kind previously described. Cells transduced by nucleic acids for ex vivo therapy can also be administered intravenously or parenterally as described above.

[0118] The pharmaceutical preparation is preferably in unit dosage form. In such form the preparation is subdivided into unit doses containing appropriate quantities of the active component. The unit dosage form can be a packaged preparation, the package containing discrete quantities of preparation, such as packeted tablets, capsules, and powders in vials or ampoules. Also, the unit dosage form can be a capsule, tablet, cachet, or lozenge itself, or it can be the appropriate number of any of these in packaged form. The composition can, if desired, also contain other compatible therapeutic agents.

[0119] The combined administration contemplates co-administration, using separate formulations or a single pharmaceutical formulation, and consecutive administration in either order, wherein preferably there is a time period while both (or all) active agents simultaneously exert their biological activities.

[0120] Effective doses of the compositions provided herein vary depending upon many different factors, including means of administration, target site, physiological state of the patient, whether the patient is human or an animal, other medications administered, and whether treatment is prophylactic or therapeutic. However, a person of ordinary skill in the art would immediately recognize appropriate and / or equivalent doses looking at dosages of approved compositions for treating and preventing cancer for guidance.

[0121] As used herein, the term “pharmaceutically acceptable” is used synonymously with “physiologically acceptable” and “pharmacologically acceptable”. A pharmaceutical composition will generally comprise agents for buffering and preservation in storage, and can include buffers and carriers for appropriate delivery, depending on the route of administration. As used herein, the terms “pharmaceutically acceptable” or “pharmacologically acceptable” refer to a material which is not biologically or otherwise undesirable, i.e., the material may be administered to an individual in a formulation or composition without causing any unacceptable biological effects or interacting in a deleterious manner with any of the components of the composition in which it is contained.

[0122] “Pharmaceutically acceptable excipient” and “pharmaceutically acceptable carrier” refer to a substance that aids the administration of an active agent to and absorption by a subject and can be included in the compositions of the present invention without causing a significant adverse toxicological effect on the patient. Non-limiting examples of pharmaceutically acceptable excipients include water, NaCl, normal saline solutions, lactated Ringer’s, normal sucrose, normal glucose, binders, fillers, disintegrants, lubricants, coatings, sweeteners, flavors, salt solutions (such as Ringer’s solution), alcohols, oils, gelatins, carbohydrates such as lactose, amylose or starch, fatty acid esters, hydroxymethycellulose, polyvinyl pyrrolidine, and colors, and the like. Such preparations can be sterilized and, if desired, mixed with auxiliary agents such as lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, coloring, and / or aromatic substances, and the like., that do not deleteriously react with the compounds of the invention. One of skill in the art will recognize that other pharmaceutical excipients are useful in the present invention.

[0123] The term “pharmaceutically acceptable salt” refers to salts derived from a variety of organic and inorganic counter ions well known in the art and include, by way of example only, sodium, potassium, calcium, magnesium, ammonium, tetraalkylammonium, and the like; and when the molecule contains a basic functionality, salts of organic or inorganic acids, such as hydrochloride, hydrobromide, tartrate, mesylate, acetate, maleate, oxalate and the like.

[0124] The term “preparation” is intended to include the formulation of the active compound with encapsulating material as a carrier providing a capsule in which the active component with or without other carriers, is surrounded by a carrier, which is thus in association with it. Similarly, cachets and lozenges are included. Tablets, powders, capsules, pills, cachets, and lozenges can be used as solid dosage forms suitable for oral administration.

[0125] The pharmaceutical preparation is optionally in unit dosage form. In such form the preparation is subdivided into unit doses containing appropriate quantities of the active component. The unit dosage form can be a packaged preparation, the package containing discrete quantities of preparation, such as packeted tablets, capsules, and powders in vials or ampoules. Also, the unit dosage form can be a capsule, tablet, cachet, or lozenge itself, or it can be the appropriate number of any of these in packaged form. The unit dosage form can be of a frozen dispersion.

[0126] The compositions of the present invention may additionally include components to provide sustained release and / or comfort. Such components include high molecular weight, anionic mucomimetic polymers, gelling polysaccharides and finely-divided drug carrier substrates. These components are discussed in greater detail in U.S. Pat. Nos. 4,911,920; 5,403,841; 5,212,162; and 4,861,760. The entire contents of these patents are incorporated herein by reference in their entirety for all purposes. The compositions of the present invention can also be delivered as microspheres for slow release in the body. For example, microspheres can be administered via intradermal injection of drug-containing microspheres, which slowly release subcutaneously (see Rao, J. Biomater Sci. Polym. Ed. 7:623-645, 1995; as biodegradable and injectable gel formulations (see, e.g., Gao Pharm. Res. 12:857-863, 1995); or, as microspheres for oral administration (see, e.g., Eyles, J. Pharm. Pharmacol. 49:669-674, 1997). In embodiments, the formulations of the compositions of the present invention can be delivered by the use of liposomes which fuse with the cellular membrane or are endocytosed, i.e., by employing receptor ligands attached to the liposome, that bind to surface membrane protein receptors of the cell resulting in endocytosis. By using liposomes, particularly where the liposome surface carries receptor ligands specific for target cells, or are otherwise preferentially directed to a specific organ, one can focus the delivery of the compositions of the present invention into the target cells in vivo. (See, e.g., Al -Muhammed, J. Microencapsul. 13:293-306, 1996; Chonn, Curr. Opin. Biotechnol. 6:698-708, 1995; Ostro, Am. J. Hosp. Pharm. 46: 1576-1587, 1989). The compositions of the present invention can also be delivered as nanoparticles.

[0127] The present invention describes methods utilizing and compositions comprising or expressing T cell epitopes, T cell epitope-containing peptides, and T cell epitope-containing proteins associated with binding to a subset of the naturally occurring MHC Class II and / or MHC Class I molecules within the human population. Compositions comprising or expressing one or more of the disclosed peptides (e.g., the amino acid sequences set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5) or polynucleotides encoding the same, covering different HLA Class II and / or MHC Class I alleles, capable of generating a treatment acting broadly on a population level are disclosed herein. As the antigen repertoire of MHC Class I and MHC Class II alleles varies from one individual to another and from one ethnic population to another, it is challenging to provide vaccines or peptide or epitopes-based immunotherapies that can be offered to subjects of any geographic region in the world or provide sufficient protection against infection across a wide segment of the populations unless numerous epitopes or peptides are included (e.g., in a vaccine). Taking into consideration the need for a single vaccine formulation that can provide protection across populations, if it desirable to provide a treatment containing or expressing proteins, peptides or epitopes that will provide protection against infection amongst the majority of the worldwide population. Also, taking into consideration the enormous costs and risks in the clinical development of new treatments and the increasing demands from regulatory bodies to meet high standards for toxicity testing, dose justification, safety and efficacy trials, it is desirable to provide treatments containing or expressing as few peptides as possible, but at the same time to be able to treat the majority of subjects in a worldwidepopulation with a single immunotherapy. Such a product should comprise as a first requirement an expression or inclusion of combination of epitopes or peptides that are able to bind the worldwide MHC Class I and / or MHC Class II allele repertoire, and the resulting peptide-MHC complexes should as a second requirement be recognized by the T cells of the subject so as to induce the desired immunological reactions.

[0128] It is an object of claims of the present invention to provide improved epitope or peptide combinations for modulating an immune response, for treating a subject for an infection or aberrant immune response, and for use in diagnostic methods and kits comprising such peptide combinations. It is another object of the invention to provide epitope or peptide combinations exhibiting very good HLA Class I and Class II coverage in a worldwide population and being immunologically potent in a worldwide population. It is another object of the invention to provide epitope or peptide combinations having good cross reactivity to other strains, including co-circulating strains (for example, mutants) of Influenza, including H5N1, etc. It is another object of the invention to provide epitope or peptide combinations of a relatively small number of epitopes or peptides yet obtaining at least 70%, and more preferably around 90- 100% donor coverage in a donor cohort representative of a worldwide population. In certain embodiments, this is achieved by selecting one or more immunodominant and / or immunoprevalent proteins (e.g., an influenza viral protein) or subsequences, portions, homologues, variants or derivatives thereof for use in the methods and compositions of the present disclosure, wherein said immunodominant and / or immunoprevalent proteins or subsequences, portions, homologues, variants or derivatives thereof comprise two or more epitopes that are immunodominant and / or immunoprevalant. In some embodiments, the two or more epitopes comprise two to ten epitopes and / or polynucleotides encoding the same. Another object of the invention is to provide epitope combinations which are so immunologically potent that even at very low doses of epitopes, the percentage of responding donors can be retained at a very high level in a donor cohort representative of a worldwide population. Another object of the invention is to provide epitope combinations which have minor risk of inducing IgE-mediated adverse events. An additional object of the invention is to provide proteins, peptides, or nucleic acids containing or expressing epitopes or combinations of such proteins, peptides or nucleic acids which have a sufficient solubility profile for being formulated in a pharmaceutical product, preferably which have acceptable estimated in vivo stability. One further objective of the invention is to select epitopes for use in the compositions and methods described herein, based on one or both of their immunodominance or immunoprevalence. A still further object of the invention is to select such epitopes and epitopes combinations not only in accordance with those embodiments previously described, but also those epitopes and epitope combinations capable of eliciting a B cell response and T cell response (e.g., selecting one or more peptides for use in the methods and compositions described herein capable of generating a T cell and antibody response in a subject).

