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WO 2015/157189 Al 15 October 2015 (15.10.2015) P O P C T (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2015/157189 Al 15 October 2015 (15.10.2015) P O P C T (51) International Patent Classification: AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, A61K 39/12 (2006.01) A61K 39/145 (2006.01) BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, A61K 39/385 (2006.01) A61K 38/00 (2006.01) DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (21) International Application Number: KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, PCT/US2015/024563 MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, (22) International Filing Date: PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, 6 April 2015 (06.04.2015) SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (25) Filing Language: English (84) Designated States (unless otherwise indicated, for every (26) Publication Language: English kind of regional protection available): ARIPO (BW, GH, (30) Priority Data: GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, 61/976,024 7 April 2014 (07.04.2014) US TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, 62/073,717 31 October 20 14 (3 1.10.20 14) US TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, 62/073,777 31 October 20 14 (3 1.10.20 14) us DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, 62/127,775 3 March 2015 (03.03.2015) us LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, (71) Applicant: THE REGENTS OF THE UNIVERSITY GW, KM, ML, MR, NE, SN, TD, TG). OF CALIFORNIA [US/US]; 1111 Franklin Street, Twelfth Floor, Oakland, California 94607-5200 (US). Declarations under Rule 4.17 : — as to applicant's entitlement to apply for and be granted a (72) Inventors: SUN, Ren; c/o Ucla Office of Intellectual Prop patent (Rule 4.1 7(H)) erty Administration, 11000 Kinross Ave., Ste 200 MC 140607, Los Angeles, California 90095-1406 (US). — as to the applicant's entitlement to claim the priority of the YOUNG, Arthur; c/o InvVax, Inc., 570 Westwood Plaza, earlier application (Rule 4.1 7(in)) Bldg. 114, Los Angeles, California 90095 (US). WU, Published: Nicholas C ; c/o Ucla Office of Intellectual Property Ad ministration, 11000 Kinross Ave., Ste 200 MC 140607, — with international search report (Art. 21(3)) Los Angeles, California 90095-1406 (US). — before the expiration of the time limit for amending the (74) Agent: SUNDBY, Suzannah K.; Canady + Lortz LLP, claims and to be republished in the event of receipt of 1050 30th Street, NW, Washington, District of Columbia amendments (Rule 48.2(h)) 20007 (US). — with sequence listing part of description (Rule 5.2(a)) (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, 00 - © (54) Title: VACCINES AND USES THEREOF (57) Abstract: Disclosed herein are methods, compositions, and vaccines formulations, kits, and reagents for developing a vaccine, ¾ e.g., a peptide-based vaccine. Also described herein are methods for identifying a peptide for use in developing a viral vaccine, such S as a viral vaccine against an influenza virus. VACCINES AND USES THEREOF [0001] CROSS-REFERENCE TO RELATED APPLICATIONS [0002] This application claims the benefit of U.S. provisional patent application nos. 61/976,024, filed April 7, 2014; 62/073,717, filed October 31, 2014; 62/073,777, filed October 31, 2014; and 62/127,775, filed March 3, 2015; which are herein incorporated by reference in their entirety. [0003] REFERENCE TO A SEQUENCE LISTFNG SUBMITTED VIA EFS-WEB [0004] The content of the ASCII text file of the sequence listing named "20150406_034044_130WOl_seq" which is 92.1 kb in size was created on April 6, 2015, and electronically submitted via EFS-Web herewith the application is incorporated herein by reference in its entirety. [0005] ACKNOWLEDGEMENT OF GOVERNMENT SUPPORT [0006] This invention was made with Government support under Grant No. AI028697 awarded by the National Institutes of Health. The Government has certain rights in the invention. [0007] BACKGROUND [0008] Influenza A virus is the most common cause of flu in humans, leading to respiratory distress and systemic illness in all ages, and occasionally hospitalization or death in susceptible young or elderly. Roughly 300,000 to 500,000 deaths per year worldwide are caused by influenza virus. In the twentieth century three major pandemics occurred (1918, 1957, and 1968), causing an estimated 50 million, 500,000, and 2 million deaths, respectively. Influenza