HIV Vaccine, Method for Producing the Same, and Method for Using the Same

Abstract

To provide HIV vaccines and methods of making and using the same.SOLUTION: Provided are: HIV-1 fusion polypeptides, polynucleotides encoding such fusion polypeptides, vectors expressing such fusion polypeptides, for use in eliciting an immune response against HIV-1; pharmaceutical and immunogenic compositions and kits comprising such fusion polypeptides, polynucleotides or vectors; and methods of use in treating and / or preventing HIV-1. Further provided are methods for design of antiviral vaccines, including vaccines to elicit an immune response against HIV-1.SELECTED DRAWING: None

Description

Technical Field

[0001] (Cross - Reference to Related Applications) This application claims the benefit under 35 U.S.C. § 119(e) of U.S. Provisional Patent Application No. 62 / 874,712, filed on Jul. 16, 2019, which is hereby incorporated by reference in its entirety for all purposes.

[0002] (Sequence Listing) This application is being filed electronically in ASCII format and includes a sequence listing which is hereby incorporated by reference in its entirety. The name of the ASCII copy created on Jun. 30, 2020 is 1314_PF_SL.txt and the size is 449,156 bytes.

Background Art

[0003] Human immunodeficiency virus type 1 (HIV - 1) infection is a severe and life - threatening disease and remains one of the major causes of morbidity and mortality worldwide, with approximately 36.9 million infected people globally and 1.1 million infected people in the United States (US) (National Center for HIV / AIDS Viral Hepatitis STD & TB Prevention: Division of HIV / AIDS Prevention, HIV in the United States and Dependent Areas. January 2019; UNAIDS, 2017 Global HIV Statistics. Fact Sheet - July 2018). Antiretroviral combination therapy (cART) for HIV - 1 infection has significantly improved morbidity and mortality by suppressing viral replication, preserving immunological function, and preventing progression to AIDS. However, despite cART, HIV - 1 infection still causes chronic immune activation and an increased risk of non - AIDS - related morbidity and mortality.

[0004] In the early stages of infection, HIV-1 integrates into the genome of memory cluster determinant 4 (CD4) T cells, a subset of which forms a long-lived reservoir of HIV-1-infected cells that persists despite treatment with antiretroviral therapy (ART) (Siliciano, et al., Nature Medicine (2003) 9(6):727-728). Eradication of the viral reservoir is an important component of HIV cure strategies. Immune-based therapies can be additional components of combination approaches to HIV cure or ART-free viral remission and can include passive administration of T cell and antibody-based vaccines, antibodies, and immunomodulatory agents.

[0005] The development of HIV T cell-specific vaccines has mainly focused on designing immunogens that provide universal coverage by addressing global HIV viral diversity. HIV-1 is defined by four groups (groups M, N, O, and P). Subtypes or clades (designations A-K) within group M, and some cross-clade recombinant forms, cause most human disease. Strategies for designing vaccines to address the vast global viral sequence diversity include computationally designed multivalent mosaic immunogens that capture common epitope variants within potential T cell epitopes (Fischer, et al., Nat Med, (2007) 13(1):100-6). These can be expressed as full-length artificial proteins or artificial recombinant proteins derived from regions with a high degree of sequence conservation (Ondondo, et al., Mol Ther, (2016) 24(4):832-42; Barouch, et al., Cell, (2013) 155(3):531-9). Subsequent versions of the in silico design algorithms led to the development of a computationally faster graph-based approach known as epigraph (Theiler, et al., Sci Rep, (2016) 6:33987). These design approaches can be used to develop a single global vaccine or to be tailored to clades prevalent within specific populations and regions. However, these approaches focus only on viral diversity and do not consider host genetic diversity that drives antigen presentation and T cell recognition, and the subsequent emergence of immune-driven escape variants.