[0129] Provided herein are methods and compositions for diagnosing, treating, and immunizing against influenza, including methods and compositions of detecting an immune response or immune cells relevant to an influenza infection. These methods and compositions include vaccines, diagnostics, therapies, reagents and kits, for modulating, eliciting, or detecting T cells responsive to one or more Influenzapeptides or proteins. The proteins and peptides described herein comprise, consist of, or consist essentially of: one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof; a fusion protein comprising one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; a pool of 2 or more peptides selected from the amino acid sequences set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a polynucleotide that encodes one or more peptides or proteins, comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof. In certain preferred embodiments, the Influenza is one or more of H5N 1 or a variant thereof. Further description and embodiments of such methods and compositions are provided in the definitions provided herein, and a person skilled in the art will recognize that the methods and compositions can be embodied in numerous variations, changes, and substitutions or as may occur to or be understood by one skilled in the art without departing from the invention.

[0130] Example 1: Immunodominance hierarchy of H5N 1 epitopes.

[0131] An analysis of human humoral and cellular response data curated in the Immune Epitope Database (IEDB36) was performed, specifically for epitopes in HP Al of the H5N1 subtype.

[0132] As a first step, the inventors queried the IEDB to retrieve H5N1 epitope data by specifying as organism the H5N1 subtype (H5N1) (organism ID: 102793, H5N1), and selecting positive assays only. Three independent queries were performed to separately retrieve B cell (B cell assay data only), CD4 T cell (MHC restriction type: class II) or CD8 T cell (MHC restriction type: class I) restricted epitopes. Combined, these three queries retrieved a total of 486 epitopes derived from over 2,000 different assays reported in 139 peer-reviewed reports and submissions (as of May 2024). Of those, 298 were associated with responses in a human host, 190 in a murine host, and 15 in other species, including dogs and chickens. (The number of epitopes does not reflect the sum of the epitopes, as some epitopes have been identified in multiple species.) Out of these, 74 epitopes were associated with CD8 T cell responses, 202 with CD4 T cell responses and 210 with B cell / antibody responses.

[0133] The inventors next investigated the immunodominance hierarchy of B cell, and CD4 and CD8 T cell responses as a function of the viral antigens. FIG. 1A summarizes the three types of responses as a function of each influenza virus antigen and lists the relative percentage of epitopes to address the most immunodominant antigens recognized.

[0134] In terms ofB cell responses, the majority of the 210 epitopes were derived from HA (74.8%; 70.5% as a monomer and 4.3% as tertiary / quatemary epitopes on the trimer), followed by M2 (11%), NA and NS 1 (3.3% each). The NP, PB1-F2, PB1, Ml, PB2, NEP, and PA antigens made up for the remaining 10.9% of B cell epitopes. In terms of CD4 T cell / class Il-restricted responses, the majority of the 202 epitopes were derived from HA (48%), followed by NP (21.8%), Ml (13.9%), and NA (8.4%). The PB1, M2, NS1, NEP, and PB2 antigens made up for the remaining 8.5% of the CD4 T cell epitopes. For CD8 T cell / class I-restricted responses, the majority of the 74 epitopes were derived from NP (45.9%), followed by Ml(12.2%), PB1 (10.8%), PA (9.5%), and PB2 (6.8%). The HA, NS1, and M2 antigens made up for the remaining 14.9% of the CD8 T cell epitopes. In conclusion, different patterns of immunodominance as a function of adaptive responses were observed. More specifically, the surface-exposed HA antigen was dominant in terms of B and CD4 T cell targets, even though this should be interpreted with caution because research is biased towards mostly focusing on HA. In general, very few NA mAbs have been characterized. Furthermore, the internal NP antigen was a dominant target of CD8 T cell responses.

[0135] Example 2: Immunodominance pattern between H5N1 and H1N1, H3N2, and H2N2.

[0136] Estimating the potential impact of a widespread H5N1 outbreak requires understanding the extent to which pre-existing immunity originating from prior vaccinations and infections cross-reacts to H5N 1. Accordingly, the inventors surveyed the IEDB and extracted B cell, and CD4 and CD8 T cell epitope data pertaining to the influenza H1N1, including pre-pandemic seasonal H1N1 and 2009 pandemic H1N1 (Organism ID: 114727), H3N2 (Organism ID: 119210) and H2N2 (Organism ID: 114729) subtypes, which have historically circulated in humans38’39, and for which immune memory is therefore expected to be prevalent. As expected, more data was available compared to H5N1, which allowed us to restrict the query to human epitope data and still obtain enough data for meaningful analysis.

[0137] Using the assay search panel to fdter by the type of experiment performed returned a total of 2,245 human epitopes. Of these, 973 epitopes were associated with T cell assays (171 CD8 and 676 CD4 and the remaining non-assigned) and 366 with B cell / antibody assays; 1,112 epitopes have been characterized for MHC binding capacity on the basis of the use of purified MHC (662), peptide elution assays (498), or X- ray structures (29). As mentioned above, the number of total epitopes does not reflect the sum of the epitopes in each category, because some epitopes were associated with multiple categories.

[0138] The data was inspected for patterns of B cell, and CD4 and CD8 T cell immunodominance as a function of viral antigen and compared to the H5N 1 data shown above. The inventors plotted the % of epitopes derived from each antigen and recognized in H5N1 versus H1N1, H3N2, and H2N2 influenza virus for CD4 and CD8 T cell responses (FIGS. 2A, 2B).

[0139] T cell responses targeted a varied number of antigens, thus allowing to test for similarity in the pattern of antigenic immunodominance at the T cell level. For both CD4 ( 0.878. p 0.0007). and CD8 (R=0.940, p<0.0001) T cells, the results revealed a high degree of correlation in immunodominance patterns between HP Al H5N 1 and seasonal IAV (FIGS. 2A, 2B). In the context of B cell responses, in both cases most of the data is associated with HA, and the number of reported epitopes for other antigens is minimal (FIG. 1A), rendering a correlation analysis statistically unmeaningful. Nevertheless, antibody responses in HP Al H5N 1 and seasonal IAV are similar in terms of predominantly targeting the HA antigen, even though this is likely to at least in part reflect research bias. Overall, this indicates a fundamental similarity between the antigen specificity of T and B cell immune responses across IAV strains.

[0140] Example 3: H1N1, H3N2, and H2N2 epitope conservation across recent H5N1 isolates.

[0141] Several studies in different virus families, including coronaviruses and flaviviruses, demonstrated that cross-reactivity at the T cell level is predictable based on sequence similarity40-43. A threshold of 67% homology was experimentally demonstrated as being associated with cross-reactivity for CD4 T cells40,41 43. and a threshold of 80% homology was experimentally demonstrated as being associated with crossreactivity for CD8 T cells42. In contrast, cross-reactivity at the antibody level between different viral antigens is in general sensitive to both sequence variation and conformational changes, and therefore is in general more difficult to predict.

[0142] To study the potential for cross-reactivity between seasonal IAV - and HP Al H5N 1 -specific immune responses, the inventors queried the IEDB for the most dominant (frequently recognized) human antibody, and CD4 and CD8 T cell epitopes derived from H1N1, H2N2 and H3N2 subtypes. Only linear epitopes were considered, since no tool is currently available to easily allow for conservation analysis of discontinuous epitopes, and this search was limited to identifying only epitopes associated with positive responses in humans. CD4 T cell, CD8 T cell, and antibody epitopes were analyzed separately. In all, this corresponded to a total of 33 possible response type / antigen combinations (3 types of epitopes X 11 antigens). For each combination, the inventors used the ImmunomeBrowser to download the associated epitope data. The inventors further fdtered for canonical size in the case of T cell epitopes, considering 8- 11 residues for CD8, and 12-25 for CD4; no size fdter was applied for antibody epitopes. Epitopes with reported positive responses in at least 2 subjects and associated with an overall Response Frequency (RF) value of 0.1 or greater44were defined as dominant. The results, identified a list of 224 CD4 epitopes, 64 CD8 epitopes, and 94 B cell epitopes.