B virus can be another culprit that causes flu in humans and is included as part of the flu vaccine each year. [0009] Viral hepatitis can be a cause of considerable morbidity and mortality in the human population, both from acute infection and chronic sequelae which can include chronic active hepatitis and cirrhosis caused by hepatitis B, C, and D. Sometimes, hepatitis such as hepatitis B further induces hepatocellular carcinoma, one of the ten most common cancers worldwide. [0010] The human immunodeficiency virus (HIV) is a lentivirus that can cause acquired immunodeficiency syndrome (AIDS). Roughly over 1 million people are infected with AIDS in the United States including about 14% whose infections have not been diagnosed. Each year, an estimated of 50,000 people in the United States are newly infected. [0011] Genetic research on influenza virus biology has been informed in large part by nucleotide variants present in clinical or laboratory and seasonal or pandemic samples, leaving a substantial part of the genome uncharacterized. Similarly, substantial parts of the hepatitis virus and HIV genomes are also uncharacterized. Elucidation of these uncharacterized regions can improve vaccines to treat and prevent diseases. [0012] SUMMARY OF THE INVENTION [0013] In some embodiments, a peptide is provided consisting of an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-53. In some embodiments, a peptide is provided comprising a sequence with 100% sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-27, 29-38, and 40-53, wherein the peptide is at most 50 amino acids in length. In some embodiments, a peptide is provided comprising a sequence with at least 70% sequence identity to at least 15 contiguous amino acids of an amino acid sequence selected from the group consisting of SEQ ID NOs: 47-53, wherein the peptide is at most 50 amino acids in length. In some embodiments, a peptide is provided comprising a sequence with at least 70%> sequence identity to at least 8 contiguous amino acids of an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-27, 32, and 40-46, wherein the peptide is at most 50 amino acids in length. In some embodiments, a peptide is provided comprising a sequence with at least 70%> sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-27, 32-38, and 40-53, wherein the peptide is at most 50 amino acids in length. In some embodiments, a peptide is provided comprising a sequence with at least 70%> sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-2, 5-15, 18-22, 26-32, and 39-46 wherein the peptide is less than 15 amino acids in length. In some embodiments, a peptide is provided comprising a sequence with at least 90%> sequence identity to an amino acid sequence of SEQ ID NO: 29 or 31, wherein the peptide is at most 50 amino acids in length. In some embodiments, a peptide is provided comprising at least 70%> sequence identity to the amino acid sequence of SEQ ID NO: 28, wherein the peptide is 8 amino acids in length. [0014] In some embodiments, any of the above peptides is attached to a lipid. In some embodiments, the lipid comprises a palmitoyl group. In some embodiments, any of the above peptides is attached to a CD4+ (helper) T cell epitope. In some embodiments, any of the above peptides is an isolated peptide. [0015] In some embodiments, a composition is provided comprising any of the above peptides, wherein the composition comprises a pharmaceutically acceptable carrier. In some embodiments, the composition further comprises an adjuvant. In some embodiments, the composition further comprises a second peptide, wherein the second peptide is not identical to any of the above peptides, wherein the second peptide is not more than 50 amino acids in length. In some embodiments, the second peptide is attached to a lipid. In some embodiments, the lipid comprises a palmitoyl group. In some embodiments, the second peptide is attached to a CD4+ (helper) T cell epitope. In some embodiments, the second peptide comprises at least 70% sequence identity to at least 8 contiguous amino acids of an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-53. In some embodiments, the second peptide comprises 100% sequence identity to at least 8 contiguous amino acids of an amino acid sequence selected from SEQ ID NOs: 1-53. In some embodiments, the second peptide comprises a sequence comprising 70%> sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-53.
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