[0006] Antigen-specific CD4+ and CD8+ T cells are associated with the control of viremia during acute infection and with the slow disease progression and control of viremia in individuals who maintain a low viral load in the absence of ART (elite controllers). Antigen-specific T cells recognize viral epitopes presented by MHC class I and II molecules. Human leukocyte antigen (HLA) class I alleles have been associated with HIV control in genome-wide association studies (GWAS) (Fellay, et al., Science, 2007. 317(5840):944-7; International, H.I.V.C.S., et al., Science, (2010)330(6010):1551-7). These proteins present antigenic peptides from sequences and induce effector and memory T cells. Current approaches to generating HIV-1 candidate vaccines focus on viral sequence diversity without appropriately modeling the process of epitope generation across various host HLA alleles. This complex process of antigen presentation and T cell priming includes proteasomal cleavage, TAP transport, cross-presentation, MHC binding and peptide-MHC complex stability, and ultimately TCR recognition (Yewdell, et al., Nat Rev Immunol, (2003)3(12):952-61). As a result, existing methods for generating T cell vaccines have met with limited success, for example, in some cases inducing as few as an average of four responses per patient (see, for example, Priddy, et al., Clin Infect Dis (2008)46(11):1769-81; Sekaly, et al., J Exp Med. (2008)205(1):7-12, and Iaccino, et al., Retrovirology. (2008)5:56).

[0007] Furthermore, highly mutated viruses such as HIV-1 pose unique challenges due to high levels of sequence diversity and the specific challenges arising from the host immune response that drives some of that diversity. The role of the adaptive immune response in driving diversity in HIV-1 is well described, leading to changes in viral sequences over time (Goulder, et al., Nature, (2001) 412(6844):334-8, Kelleher, et al., J Exp Med, (2001) 193(3):375-86, Schneidewind, et al., J Virol, (2007) 81(22):12382-93, Kawashima, et al., Nature, (2009) 458(7238):641-5, Leslie, et al., Nat Med, (2004) 10(3):282-9, Phillips, et al., Nature, (1991) 354(6353):453-9). Most of that diversity is driven by cytotoxic T lymphocytes that recognize peptide epitopes presented on MHC class I alleles. The selective pressure imposed by these T cell responses during chronic infection leads to adaptation of the HIV sequence. This sequence evolution drives diversity of HIV-1 within individuals and across populations (Kawashima, et al., supra, Phillips, et al., supra). Furthermore, viral sequences have mutations that allow them to hide from host defenses. These sequences may resemble self-peptides or peptide sequences that induce central or peripheral tolerance. Standard vaccine design approaches may not be able to cope with viral sequence variants and may lead to inefficient use of vaccine potency by including sequences that can induce responses that cross-react with self-antigens. The impact of vaccines on human health cannot be overstated. Most of these are preventive vaccines, which are effective in inducing normal neutralizing antibodies against infectious disease targets. The development of therapeutic vaccines has made great progress in cancer immunotherapy, which has focused on developing vaccines that generate antigen-specific T cells. Many tumor-associated or tumor-specific antigens are self-antigens and require the design of vaccines that need to overcome immune tolerance. Recent innovations in the identification and prediction of neoantigens arising from cancer-specific mutations have led to promising targets that may not be influenced by central or peripheral tolerance mechanisms. Various informatics strategies have been established to assist in the identification of neoantigens and predict their ability to induce strong T cell responses (see, for example, Bulik-Sullivan, et al., Nature Biotech (2019) 37:55-63). In the development of therapeutic vaccines against HIV, the antigen targets are defined by the virus. Tools for effectively presenting viral sequences and predicting their ability to stimulate an immune response are not well defined. This is related to the context of HIV, in which a very diverse quasispecies is established due to a high mutation rate combined with host immune-mediated selection pressure. Therefore, the inventors have developed informatics tools that can identify conserved viral sequences in a population-based consensus sequence or, by individual deep sequencing of isolates, are useful in designing HIV vaccine immunogens and can predict presentation, T cell priming, and HLA-driven escape pathways.

Prior Art Documents

Non-Patent Documents

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Summary of the Invention

Means for Solving the Problems

[0009] In this specification, at least the following embodiments are provided. Additional embodiments are described in the detailed embodiments and examples of this specification. Fusion polypeptide

[0010] Embodiment 1: A fusion polypeptide comprising a plurality of polypeptide segments of one or more human immunodeficiency virus - 1 (HIV - 1) proteins encoded by one or more HIV genes selected from Gag, Nef, Env, Pol, Rev, Tat, Rev, Vif, Vpr, and Vpu.