[0143] Next, utilizing the sequence conservation tool provided in the IEDB Analysis Resource (IEDB- AR45), the inventors examined the degree of sequence conservation of these human seasonal IAV dominant epitopes in the HP Al H5N 1 isolate A / Anhui / 1 / 2005 H5N 1 , taken as a prototype HPAI of the H5N 1 subtype genome. The results indicate that 9.8% of CD4 and 32.8% CD8 epitopes were fully conserved (100% sequence identity). By contrast, only one (1.1%) of the B cell epitopes was fully conserved. Furthermore, it was noted in total 56.7% of CD4 and 62.5% CD8 T cell epitopes are conserved above the 67% and 80% sequence identity thresholds associated with experimentally verified cross-reactivity for CD4 and CD8 T cell responses, respectively40-43. The inventors also analyzed conservation in 6 different recent clade 2.3.4.4b H5N1 isolates from the Americas from several animal species during the 2023-2024 period and noted an overall similar level of conservation. These virus isolates represent 5 genotypes and include the B3. 13 genotype that currently circulating in dairy cattle and causing concern over its pandemic potential.

[0144] The inventors next determined if the level of conservation between the prototype strain (from 2005) and across the more recent clade 2.3.4.4b H5N1 isolates / genotypes was different and decreased, which would raise concerns on the ability of the immune system primed with circulating IAV to cross-recognize the avian ones if exposed. Notably, the average conservation was similar or even significantly increased as compared to the prototype (FIGS. 1B-1D).

[0145] In general, it is appreciated that the targets of humoral and cellular immune responses only partially overlap. In the case of influenza virus, antibody responses target the more variable and surface-accessible HA and NA antigens. In the case of clade 2.3.4.4b H5N1, based on the sequence similarity of the N1 component, extensive cross-reactivity at the level of antibody response is expected. There is data to support this notion10 11. The IEDB only reports defined epitopes and there are reports describing at least four different supersites (HA central stalk, HA anchor, active site of NA, sialic acid binding site of HA) that are targeted by HA and NA cross-reactive antibodies. Furthermore, it is also expected that anti-HA stalk antibodies induced by H1N1 will cross-react to clade 2.3 ,4.4b H5 HA since they were detectible in humans against clade 2.3.4.4 H5 HA dependent on age and exposure history13. However, the globular head domain of HA (which is the main target of neutralizing antibodies) is very plastic and the H5 head domain differs drastically from Hl or H3 head domains. By contrast, a significant fraction of T cell responses target virion and non-structural antigens, which are significantly more conserved, thus contributing to a higher potential for cross-reactivity of T cell responses. These mechanisms are also exemplified by the SARS-CoV-2 pandemic; sequence variation often led to escape from antibodies, but this was not observed in the context of T cell recognition46-53.

[0146] Example 4: T cell immune responses against the human seasonal IAV dominant epitopes and their HPAI H5N1 counterparts.

[0147] To further evaluate the biological significance of the conservation of epitopes from H1N1, H2N2, and H3N2 (non-avian human strains) the inventors synthesized the dominant T cell epitopes identified in humans and their corresponding HP Al H5N1 isolate A / Anhui / 1 / 2005 H5N1 peptides. These peptides were then pooled in four different MegaPools (MPs)54corresponding to human and avian CD4 or CD8 MPs. These newly designed pools were used to measure CD4+ and CD8+ T cell responses using PBMCs from 20 healthy controls (HC) collected from Oct 2021 to July 2022. The results in FIGS. 3A TO 3G show significant reactivity against the human non-avian MPs using T cells derived from these donors. When antigen-specific responses of the human non-avian MPs were compared to the avian MPs, in the case of CD4+AIM+, CD4+GranzymeB+ and CD4+IFN-y+ T cell responses (FIG. 3A-3C) no significant differences between non-avian and avian CD4 MPs were noted (CD4+AIM+, p=0.3385, ratio=0.886; CD4+GranzymeB+, p=0.4423, ratio=0.7818; CD4+IFN-y+, p=0.9515, ratio=9463).

[0148] Because of the lower sensitivity of the AIM assays in detecting CD8+ responses, the inventors focused on CD8+GranzymeB+ and CD8+IFN-y+ T cell responses. No significant differences were observed between non-avian and avian CD8 MPs (CD8+GranzymeB+; p=0.3125, ratio=0.726; CD8+IFN- y+, p=0.2969, ratio=0.7141) (FIG. 3D-3E) despite the relatively low level of responses likely due to the limited number of epitopes in the MPs. Better overall responses were seen when the CD4 MPs, which spanned a large fraction of IAV genome and a larger number of peptides, were used to detect CD8 T cell responses (CD8+GranzymeB+; p=0.5897, ratio=0.8325; CD8+IFN-y+, p=0.8999, ratio=0.8741) (FIG. 3F- 3G). Overall, these data demonstrate that the existing lAV-specific T cell responses are largely preserved when in terms of recognition of the corresponding HP Al H5N1 sequences.

[0149] Materials and Methods: Querying influenza epitopes in IEDB database. B cell (antibody), and CD4 (Class II) and CD8 (Class I) T cell, epitopes were extracted from the IEDB database (www.IEDB.org)36on May 7th, 2024, using the following organisms: influenza H1N1 (Organism ID: 114727), H3N2 (Organism ID: 119210), H2N2 (Organism ID: 114729), or H5N1 (Organism ID: 102793). The query included positive assays only, with the host specified as Human. Separate queries were performed for T cell Class I and Class II epitopes by selecting either MHC restriction type Class I for CD8 epitopes or Class II for CD4 epitopes. CD8 and CD4 epitopes were further filtered on size criteria, to include only lengths of 8-11 or 12-25 residues, respectively, to comport with canonical epitopes sizes. B cell epitopes were also queried separately, with no size criteria implemented. The data reported and curated in the IEDB does not consistently identify clades, thus the granularity of the analysis was limited to the H5N 1 subtype level; and the H1N1, H3N2, H2N2 subtype and human host level.

[0150] Conservation analyses. Conservation analyses were performed using the Conservation tool available in the IEDB Analysis Resource (IEDB-AR)74for non-avian epitopes based on the IEDB epitope query for H1N1, H3N2 and H2N2, as listed in Table SI. The epitopes were divided into the different influenza antigens and ran separately against the 2005 prototype HP Al H5N 1 isolate EPI ISL 24603 and six different isolates collected in 2023-2024 (EPI_ISL_18731617; EPI_ISL_1909448;EPI ISL 19094639; EPI ISL 18945317; EPI ISL 17964970; EPI ISL 19151399). The resulting conservancy values were then compiled to count the number of epitopes meeting specified thresholds of conservation (100%, >80% and >67%), mirroring cutoffs previously validated experimentally to predict cross-reactivity for CD84275and CD440’41’43, respectively.

[0151] Preparation of peptide pools. Based on conservation analyses, the inventors synthesized sets of CD4 (n=224, non-avian CD4) and CD8 (n=64, non-avian CD8) epitopes from non-avian strains, as well as the corresponding CD4 (n=219, avian CD4) and CD8 (n=40, avian CD8) epitopes from avian strains, excluding duplicate peptides. The synthesized peptides were individually resuspended in dimethyl sulfoxide (DMSO; Sigma) at a concentration of 20 mg / ml. Subsequently, the peptides were pooled, lyophilized, and resuspended at a final concentration of 1 mg / ml in DMSO.

[0152] Human subjects and peripheral blood mononuclear cells (PBMC) isolation. Blood samples, leftover from a previous research study and eligible to be used for the current study, were utilized from healthy adult donors (n=20) obtained from the La Jolla Institute for Immunology Clinical Core in San Diego, California (under IRB protocol VD-101). Donors were 22-61 years old (median 38), consisting of 65% females and 35% males. The cohort was 75% White / not Hispanic or Latino, 5% Asian, and 20% more than one race. The samples were collected between October 2021 and July 2022. Whole blood was drawn into heparin-coated blood bags and processed according to a previously established protocol76. PBMCs were isolated and cryopreserved in cell recovery media containing 10% DMSO, supplemented with 10% heat- inactivated fetal bovine serum (FBS; Hyclone Laboratories, Logan, UT). The cryopreserved PBMCs were then stored in liquid nitrogen until used in subsequent assays.

[0153] Activation-induced markers (AIM) and intracellular cytokine staining (ICS) assay. The samples were tested using a combined AIM and ICS (AIM / ICS) assay, as previously described76. Briefly, cryopreserved PBMCs were thawed in RPMI 1640 media supplemented with 5% human AB serum (Gemini Bioproduct) and benzonase (20 pl / 10ml, EMD Milipore Corp). A total of 2xl06cells per well in 96-well U-bottom plates (GenClone) were stimulated for 24 hours in the presence of non-avian and avian MPs (1 pg / ml). Equimolar amounts of DMSO were used in quadruplicate as a negative control, while phytohemagglutinin (PHA; 1 pg / ml, Roche) was used as a positive control.

[0154] After 20h of incubation at 37°C, 5% CO2, cells were incubated in the presence of Golgi Plug (Brefeldin A) and Golgi Stop (Monensin) (both BD Bioscience) for an additional 4h to allow the accumulation of intracellular cytokines and CD137 APC (1: 100; Biolegend, clone 4B4-1, Cat# 309810) to prevent re-intemalization.

[0155] After 24 hours of cumulative stimulation, membrane staining was conducted for 30 min at 4°C using the following antibodies: CD8 BUV496 (2: 100; BD Biosciences; clone RPA-T8; Cat# 612942), CD4 Brilliant Violet (BV) 605 (2: 100; BD Biosciences; clone RPA-T4; Cat# 562658), and CD3 Alexa Fluor 700 (1: 100; eBioscience; clone UCHT1; Cat# 56-0038-42). LIVE / DEAD Fixable NIR stain APC-ef780 (0.05: 100; Invitrogen; Cat# L34975) was used to mark viable cells. CD 14 APC-ef780 (1: 100; clone 61D3; eBioscience; Cat# 47-0419-42) and CD19 APC-ef780 (1: 100; eBioscience; clone HIB19; Cat# 47-0199- 42) were both used to exclude monocytes and B cells in the dump channel. For AIM-specific T cell identification, CD 137 APC (2: 100) and CD69 BV786 (1: 100; BD Biosciences; clone FN50; Cat# 563834) were used for CD8+ T cells, while CD137 APC (2: 100) and 0X40 PE-Cy7 (2: 100; Biolegend; clone Ber- ACT35; Cat# 350012) were used for CD4+ T cells.

[0156] Next, cells were fixed with 4% paraformaldehyde (PFA) solution for 10 min at 4°C, followed by permeabilization with saponin buffer and blocking with 10% human AB serum. ICS was performed for 30 min at 4°C with antibodies detecting cytokines, including IFN-y FITC (1: 100; Invitrogen; clone 4S.B3; Cat# 11-7319-82) and Granzyme B PE (1: 100; Invitrogen; clone GB11; Cat# 12-8899-41). The cells were washed with PBS, resuspended in 120pL of PBS per well, and acquired by a ZE5 cell analyzer (Bio-Rad laboratories). Raw FCS files were analyzed with FlowJo software (Tree Star).

[0157] Quantification and statistical analyses. Correlation analyses were performed by Spearman correlation; r and two-tailed p values are listed in each Figure. Conservancy analysis comparing prototype H5N1 isolate and six more recent H5N1 isolates was performed by one sample T-test. Fold-Change conservancy is calculated by dividing the average conservation for the six isolates by the prototype isolate.

[0158] The frequencies of non-avian and avian MP-specific T cells were determined using AIM and CD137+ICS gating strategies. The percentages of the quadruplicate DMSO wells were averaged, and this background was subtracted from each MP-stimulated population. The stimulation index (SI) was calculated by dividing the percentage of positive cells after MP stimulation by averaged DMSO background. For each gated population, the Limit of Detection (LOD) was determined by the two-fold lower confidence interval (CI) of the geometric mean, and the Limit of Sensitivity (LOS) was based on the median plus two-foldstandard deviation (SD) of T cell reactivity in the DMSO wells. A response was considered positive if the DMSO background-subtracted value was greater than the LOS and the SI was greater than 2. Data and statistical analyses were performed in FlowJo 10 and Graphpad Prism 10.2. The comparisons are performed by paired Wilcoxon test and the significance of the ratio is analyzed by one-sample Wilcoxon test compared with a hypothetical medina of 1. The ratios between non-avian and avian MPs-specific responses are calculated if either value is above the LOS.

[0159] Table 1: Dominant non-avian influenza A epitopes.

[0160] Table 2: Avian CD4

[0161] Table 3: Avian CD8

[0162] Table 4: Non-Avian CD4

[0163] Table 5: Non-Avian CD8

[0164] It is contemplated that any aspects of the disclosure discussed in this specification can be implemented with respect to any method, kit, reagent, or composition of the disclosure, and vice versa. Furthermore, compositions of the disclosure can be used to achieve methods of the disclosure.

[0165] It will be understood that particular aspects described herein are shown by way of illustration and not as limitations of the disclosure. The principal features of this disclosure can be employed in various aspects without departing from the scope of the disclosure. Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, numerous equivalents to the specific procedures described herein. Such equivalents are considered to be within the scope of this disclosure and are covered by the claims.

[0166] All publications and patent applications mentioned in the specification are indicative of the level of skill of those skilled in the art to which this disclosure pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.

[0167] The use of the word “a” or “an” when used in conjunction with the term “comprising” in the claims and / or the specification may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one,” and “one or more than one.” The use of the term “or” in the claims is used to mean “and / or” unless explicitly indicated to refer to alternatives only or the alternatives are mutually exclusive, although the disclosure supports a definition that refers to only alternatives and “and / or.” Throughout this application, the term “about” is used to indicate that a value includes the inherent variation of error for the device, the method being employed to determine the value, or the variation that exists among the study subjects.

[0168] As used in this specification and claim(s), the words “comprising” (and any form of comprising, such as “comprise” and “comprises”), “having” (and any form of having, such as “have” and “has”), “including” (and any form of including, such as “includes” and “include”) or “containing” (and any form of containing, such as “contains” and “contain”) are inclusive or open-ended and do not exclude additional, unrecited elements or method steps. In aspects of any of the compositions and methods provided herein, “comprising” may be replaced with “consisting essentially of’ or “consisting of’. As used herein, the phrase “consisting essentially of’ requires the specified integer(s) or steps as well as those that do not materially affect the character or function of the claimed invention. As used herein, the term “consisting” is used to indicate the presence of the recited integer (e.g., a feature, an element, a characteristic, a property, a method / process step or a limitation) or group of integers (e.g., feature(s), element(s), characteristic(s), propertie(s), method / process steps or limitation(s)) only.

[0169] The term “or combinations thereof’ as used herein refers to all permutations and combinations of the listed items preceding the term. For example, “A, B, C, or combinations thereof’ is intended to includeat least one of: A, B, C, AB, AC, BC, or ABC, and if order is important in a particular context, also BA, CA, CB, CBA, BCA, ACB, BAC, or CAB. Continuing with this example, expressly included are combinations that contain repeats of one or more item or term, such as BB, AAA, AB, BBC, AAABCCCC, CBBAAA, CABABB, and so forth. The skilled artisan will understand that typically there is no limit on the number of items or terms in any combination, unless otherwise apparent from the context.

[0170] As used herein, words of approximation such as, without limitation, “about”, "substantial" or "substantially" refers to a condition that when so modified is understood to not necessarily be absolute or perfect but would be considered close enough to those of ordinary skill in the art to warrant designating the condition as being present. The extent to which the description may vary will depend on how great a change can be instituted and still have one of ordinary skilled in the art recognize the modified feature as still having the required characteristics and capabilities of the unmodified feature. In general, but subject to the preceding discussion, a numerical value herein that is modified by a word of approximation such as “about” may vary from the stated value by at least ±1, 2, 3, 4, 5, 6, 7, 10, 12 or 15%.

[0171] Additionally, the section headings herein are provided for consistency with the suggestions under 37 CFR 1.77 or otherwise to provide organizational cues. These headings shall not limit or characterize the disclosure(s) set out in any claims that may issue from this disclosure. Specifically, and by way of example, although the headings refer to a “Field of Invention,” such claims should not be limited by the language under this heading to describe the so-called technical field. Further, a description of technology in the “Background” section is not to be construed as an admission that technology is prior art to any disclosure(s) in this disclosure. Neither is the “Summary” to be considered a characterization of the disclosure(s) set forth in issued claims. Furthermore, any reference in this disclosure to “invention” in the singular should not be used to argue that there is only a single point of novelty in this disclosure. Multiple inventions may be set forth according to the limitations of the multiple claims issuing from this disclosure, and such claims accordingly define the invention(s), and their equivalents, that are protected thereby. In all instances, the scope of such claims shall be considered on their own merits in light of this disclosure but should not be constrained by the headings set forth herein.