[0011] Embodiment 2: The fusion polypeptide according to Embodiment 1, wherein the plurality of polypeptide segments contain or consist of only polypeptide segments encoded by the HIV-1 genes Env, Gag, Nef and Pol, and for example do not contain polypeptide segments encoded by the HIV-1 Tat, Rev, Vif, Vpr and / or Vpu genes.

[0012] Embodiment 3: The fusion polypeptide according to Embodiment 1, wherein the plurality of polypeptide segments contain or consist of only polypeptide segments encoded by the HIV-1 genes Gag, Nef and Pol, and for example do not contain polypeptide segments encoded by the HIV-1 Env, Tat, Rev, Vif, Vpr and / or Vpu genes.

[0013] Embodiment 4: The fusion polypeptide according to Embodiment 1, wherein the plurality of polypeptide segments contain or consist of only polypeptide segments encoded by the HIV-1 genes Gag and Nef, and for example do not contain polypeptide segments encoded by the HIV-1 Env, Pol, Tat, Rev, Vif, Vpr and / or Vpu genes.

[0014] Embodiment 5: The fusion polypeptide according to Embodiment 1, wherein the plurality of polypeptide segments contain or consist of only polypeptide segments encoded by the HIV-1 genes Pol and Nef, and for example do not contain polypeptide segments encoded by the HIV-1 Env, Gag, Tat, Rev, Vif, Vpr and / or Vpu genes.

[0015] Embodiment 6: The fusion polypeptide according to Embodiment 1, wherein the plurality of polypeptide segments contain or consist of only polypeptide segments encoded by the HIV-1 genes Pol and Env, and for example do not contain polypeptide segments encoded by the HIV-1 Gag, Nef, Tat, Rev, Vif, Vpr and / or Vpu genes.

[0016] Embodiment 7: The fusion polypeptide according to Embodiment 1, wherein the plurality of polypeptide segments only contain or consist of polypeptide segments encoded by the HIV-1 Pol gene, and for example, do not contain polypeptide segments encoded by the HIV-1 Env, Gag, Nef, Tat, Rev, Vif, Vpr, and / or Vpu genes.

[0017] Embodiment 8: The fusion polypeptide according to any one of Embodiments 1 to 7, wherein the plurality of polypeptide segments do not contain segments encoded by one, two, three, or four of the HIV Tat, Rev, Vif, Vpr, and Vpu genes.

[0018] Embodiment 9: The fusion polypeptide according to any one of Embodiments 1 to 8, wherein the polypeptide segment is derived from a conserved region within a population of viral proteome sequences.

[0019] Embodiment 10: The fusion polypeptide according to Embodiment 9, wherein the conserved region is more than 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% conserved among HIV-1 subtypes in a population of patients.

[0020] Embodiment 11: The fusion polypeptide according to any one of Embodiments 9 to 10, wherein the conserved region is conserved among one or more of HIV-1 clades A to K, for example, one or more of clades A, B, C, D, and G, or one or more recombinant forms of HIV-1 clades A to K, and combinations thereof.

[0021] Embodiment 12: The fusion polypeptide according to any one of Embodiments 1 to 11, comprising at least 5 and at most 40 polypeptide segments, for example, 5 polypeptide segments and at most 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40 polypeptide segments.

[0022] Embodiment 13: The fusion polypeptide according to any one of Embodiments 1 to 12, wherein each polypeptide segment is at least 8 amino acids in length and at most about 30, for example, at most about 50, for example, at most about 100, for example, at most about 250 amino acids in length, for example, at least 8 amino acids in length and at most 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240 or 250 amino acids in length.

[0023] Embodiment 14: The fusion polypeptide according to any one of Embodiments 1 to 13, wherein the total length of the fusion polypeptide is at least about 350 amino acids and at most about 1000 amino acids, for example, at least about 350 amino acids and at most about 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990 or 1000 amino acids.