[0172] All of the compositions and / or methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this disclosure have been described in terms of preferred aspects, it will be apparent to those of skill in the art that variations may be applied to the compositions and / or methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the disclosure. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the disclosure as defined by the appended claims.

[0173] To aid the Patent Office, and any readers of any patent issued on this application in interpreting the claims appended hereto, applicants wish to note that they do not intend any of the appended claims to invoke paragraph 6 of 35 U.S.C. § 112, U.S.C. § 112 paragraph (f), or equivalent, as it exists on the date of filing hereof unless the words “means for” or “step for” are explicitly used in the particular claim.

[0174] For each of the claims, each dependent claim can depend both from the independent claim and from each of the prior dependent claims for each and every claim so long as the prior claim provides a proper antecedent basis for a claim term or element.

Claims

WHAT IS CLAIMED IS:

1. A composition comprising: one or more peptides or proteins, comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof; a fusion protein comprising one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; or a pool of 2 or more or more peptides comprising, consisting of, or consisting essentially of amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; or a polynucleotide that encodes one or more peptides or proteins, comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof.

2. The composition of claim 1, wherein the one or more peptides or proteins comprises, or wherein the fusion protein comprises 2 or more or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof.

3. The composition of claim 1 or claim 2, wherein the amino acid sequence is selected from an influenza T cell epitope selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5.

4. The composition of claim 1 or claim 2, wherein the composition comprises one or more H5N 1 peptides amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof; a fusion protein comprising one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; or a pool of 2 or more peptides selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; or a polynucleotide that encodes one or more peptides or proteins, comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof.

5. The composition of any one of claims 1 to 4, wherein the peptide or protein comprises an influenza T cell epitope.

6. The composition of any one of claims 1 to 5, wherein the one or more peptides or proteins comprises an influenza CD8+ or CD4+ T cell epitope.

7. The composition of any one of claims 1 to 6, wherein the Influenza is H5N 1 and the H5N 1 T cell epitope is not conserved in another influenza.

8. The composition of any one of claims 1 to 6, wherein the Influenza is H5N 1 and the H5N5 T cell epitope is conserved in another influenza.

9. The composition of any one of claims 1 to 8, wherein one or more peptides or proteins has alength from about 9-15, 15-20, 20-25, 25-30, 30-40, 40-50, 50-75 or 75-100 amino acids.

10. The composition of any one of claims 1 to 9, wherein the one or more peptides or proteins elicits, stimulates, induces, promotes, increases or enhances a T cell response to an influenza.

11. The composition of claim 10, wherein the one or more peptides or proteins that elicits, stimulates, induces, promotes, increases or enhances the T cell response to the Influenza is an influenza protein or peptide, or a variant, homologue, derivative or subsequence thereof.

12. The composition of any one of claims 1 to 11, further comprising formulating the one or more peptides or proteins into an immunogenic formulation with an adjuvant.

13. The composition of claim 12, wherein the adjuvant is selected from the group consisting of adjuvant is selected from the group consisting of alum, aluminum hydroxide, aluminum phosphate, calcium phosphate hydroxide, cytosine-guanosine oligonucleotide (CpG-ODN) sequence, granulocyte macrophage colony stimulating factor (GM-CSF), monophosphoryl lipid A (MPL), poly(I:C), MF59, Quil A, N-acetyl muramyl-L-alanyl-D-isoglutamine (MDP), FIA, montanide, poly (DL-lactide- coglycolide), squalene, virosome, AS03, ASO4, IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-10, IL- 12, IL-15, IL-17, IL-18, STING, CD40L, pathogen-associated molecular patterns (PAMPs), damage- associated molecular pattern molecules (DAMPs), Freund’s complete adjuvant, Freund’s incomplete adjuvant, transforming growth factor (TGF)-beta antibody or antagonists, A2aR antagonists, lipopolysaccharides (LPS), Fas ligand, Trail, lymphotactin, Mannan (M-FP), APG-2, Hsp70 and Hsp90, pattern recognition receptor ligands, TLR3 ligands, TLR4 ligands, TLR5 ligands, TLR7 / 8 ligands, and TLR9 ligands.

14. The composition of any one of claims 1 to 13, wherein the composition further comprises a modulator of immune response.

15. The composition of claim 14, wherein the modulator of immune response is a modulator of the innate immune response.

16. The composition of claim 14 or claim 15, wherein the modulator is Interleukin-6 (IL-6), Interferon-gamma (IFN-y), Transforming growth factor beta (TGF-[3), or Interleukin- 10 (IL-10), or an agonist or antagonist thereof.

17. A composition comprising monomers or multimers of: peptides or proteins comprising, consisting of, or consisting essentially of: one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, concatemers, subsequences, portions, homologues, variants or derivatives thereof; a fusion protein comprising one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; or a polynucleotide that encodes one or more peptides or proteins, comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof.

18. A composition comprising one or more peptide-major histocompatibility complex (MHC) monomers or multimers, wherein the peptide-MHC monomer or multimer comprises a peptide comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, in a groove of the MHC monomer or multimer.

19. A composition comprising: one or more peptides or proteins comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof; a fusion protein comprising one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; a pool of 2 or more peptides selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; or a polynucleotide that encodes one or more peptides or proteins, comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof.

20. The composition of claim 19, wherein the one or more peptides or proteins comprises, or wherein the fusion protein comprises, 2 or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof.

21. The composition of claim 19 or claim 20, wherein the protein or peptide comprises a H5N1 T cell epitope.

22. The composition of any one of claims 19 to 21, wherein the one or more peptides or proteins comprises a H5N1 CD8+ or CD4+ T cell epitope.

23. The composition of any one of claims 19 to 22, wherein the H5N 1 T cell epitope is not conserved in another influenza.

24. The composition of any one of claims 19 to 22, wherein the H5N1 T cell epitope is conserved in another influenza.

25. The composition of any one of claims 19 to 24, wherein one or more peptides or proteins has a length from about 9-15, 15-20, 20-25, 25-30, 30-40, 40-50, 50-75 or 75-100 amino acids.

26. The composition of any one of claims 19 to 25, wherein the one or more peptides or proteins elicits, stimulates, induces, promotes, increases or enhances a T cell response to H5N1.

27. The composition of any one of claims 19 to 26, wherein the one or more peptides or proteins that elicits, stimulates, induces, promotes, increases or enhances the T cell response to H5N1 is a H5N1 protein or peptide, or a variant, homologue, derivative or subsequence thereof.

28. The composition of any one of claims 19 to 27, further comprising formulating the one or more peptides or proteins into an immunogenic formulation with an adjuvant.

29. The composition of claim 28, wherein the adjuvant is selected from the group consisting ofadjuvant is selected from the group consisting of alum, aluminum hydroxide, aluminum phosphate, calcium phosphate hydroxide, cytosine-guanosine oligonucleotide (CpG-ODN) sequence, granulocyte macrophage colony stimulating factor (GM-CSF), monophosphoryl lipid A (MPL), poly(I:C), MF59, Quil A, N-acetyl muramyl-L-alanyl-D-isoglutamine (MDP), FIA, montanide, poly (DL-lactide- coglycolide), squalene, virosome, AS03, ASO4, IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-10, IL- 12, IL-15, IL-17, IL-18, STING, CD40L, pathogen-associated molecular patterns (PAMPs), damage- associated molecular pattern molecules (DAMPs), Freund’s complete adjuvant, Freund’s incomplete adjuvant, transforming growth factor (TGF)-beta antibody or antagonists, A2aR antagonists, lipopolysaccharides (LPS), Fas ligand, Trail, lymphotactin, Mannan (M-FP), APG-2, Hsp70 and Hsp90, pattern recognition receptor ligands, TLR3 ligands, TLR4 ligands, TLR5 ligands, TLR7 / 8 ligands, and TLR9 ligands.

30. The composition of any one of claims 19 to 29, wherein the composition further comprises a modulator of immune response.

31. The composition of claim 30, wherein the modulator of immune response is a modulator of the innate immune response.

32. The composition of claim 30 or claim 31, wherein the modulator is Interleukin-6 (IL-6), Interferon-gamma (IFN-g), Transforming growth factor beta (TGF-B), or Interleukin- 10 (IL- 10), or an agonist or antagonist thereof.