[0024] Embodiment 15: The full length of the fusion polypeptide is at least about 500 amino acids and at most about 1000 amino acids, for example, at least about 500 amino acids and at most about 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990 or 1000 amino acids, and is the fusion polypeptide according to any one of Embodiments 1 to 13.

[0025] Embodiment 16: The full length of the fusion polypeptide contains only or consists of polypeptide segments encoded by the HIV-1 genes Gag, Nef, and Pol, is at least about 700 amino acids in length and at most about 800 amino acids in length, for example, at least about 700 amino acids in length and at most about 710, 720, 730, 740, 750, 760, 770, 780, 790, or 800 amino acids in length, and is the fusion polypeptide according to any one of Embodiments 1 to 13 (for example, SEQ ID NOs: 345 to 350, 422 to 423 are exemplary fusion polypeptides).

[0026] Embodiment 17: The full length of the fusion polypeptide contains only or consists of polypeptide segments encoded by the HIV-1 genes Gag and Nef, and including an optional N-terminal signal peptide, is at least about 340 amino acids in length and at most about 500 amino acids in length, for example, at least about 340 amino acids in length and at most about 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, or 500 amino acids in length, and is the fusion polypeptide according to any one of Embodiments 1 to 13 (for example, SEQ ID NOs: 351 to 356, 430 are exemplary fusion polypeptides).

[0027] Embodiment 18: The full length of the fusion polypeptide comprises only or consists of polypeptide segments encoded by the HIV-1 genes Pol and Env, and is at least about 335 amino acids in length and up to about 970 amino acids in length, including an optional N-terminal signal peptide, for example, at least about 335 amino acids in length and up to about 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910, 920, 930, 940, 950, 960 or 970 amino acids in length. The fusion polypeptide according to any one of Embodiments 1 to 13 (for example, SEQ ID NOs: 357 to 366 are exemplary fusion polypeptides).

[0028] Embodiment 19: The full length of the fusion polypeptide comprises only or consists of polypeptide segments encoded by the HIV-1 gene Pol, and is at least about 645 amino acids in length and up to about 675 amino acids in length, for example, at least about 645 amino acids in length and up to about 650, 655, 660, 670, 675, or 680 amino acids in length. The fusion polypeptide according to any one of Embodiments 1 to 13 (for example, SEQ ID NOs: 407 to 410 are exemplary fusion polypeptides).

[0029] Embodiment 20: The full length of the fusion polypeptide comprises only or consists of polypeptide segments encoded by the HIV-1 genes Env, Gag, Nef, and Pol, and is at least about 360 amino acids in length and at most about 510 amino acids in length, including an optional N-terminal signal peptide, for example, at least about 360 amino acids and at most about 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, or 510 amino acids in length, the fusion polypeptide according to any one of Embodiments 1 to 13 (for example, SEQ ID NOs: 367 to 371, 424, 431 to 435 are exemplary fusion polypeptides).

[0030] Embodiment 21: The full length of the fusion polypeptide comprises only or consists of polypeptide segments encoded by the HIV-1 genes Env, Gag, Nef, and Pol, and is at least about 760 amino acids in length and at most about 955 amino acids in length, including an optional N-terminal signal peptide, for example, at least about 760 amino acids and at most about 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910, 920, 930, 940, 950, 955 amino acids in length, the fusion polypeptide according to any one of Embodiments 1 to 13 (for example, SEQ ID NOs: 373 to 377, 411 are exemplary fusion polypeptides).

[0031] Embodiment 22: The full length of the fusion polypeptide is 800 amino acids or less, for example, 795, 790, 785, 780, 775, 770, 765, 760, 755, 750, 745, 740, 735, 730, 725, 720, 715, 710, 705, or 700 amino acids or less, the fusion polypeptide according to any one of Embodiments 1 to 14.

[0032] Embodiment 23: Each polypeptide segment comprises or consists of one or more predicted T cell epitopes, the fusion polypeptide according to any one of Embodiments 1 to 22.

[0033] Embodiment 24: A fusion polypeptide according to any one of Embodiments 1 to 23, which binds to or comprises one or more polypeptide segments presented by one or more human HLA class I alleles (for example, 1, 2, 3, 4, 5, or 6 alleles), for example, within a single subject or among multiple patients.

[0034] Embodiment 25: A fusion polypeptide according to any one of Embodiments 1 to 24, which binds to or comprises one or more polypeptide segments presented by at least one human HLA class I molecule, for example, human A * 0201 HLA class I molecule.

[0035] Embodiment 26: A fusion polypeptide according to any one of Embodiments 1 to 25, which comprises one or more 8mer, 9mer, and / or 10mer polypeptide segments presented by one or more human HLA class I alleles (for example, 1, 2, 3, 4, 5, or 6 alleles), for example, within a single subject.

[0036] Embodiment 27: A fusion polypeptide according to any one of Embodiments 1 to 25, which comprises one or more 25mer polypeptide segments, and each 25mer polypeptide segment comprises one or more 8mer, 9mer, and / or 10mer polypeptide segments presented by one or more human HLA class I alleles (for example, 1, 2, 3, 4, 5, or 6 alleles), for example, within a single subject.

[0037] Embodiment 28: A fusion polypeptide according to any one of Embodiments 1 to 27, which comprises one or more polypeptide segments intracellularly processed and presented by one or more human HLA class II alleles (for example, 1, 2, 3, 4, 5, or 6 alleles), for example, within a single subject.

[0038] Embodiment 29: The fusion polypeptide according to any one of Embodiments 1 to 28, wherein one or more of the polypeptide segments abut or are fused to an adjacent segment.

[0039] Embodiment 30: The fusion polypeptide according to any one of Embodiments 1 to 28, wherein one or more of the polypeptide segments are linked to an adjacent segment by one or more peptide linkers.

[0040] Embodiment 31: The fusion polypeptide according to Embodiment 30, wherein one or more peptide linkers are selected from one or more of a polyalanine linker, a polyglycine linker, a cleavable linker, a flexible linker, a rigid linker, a Nef linking sequence, and combinations thereof.

[0041] Embodiment 32: The fusion polypeptide according to Embodiment 31, wherein the polyalanine linker comprises or consists of 2 or 3 consecutive alanine residues, such as AA, AAA (SEQ ID NO: 378), AAY (SEQ ID NO: 379) or AAX (SEQ ID NO: 380), and X is any amino acid (e.g., A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, Y).

[0042] Embodiment 33: The fusion polypeptide according to Embodiment 31, wherein the flexible linker or the polyglycine linker comprises or consists of GG, GGS (SEQ ID NO: 419), GSG (SEQ ID NO: 420) or GGGS (SEQ ID NO: 421).

[0043] Embodiment 34: The fusion polypeptide according to Embodiment 31, wherein the cleavable linker is selected from 2A cleavable peptides (e.g., foot-and-mouth disease virus (F2A), equine rhinitis A virus (E2A), porcine teschovirus-1 (P2A) and Thosea asigna virus (T2A)), furin recognition / cleavage sequences (e.g., REKR (SEQ ID NO: 382), RRKR (SEQ ID NO: 383), RAKR (SEQ ID NO: 381)), Nef linking sequences, and combinations, derivatives or variants thereof.

[0044] Embodiment 35: The fusion polypeptide according to Embodiment 34, wherein the cleavable linker comprises, or consists of, a furin recognition / cleavage site selected from the group consisting of RAKR (SEQ ID NO: 381), REKR (SEQ ID NO: 382), and RRKR (SEQ ID NO: 383).