33. A composition comprising monomers or multimers of: one or more peptides or proteins comprising, consisting of, or consisting essentially of: one or more H5N1 amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, concatemers, subsequences, portions, homologues, variants or derivatives thereof; a fusion protein comprising one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; or a polynucleotide that encodes one or more peptides or proteins, comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof.

34. A composition comprising one or more peptide-major histocompatibility complex (MHC) monomers or multimers, wherein the peptide-MHC monomer or multimer comprises a peptide comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, in a groove of the (MHC) monomer or multimer.

35. A method for detecting the presence of: (i) an influenza or (ii) an immune response relevant to Influenza infections, vaccines or therapies, including T cells responsive to one or more Influenza peptides, comprising: providing one or more proteins or peptides for detection of an amount or a relative amount of, and / or the activity of, and / or the state of antigen-specific T-cells;contacting a biological sample suspected of having Influenza-specific T-cells to one or more proteins or peptides for detection; and detecting an amount or a relative amount of, and / or the activity of, and / or the state of antigenspecific T-cells in the biological sample, wherein the one or more proteins or peptides for detection comprise one or more amino acid sequences set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or comprise a pool of 2 or more or more amino acid sequences set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5.

36. The method of claim 35, wherein detecting the amount or a relative amount of, and / or activity of antigen-specific T-cells comprises one or more steps of identification or detection of the antigen-specific T-cells and measuring the amount of the antigen-specific T-cells.

37. The method of claim 35 or claim 36, wherein the one or more peptides or proteins comprises 2 or more amino acid sequences selected from those set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5.

38. The method of any one of claims 35 to 37, wherein the detecting the amount or a relative amount of, and / or activity of antigen-specific T-cells comprises indirect detection and / or direct detection.

39. The method of any one of claims 35 to 38, wherein the method of detecting an immune response relevant to the Influenza comprises the following steps: providing an MHC monomer or an MHC multimer; contacting a population T-cells to the MHC monomer or MHC multimer; and measuring the number, activity or state of T-cells specific for the MHC monomer or MHC multimer.

40. The method of claim 39, wherein the MHC monomer or MHC multimer comprises a protein or peptide of the Influenza.

41. The method of claim 35, wherein the protein or peptide comprises a CD8+ or CD4+ T cell epitope.

42. The method of claim 41, wherein the T cell epitope is not conserved in another Influenza.

43. The method of claim 41, wherein the T cell epitope is conserved in another Influenza.

44. The method of any one of claims 35 to 43, wherein the protein or peptide has a length from about9-15, 15-20, 20-25, 25-30, 30-40, 40-50, 50-75 or 75-100 amino acids.

45. The method of any one of claims 35 to 44, wherein the proteins or peptides comprise 2 or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof.

46. The method of any one of claims 35 to 44, further comprising detecting the presence or amount of the one or more peptides in a biological sample, or a response thereto, which is diagnostic of an Influenza infection.

47. The method of any one of claims 35 to 46, wherein detecting an amount or a relative amount of, and / or the activity of, and / or the state of antigen-specific T-cells in the biological sample comprises measuring one or more of a cytokine or lymphokine secretion assay, T cell proliferation,immunoprecipitation, immunoassay, ELISA, radioimmunoassay, immunofluorescence assay, Western Blot, FACS analysis, a competitive immunoassay, a noncompetitive immunoassay, a homogeneous immunoassay a heterogeneous immunoassay, a bioassay, a reporter assay, a luciferase assay, a microarray, a surface plasmon resonance detector, a florescence resonance energy transfer, immunocytochemistry, or a cell mediated assay, or a cytokine proliferation assay.

48. The method of any one of claims 35 to 47, further comprising administering a treatment comprising the composition of any one of claims 1-34 to the subject from which the biological sample was drawn that increases the amount or relative amount of, and / or activity of the antigen-specific T-cells.

49. A method for detecting the presence of: (i) H5N 1 or (ii) an immune response relevant to H5N 1 infections, vaccines or therapies, including T cells responsive to one or more H5N1 peptides, comprising: providing one or more proteins or peptides for detection of an amount or a relative amount of, and / or the activity of, and / or the state of antigen-specific T-cells; contacting a biological sample suspected of having H5N1 -specific T-cells to one or more proteins or peptides for detection; and detecting an amount or a relative amount of, and / or the activity of, and / or the state of antigenspecific T-cells in the biological sample, wherein the one or more proteins or peptides for detection comprise one or more amino acid sequences selected from those set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or comprise a pool of 2 or more amino acid sequences selected from those set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5.

50. The method of claim 49, wherein detecting the amount or a relative amount of, and / or activity of antigen-specific T-cells comprises one or more steps of identification or detection of the antigen-specific T-cells and measuring the amount of the antigen-specific T-cells.

51. The method of claim 49 or claim 50, wherein the one or more peptides or proteins comprises 2 or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5.

52. The method of any one of claims 49 to 51, wherein the detecting the amount or a relative amount of, and / or activity of antigen-specific T-cells comprises indirect detection and / or direct detection.

53. The method of any one of claims 49 to 52, wherein the method of detecting an immune response relevant to H5N1 comprises the following steps: providing an MHC monomer or an MHC multimer; contacting a population T-cells to the MHC monomer or MHC multimer; and measuring the number, activity or state of T-cells specific for the MHC monomer or MHC multimer.

54. The method of claim 53, wherein the MHC monomer or MHC multimer comprises a protein or peptide of H5N 1.

55. The method of claim 54, wherein the protein or peptide comprises a H5N1 CD8+ or CD4+ T cell epitope.

56. The method of claim 55, wherein the H5N1 T cell epitope is not conserved in another Influenza.

57. The method of claim 55, wherein the H5N1 T cell epitope is conserved in another Influenza.

58. The method of any one of claims 49 to 57, wherein the protein or peptide has a length from about9-15, 15-20, 20-25, 25-30, 30-40, 40-50, 50-75 or 75-100 amino acids.

59. The method of any one of claims 49 to 58, wherein the proteins or peptides comprise 2 or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof.

60. The method of any one of claims 49 to 59, further comprising detecting the presence or amount of the one or more peptides in a biological sample, or a response thereto, which is diagnostic of a H5N 1 infection.

61. The method of any one of claims 49 to 60, wherein detecting an amount or a relative amount of, and / or the activity of, and / or the state of antigen-specific T-cells in the biological sample comprises measuring one or more of a cytokine or lymphokine secretion assay, T cell proliferation, immunoprecipitation, immunoassay, ELISA, radioimmunoassay, immunofluorescence assay, Western Blot, FACS analysis, a competitive immunoassay, a noncompetitive immunoassay, a homogeneous immunoassay a heterogeneous immunoassay, a bioassay, a reporter assay, a luciferase assay, a microarray, a surface plasmon resonance detector, a florescence resonance energy transfer, immunocytochemistry, or a cell mediated assay, or a cytokine proliferation assay.

62. The method of any one of claims 49 to 61, further comprising administering a treatment comprising the composition of any one of claims 1-34 to the subject from which the biological sample was drawn that increases the amount or relative amount of, and / or activity of the antigen-specific T-cells.

63. A method detecting an influenza infection or exposure in a subject, the method comprising, consisting of, or consisting essentially of: contacting a biological sample from a subject with a composition of any one of claims 1 to 36; and determining if the composition elicits an immune response from the contacted cells, wherein the presence of an immune response indicates that the subject has been exposed to or infected with Influenza.

64. The method of claim 63, wherein the sample comprises T cells.

65. The method of claim 63 or claim 64, wherein the response comprises inducing, increasing, promoting or stimulating anti-influenza activity of T cells.

66. The method of claim 63 or claim 65, wherein the T cells are CD8+ or CD4+ T cells.

67. The method of any one of claims 63 to 66, wherein the method comprises determining whether the subject has been infected by or exposed to the Influenza more than once by determining if the subject elicits a secondary T cell immune response profile that is different from a primary T cell immune response profile.

68. The method of any one of claims 63 to 67, further comprising diagnosing an influenza infection or exposure in a subject, the method comprising contacting a biological sample from a subject with acomposition of any one of claims 1 to 34, and determining if the composition elicits a T cell immune response, wherein the T cell immune response identifies that the subject has been infected with or exposed to an influenza.

69. The method of any one of claims 63 to 68, wherein the method is conducted three or more days following the date of suspected infection by or exposure to an influenza.

70. A method detecting H5N1 infection or exposure in a subject, the method comprising, consisting of, or consisting essentially of: contacting a biological sample from a subject with a composition of any one of claims 19 to 36; and determining if the composition elicits an immune response from the contacted cells, wherein the presence of an immune response indicates that the subject has been exposed to or infected with H5N1.