[0045] Embodiment 36: The fusion polypeptide according to Embodiment 34 or 35, wherein the cleavable linker comprises, or consists of, an amino acid sequence that is at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least 99% identical to ATNFSLLKQAGDVEENPGP (SEQ ID NO: 384), APVKQTLNFDLLKLAGDVESNPGP (SEQ ID NO: 385), RAKRAPVKQTLNFDLLKLAGDVESNPGP (SEQ ID NO: 386), QCTNYALLKLAGDVESNPGP (SEQ ID NO: 387), or EGRGSLLTCGDVEENPGP (SEQ ID NO: 388), or comprises, or consists of, the amino acid sequence of ATNFSLLKQAGDVEENPGP (SEQ ID NO: 384), APVKQTLNFDLLKLAGDVESNPGP (SEQ ID NO: 385), RAKRAPVKQTLNFDLLKLAGDVESNPGP (SEQ ID NO: 386), QCTNYALLKLAGDVESNPGP (SEQ ID NO: 387), or EGRGSLLTCGDVEENPGP (SEQ ID NO: 388).

[0046] Embodiment 37: The fusion polypeptide according to Embodiment 31, wherein the Nef linker sequence comprises, or consists of, an amino acid sequence that is at least 95%, 96%, 97%, 98%, or 99% identical to VHAGPIA (SEQ ID NO: 389), VHAGPVA (SEQ ID NO: 390), or GALDI (SEQ ID NO: 391), or comprises, or consists of, an amino acid sequence selected from VHAGPIA (SEQ ID NO: 389), VHAGPVA (SEQ ID NO: 390), and GALDI (SEQ ID NO: 391).

[0047] Embodiment 38: The fusion polypeptide according to any one of Embodiments 1 to 37, wherein a plurality of polypeptide segments include at least two polypeptide segments selected from SEQ ID NOs: 1 to 344, for example, at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, or more polypeptide segments.

[0048] Embodiment 39: The fusion polypeptide according to any one of Embodiments 1 to 38, wherein a plurality of polypeptide segments include one or more segments of one or more viral proteins encoded by the HIV-1 Gag gene, or a fragment or partial sequence thereof.

[0049] Embodiment 40: The fusion polypeptide according to Embodiment 39, wherein one or more viral proteins encoded by the HIV-1 Gag gene are selected from p7, p17, and p24, and the fusion polypeptide does not include any p6 protein.

[0050] Embodiment 41: A plurality of polypeptide segments include · SEQ ID NOs: 68 to 146 and 339 to 342, · SEQ ID NOs: 68, 69, 72, 73, 74, 75, 76, 77, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 92, 93, 101, 102, 103, 104, 109, 110, 115, 116, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 139, 140, 141, 142, 143, 144, 145, and 146, · SEQ ID NOs: 76, 77, 86, 87, and 92 to 124, · SEQ ID NOs: 76, 77, 86, 87, 94, and 95, · SEQ ID NOs: 76, 86, and 94, · SEQ ID NOs: 77, 87, and 95, · SEQ ID NOs: 68 to 79 and 92 to 124, · SEQ ID NOs: 70 - 71, 76 - 77, and 94 - 95, · SEQ ID NOs: 78, 79, 96, 99, 100, 107, 108, 113, 114, 121, 122, 123, 124, 137, and 138, · SEQ ID NOs: 78, 99, 107, 113, 121, 123, and 137, · SEQ ID NOs: 78, 79, 90, 91, 97, 98, 99, 100, 105, 106, 107, 108, 111, 112, 113, 114, 117, 118, 119, 120, 121, 122, 123, 124, 137, and 138, · SEQ ID NOs: 78, 90, 97, 105, 111, 117, 119, and 137, and · at least two polypeptide segments comprising, or consisting of, an amino acid sequence selected from SEQ ID NOs: 78 and 137, for example, at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, or more segments, of the fusion polypeptide according to embodiment 39 or 40.

[0051] Embodiment 42: At least two polypeptide segments, for example, at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more segments, comprising, or consisting of, an HIV-1 Gag amino acid sequence corresponding to amino acid residue positions selected from 31 - 53, 37 - 51, 142 - 166, 175 - 199, 183 - 191, 257 - 282, 257 - 290, 265 - 282, 288 - 313, 288 - 321, 296 - 313, 333 - 357, 337 - 361, 341 - 349, 345 - 353, and 429 - 444, of the fusion polypeptide according to any one of embodiments 39 - 41, wherein the amino acid positions are based on SEQ ID NO: 404.