71. The method of claim 70, wherein the sample comprises T cells.

72. The method of claim 70 or claim 71, wherein the response comprises inducing, increasing, promoting or stimulating anti-H5Nl activity of T cells.

73. The method of claim 71 or claim 72, wherein the T cells are CD8+ or CD4+ T cells.

74. The method of any one of claims 70 to 73, wherein the method comprises determining whether the subject has been infected by or exposed to H5N1 more than once by determining if the subject elicits a secondary T cell immune response profde that is different from a primary T cell immune response profde.

75. The method of any one of claims 70 to 74, further comprising diagnosing a H5N1 infection or exposure in a subject, the method comprising contacting a biological sample from a subject with a composition of any one of claims 19 to 34; and determining if the composition elicits a T cell immune response, wherein the T cell immune response identifies that the subject has been infected with or exposed to H5N 1.

76. The method of any one of claims 70 to 75, wherein the method is conducted three or more days following the date of suspected infection by or exposure to an influenza.

77. A kit for the detection of Influenza or an immune response to Influenza in a subject comprising, consisting of or consisting essentially of: one or more T cells that specifically detect the presence of: one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof; or a fusion protein comprising one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; or a pool of 2 or more or more peptides selected from the amino acid sequences set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5.

78. The kit of claim 77, wherein the one or more amino acid sequences are selected from an influenza T cell epitope set forth in any one of SEQ ID NOS: 1 to 929 or Tables 1 to 5.

79. The kit of claim 77 or claim 78, wherein the composition comprises: one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof; a fusion protein comprising one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; or a pool of 2 or more peptides selected from the amino acid sequences selected from those set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5.

80. The kit of any one of claims 77 to 79, wherein the amino acid sequence comprises an influenza CD8+ or CD4+ T cell epitope.

81. The kit of claim 78 or claim 80, wherein the T cell epitope is not conserved in another Influenza.

82. The kit of claim 78 or claim 80, wherein the T cell epitope is conserved in another Influenza.

83. The kit of any one of claims 77 to 82, wherein the fusion protein has a length from about 9-15,15-20, 20-25, 25-30, 30-40, 40-50, 50-75 or 75-100 amino acids.

84. The kit of any one of claims 77 to 83, wherein the kit includes instruction for a diagnostic method, a process, a composition, a product, a service or component part thereof for the detection of: (i) Influenza or (ii) an immune response relevant to Influenza infections, vaccines or therapies, including T cells responsive to Influenza.

85. The kit of any one of claims 77 to 84, wherein the kit includes reagents for detecting an amount or a relative amount of, and / or the activity of, and / or the state of antigen-specific T-cells in the biological sample comprises measuring one or more of a cytokine or lymphokine secretion assay, T cell proliferation, immunoprecipitation, immunoassay, ELISA, radioimmunoassay, immunofluorescence assay, Western Blot, FACS analysis, a competitive immunoassay, a noncompetitive immunoassay, a homogeneous immunoassay a heterogeneous immunoassay, a bioassay, a reporter assay, a luciferase assay, a microarray, a surface plasmon resonance detector, a florescence resonance energy transfer, immunocytochemistry, or a cell mediated assay, or a cytokine proliferation assay.

86. The kit of any one of claims 77 to 85, wherein the kit includes reagents for determining a Human Leukocyte Antigen (HLA) profile of a subject, and selecting peptides that are presented by the HLA profile of the subject for detecting an immune response to Influenza.

87. A kit for the detection of H5N 1 or an immune response to H5N 1 in a subject comprising, consisting of or consisting essentially of: one or more T cells that specifically detect the presence of: one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof; a fusion protein comprising one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; or a pool of 2 or more peptides selected from the amino acid sequences selected from those set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5.

88. The kit of claim 87, wherein the one or more amino acid sequences is selected from a H5N 1 CD4 T cell epitope selected from any one of SEQ ID NOS: 1 to 929 or Tables 1 to 5; or both.

89. The kit of claims 87 to 88, wherein the amino acid sequence comprises a H5N1 CD8+ or CD4+ T cell epitope.

90. The kit of claim 89, wherein the H5N1 T cell epitope is not conserved in another Influenza.

91. The kit of claim 89, wherein the H5N1 T cell epitope is conserved in another Influenza.

92. The kit of any one of claims 87 to 91, wherein the fusion protein has a length from about 9-15,15-20, 20-25, 25-30, 30-40, 40-50, 50-75 or 75-100 amino acids.

93. The kit of any one of claims 87 to 92, wherein the kit includes instruction for a diagnostic method, a process, a composition, a product, a service or component part thereof for the detection of: (i) H5N1 or (ii) an immune response relevant to H5N1 infections, vaccines or therapies, including T cells responsive to H5N 1.

94. The kit of any one of claims 87 to 93, wherein the kit includes reagents for detecting an amount or a relative amount of, and / or the activity of, and / or the state of antigen-specific T-cells in the biological sample comprises measuring one or more of a cytokine or lymphokine secretion assay, T cell proliferation, immunoprecipitation, immunoassay, ELISA, radioimmunoassay, immunofluorescence assay, Western Blot, FACS analysis, a competitive immunoassay, a noncompetitive immunoassay, a homogeneous immunoassay a heterogeneous immunoassay, a bioassay, a reporter assay, a luciferase assay, a microarray, a surface plasmon resonance detector, a florescence resonance energy transfer, immunocytochemistry, or a cell mediated assay, or a cytokine proliferation assay.

95. The kit of any one of claims 87 to 94, wherein the kit includes reagents for determining a Human Leukocyte Antigen (HLA) profile of a subject, and selecting peptides that are presented by the HLA profile of the subject for detecting an immune response to H5N 1.

96. A method of stimulating, inducing, promoting, increasing, or enhancing an immune response against an influenza in a subject, comprising: administering a composition of claims 1 to 34, in an amount sufficient to stimulate, induce, promote, increase, or enhance an immune response against the Influenza in the subject.

97. The method of claim 96, wherein the immune response provides the subject with protection against an influenza infection or pathology, or one or more physiological conditions, disorders, illnesses, diseases or symptoms caused by or associated with Influenza infection or pathology.

98. The method of claim 96 or claim 97, wherein the immune response is specific to: one or more H5N1 peptides selected from the amino acid sequences set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof.

99. A method of stimulating, inducing, promoting, increasing, or enhancing an immune response against H5N1 in a subject, comprising: administering a composition of claims to 19 to 34, in an amount sufficient to stimulate, induce, promote, increase, or enhance an immune response against H5N1 in the subject.

100. The method of claim 99, wherein the immune response provides the subject with protection against a H5N 1 infection or pathology, or one or more physiological conditions, disorders, illnesses, diseases or symptoms caused by or associated with H5N1 infection or pathology.

101. The method of claim 99 or claim 100, wherein the immune response is specific to: one or more Influenza viralpeptides selected from the amino acid sequences selected from those set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof.

102. A method of stimulating, inducing, promoting, increasing, or enhancing an immune response against H5N1 in a subject, comprising: administering to a subject an amount of a protein or peptide or a polynucleotide that expresses the protein or peptide comprising, consisting of or consisting essentially of an amino acid sequence of the Influenza viral protein or peptide, or a variant, homologue, derivative or subsequence thereof, wherein the protein or peptide comprises at least two peptides selected from the amino acid sequences set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5 or a subsequence, portion, homologue, variant or derivative thereof, in an amount sufficient to prevent, stimulate, induce, promote, increase, immunize against, or enhance an immune response against H5N1 in the subject.

103. The method of claim 102, wherein the immune response provides the subject with protection against H5N 1 infection or pathology, or one or more physiological conditions, disorders, illnesses, diseases or symptoms caused by or associated with H5N1 infection or pathology.

104. A method of treating, preventing, or immunizing a subject against H5N 1 infection, comprising administering to a subject an amount of a protein, peptide or a polynucleotide that expresses the protein or peptide comprising, consisting of, or consisting essentially of an amino acid sequence of an influenza protein or peptide, or a variant, homologue, derivative or subsequence thereof, wherein the protein or peptide comprises at least two amino acid sequences selected from any one of SEQ ID NOS: 1 to 929 or Tables 1 to 5 or a subsequence, portion, homologue, variant or derivative thereof, in an amount sufficient to treat, prevent, or immunize the subject for H5N 1 infection, wherein the protein or peptide comprises or consists of an influenza T cell epitope that elicits, stimulates, induces, promotes, increases, or enhances an anti-H5Nl T cell immune response.