[0052] Embodiment 43: A fusion polypeptide according to any one of Embodiments 39 to 42, wherein the plurality of polypeptide segments do not include one, two, three, four, five, or more polypeptide segments that include or consist of an HIV-1 Gag amino acid sequence or a partial sequence thereof corresponding to amino acid residue positions selected from 1 to 30, 54 to 127, 138 to 146, 370 to 428, and 445 to 500, and the amino acid positions are based on SEQ ID NO: 404.

[0053] Embodiment 44: A fusion polypeptide according to any one of Embodiments 39 to 43, wherein the plurality of polypeptide segments do not include one, two, three, four, five, or more polypeptide segments that include or consist of an HIV-1 Gag amino acid sequence of any one of SEQ ID NOs: 444 to 448, or a sequence or a partial sequence thereof that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to any one of SEQ ID NOs: 444 to 448.

[0054] Embodiment 45: A fusion polypeptide according to any one of Embodiments 1 to 44, wherein the plurality of polypeptide segments include one or more segments of a viral protein encoded by the HIV-1 Nef gene.

[0055] Embodiment 46: The plurality of polypeptide segments are · SEQ ID NOs: 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, and 172, · SEQ ID NOs: 147, 148, 149, 150, 155, 156, 157, 158, 159, 160, 166, 167, 168, 169, 170, and 171, · SEQ ID NOs: 149 to 152, · SEQ ID NOs: 151 and 152, · SEQ ID NOs: 149, 150, 151, 152, 159, 160, 161, 162, 163, 164, 166, 167, 168, 169, 170, 171, 172, 173 and 174, · SEQ ID NOs: 151, 152, 161 and 162, · SEQ ID NOs: 151 and 152, · SEQ ID NOs: 153, 154, 172 and 173, · SEQ ID NOs: 153 and 172, · SEQ ID NOs: 153, 154, 155, 156, 157, 158, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172 and 173, · SEQ ID NOs: 153 and 165, and · at least one polypeptide segment comprising or consisting of an amino acid sequence selected from SEQ ID NO: 153, for example, at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more segments, the fusion polypeptide according to embodiment 45.

[0056] Embodiment 47: A fusion polypeptide according to embodiment 45 or 46, wherein a plurality of polypeptide segments comprise or consist of an HIV-1 Nef amino acid sequence corresponding to amino acid residue positions selected from 64 - 102, 81 - 102, 88 - 97, 91 - 99, 130 - 148, 130 - 154, 134 - 142, 134 - 148, 136 - 148, 137 - 145, 137 - 145 and 117 - 154, for example, at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more segments, and the amino acid positions are based on SEQ ID NO: 405.

[0057] Embodiment 48: A fusion polypeptide according to any one of Embodiments 45 to 47, wherein the plurality of polypeptide segments do not include one, two, three, or more polypeptide segments that include or consist of an HIV-1 Nef amino acid sequence or a partial sequence thereof corresponding to amino acid residue positions selected from 1 to 63, 103 to 116, and 155 to 206, and the amino acid positions are based on SEQ ID NO: 405.

[0058] Embodiment 49: A fusion polypeptide according to any one of Embodiments 45 to 48, wherein the plurality of polypeptide segments do not include one, two, three, or more polypeptide segments that include or consist of an HIV-1 Nef amino acid sequence of any one of SEQ ID NOs: 449 to 451, or a sequence or a partial sequence thereof that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to any one of SEQ ID NOs: 449 to 451.

[0059] Embodiment 50: A fusion polypeptide according to any one of Embodiments 1 to 49, wherein the plurality of polypeptide segments include or consist of one or more segments of viral proteins encoded by the HIV-1 Gag and Nef genes.