105. The method of claim 104, wherein the one or more amino acid sequences are selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof; a fusion protein comprising one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; or a pool of 2 or more peptides selected from the amino acid sequences selected from those set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5.

106. The method of claim 104, wherein the anti-H5Nl T cell response is a CD8+, a CD4+ T cell response, or both.

107. The method of any of claims 104 to 106, wherein the T cell epitope is conserved across two or more clinical isolates of H5N 1 or two or more circulating forms of H5N 1.

108. The method of claim 107, wherein the H5N1 infection is an acute infection.

109. The method of any one of claims 104 to 108, wherein the subject is a mammal or a human.

110. The method of any one of claims 104 to 109, wherein the method reduces Influenza viral titer, increases or stimulates Influenza viral clearance, reduces or inhibits Influenza viral proliferation, reduces or inhibits increases in Influenza viral titer or Influenza viral proliferation, reduces the amount of an influenza viral protein or the amount of an influenza viral nucleic acid, or reduces or inhibits synthesis of an influenza viral protein or an influenza viral nucleic acid.

111. The method of any one of claims 104 to 110, wherein the method reduces one or more adverse physiological conditions, disorders, illness, diseases, symptoms or complications caused by or associated with H5N 1 infection or pathology.

112. The method of any one of claims 104 to 111, wherein the method improves one or more adverse physiological conditions, disorders, illness, diseases, symptoms or complications caused by or associated with H5N 1 infection or pathology.

113. The method of claim 111 or claim 112, wherein the symptom is fever or chills, joint pain, fatigue, muscle or body aches, headache, nausea or vomiting, diarrhea, conjunctivitis or rash.

114. The method of any one of claims 104 to 113, wherein the method reduces or inhibits susceptibility to H5N1 infection or pathology.

115. The method of any one of claims 104 to 113, wherein the protein or peptide, or a subsequence, portion, homologue, variant or derivative thereof, is administered prior to, substantially contemporaneously with or following exposure to or infection of the subject with H5N 1.

116. The method of any one of claims 104 to 115, wherein a plurality of H5N 1 T cell epitopes are administered prior to, substantially contemporaneously with or following exposure to or infection of the subject with H5N 1.

117. The method of any one of claims 104 to 116, wherein the protein or peptide, or a subsequence, portion, homologue, variant or derivative thereof is administered within 2-72 hours, 2-48 hours, 4-24 hours, 4-18 hours, or 6-12 hours after a symptom of H5N1 infection or exposure develops.

118. The method of any one of claims 104 to 117, wherein the protein or peptide, or a subsequence, portion, homologue, variant or derivative thereof is administered prior to exposure to or infection of the subject with H5N 1.

119. The method of any one of claims 104 to 118, wherein the method further comprises administering a modulator of immune response prior to, substantially contemporaneously with or following the administration to the subject of an amount of a protein or peptide.

120. The method of claim 119, wherein the modulator of immune response is a modulator of the innate immune response.

121. The method of claim 119 or claim 120, wherein the modulator is IL-6, IFN-y, TGF-[3, or IL-10,or an agonist or antagonist thereof.

122. A method of treating, preventing, or immunizing a subject against H5N 1 infection, comprising administering to a subject the composition of any one of claims 1-36 in an amount sufficient to treat, prevent, or immunize the subject for H5N1 infection.

123. The method of claim 122, wherein the H5N1 infection is an acute infection.

124. The method of claim 122, wherein the method reduces Influenza viral titer, increases or stimulates Influenza viral clearance, reduces or inhibits Influenza viral proliferation, reduces or inhibits increases in Influenza viral titer or Influenza viral proliferation, reduces the amount of an influenza viral protein or the amount of an influenza viral nucleic acid, or reduces or inhibits synthesis of an influenza viral protein or an influenza viral nucleic acid.

125. The method of any one of claims 122 to 124, wherein the method reduces one or more adverse physiological conditions, disorders, illness, diseases, symptoms or complications caused by or associated with H5N 1 infection or pathology.

126. The method of any one of claims 122 to 125, wherein the method improves one or more adverse physiological conditions, disorders, illness, diseases, symptoms or complications caused by or associated with H5N 1 infection or pathology.

127. The method of claim 125 or claim 126, wherein the symptom is fever or chills, joint pain, fatigue, muscle or body aches, headache, nausea or vomiting, diarrhea, conjunctivitis or rash.

128. The method of any one of claims 122 to 127, wherein the method reduces or inhibits susceptibility to H5N1 infection or pathology.

129. The method of any one of claims 122 to 128, wherein the composition is administered prior to, substantially contemporaneously with or following exposure to or infection of the subject with H5N 1.

130. The method of any one of claims 122 to 128, wherein the composition is administered prior to, substantially contemporaneously with or following exposure to or infection of the subject with H5N 1.

131. The method of any one of claims 122 to 130, wherein the composition is administered within 2- 72 hours, 2-48 hours, 4-24 hours, 4-18 hours, or 6-12 hours after a symptom of H5N1 infection or exposure develops.

132. The method of any one of claims 122 to 130, wherein the composition is administered prior to exposure to or infection of the subject with H5N1.

133. A peptide or peptides that are immunoprevalent or immunodominant in a virus obtained by a method consisting of, or consisting essentially of: obtaining an amino acid sequence of the virus; determining one or more sets of overlapping peptides spanning one or more viral antigen using unbiased selection; synthesizing one or more pools of viral peptides comprising the one or more sets of overlapping peptides; combining the one or more pools of viral peptides with Class I major histocompatibility proteins(MHC), Class II MHC, or both Class I and Class II MHC to form peptide-MHC complexes; contacting the peptide-MHC complexes with T cells from subjects exposed to the viral; determining which pools triggered cytokine release by the T cells; and deconvoluting from the pool of peptides that elicited cytokine release by the T cells, which peptide or peptides are immunoprevalent or immunodominant in the pool.

134. The peptide or peptides of claim 133, wherein the virus is an influenza.

135. The peptide or peptides of claim 134, wherein the Influenza is H5N1.

136. The peptide or peptides of any one of claims 133 to 135, wherein the immunodominant peptides are selected from 1, 2 or more peptides selected from the amino acid sequences set forth in SEQ ID NOS:1 to 929 or Tables 1 to 5.

137. The peptide or peptides of any one of claims 133 to 136, wherein the immunodominant peptides are selected from 1, 2 or more peptides selected from the amino acid sequences selected from those set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5.

138. A method of selecting an immunoprevalent or immunodominant peptide or protein of a virus comprising, consisting of, or consisting essentially of: obtaining an amino acid sequence of the virus; determining one or more sets of overlapping peptides spanning one or more virus antigen using unbiased selection; synthesizing one or more pools of virus peptides comprising the one or more sets of overlapping peptides; combining the one or more pools of viral peptides with Class I major histocompatibility proteins (MHC), Class II MHC, or both Class I and Class II MHC to form peptide-MHC complexes; contacting the peptide-MHC complexes with T cells from subjects exposed to the virus; determining which pools triggered cytokine release by the T cells; and deconvoluting from the pool of peptides that elicited cytokine release by the T cells, which peptide or peptides are immunoprevalent or immunodominant in the pool.

139. The method of claim 138, wherein the virus is an influenza.

140. The method of claim 139, wherein the Influenza is H5N 1.

141. The method of any one of claim 138 to 140, wherein the immunodominant peptides are selected from 1, 2 or more peptides selected from the amino acid sequences set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5.

142. The method of any one of claims 138 to 141, wherein the immunodominant peptides are selected from 1, 2 or more peptides selected from the amino acid sequences selected from those set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5.

143. A polynucleotide that expresses one or more peptides or proteins, comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof;a fusion protein comprising one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; or a pool of 2 or more or more peptides comprising, consisting of, or consisting essentially of amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5.

144. A vector that comprises the polynucleotide of claim 143.

145. The vector of claim 144, wherein the vector is a viral vector.

146. A host cell that comprises the vector of claim 144 or claim 145.

147. A polynucleotide that expresses: one or more peptides or proteins comprising, consisting of, or consisting essentially of an amino acid sequence selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5, or a subsequence, portion, homologue, variant or derivative thereof; a fusion protein comprising one or more amino acid sequences selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables 1 to 5; or a pool of 2 or more peptides selected from any sequence set forth in SEQ ID NOS: 1 to 929 or Tables I to 5.

148. A vector that comprises the polynucleotide of claim 147.

149. The vector of claim 148, wherein the vector is a viral vector.

150. A host cell that comprises the vector of claim 148 or claim 149.

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