[0060] Embodiment 51: The plurality of polypeptide segments are · SEQ ID NOs: 68 to 79 and 92 to 124, 149, 150, 151, 152, 159, 160, 161, 162, 163, 164, 166, 167, 168, 169, 170, 171, 172, 173, and 174, · SEQ ID NOs: 70, 71, 76, 77, 94, 95, 151, 152, 161, and 162, · SEQ ID NOs: 70, 76, 94, 151, and 161, and · At least two polypeptide segments, for example, at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, or more segments, comprising or consisting of an amino acid sequence selected from SEQ ID NOs: 71, 77, 95, 152, and 162, of the fusion polypeptide according to Embodiment 50.

[0061] Embodiment 52: In the order from the N-terminus to the C-terminus, optionally joined or connected by one or more linkers, · SEQ ID NOs: 70, 76, 94, 151, and 161, or · The fusion polypeptide according to any one of Embodiments 1 to 4 and 8 to 51, comprising or consisting of polypeptide segments of SEQ ID NOs: 71, 77, 95, 152, and 162.

[0062] Embodiment 53: The fusion polypeptide according to any one of Embodiments 1 to 52, wherein a plurality of polypeptide segments comprise or consist of an amino acid sequence of any one of SEQ ID NOs: 351 to 356 and 430, or a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to any one of SEQ ID NOs: 351 to 356 and 430.

[0063] Embodiment 54: The fusion polypeptide according to any one of Embodiments 1, 2, 6, and 9 to 53, wherein a plurality of polypeptide segments comprise one or more segments of one or more viral proteins encoded by the HIV-1 Env gene.

[0064] Embodiment 55: The fusion polypeptide according to Embodiment 54, wherein one or more viral proteins encoded by the HIV-1 Env gene are selected from gp120 and gp41.

[0065] Embodiment 56: A plurality of polypeptide segments are · SEQ ID NOs: 1 to 67 and 338, · SEQ ID NOs: 2, 3, 8, 9, 13, 14, 17, 18, 23, 24, 25, 26, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 58, 59, 62, 63, 64, 65, 66 and 67, · SEQ ID NOs: 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 28, 29, 30, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 and 338, · SEQ ID NOs: 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 28, 29, 30, 37, 38, 41 and 42, · SEQ ID NOs: 28, 29, 30 and 41 to 56, · SEQ ID NOs: 28, 29, 41 and 42, · SEQ ID NOs: 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 37 and 38, · SEQ ID NOs: 4, 5, 11, 12, 37 and 38, · SEQ ID NOs: 6, 7, 15, 16, 21, 22, 30, 60 and 61, · SEQ ID NOs: 6, 15, 21, 30 and 60, · SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 14, 15, 16, 19, 20, 27, 55, 56, 57, 58, 59, 60, 61 and 338, · SEQ ID NOs: 1, 10, 19, 27, 55, 56 and 57, and · At least two polypeptide segments comprising or consisting of amino acid sequences selected from SEQ ID NOs: 6, 15 and 60, for example, at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40 or more segments, the fusion polypeptide according to Embodiment 54 or 55.

[0066] Embodiment 57: A fusion polypeptide according to any one of Embodiments 54-56, wherein a plurality of polypeptide segments comprise or consist of an HIV-1 Env amino acid sequence corresponding to amino acid residue positions selected from 28-52, 34-48, 34-47, 36-44, 59-83, 64-83, 66-83, 67-75, 113-137, 235-259, 586-594, 586-610, 589-606, and 594-602, for example, at least 2 polypeptide segments, such as at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or more segments, and the amino acid positions are based on SEQ ID NO: 403.

[0067] Embodiment 58: A fusion polypeptide according to any one of Embodiments 54-57, wherein a plurality of polypeptide segments do not include 1, 2, 3, 4, 5, 6, or more polypeptide segments that comprise or consist of an HIV-1 Env amino acid sequence or a partial sequence thereof corresponding to amino acid residue positions selected from 1-27, 53-58, 84-112, 138-234, 269-474, 490-501, 611-856, and the amino acid positions are based on SEQ ID NO: 403.

[0068] Embodiment 59: A fusion polypeptide according to any one of Embodiments 54-57, wherein a plurality of polypeptide segments do not include 1, 2, 3, 4, 5, or more polypeptide segments that comprise or consist of an HIV-1 Env amino acid sequence of any one of SEQ ID NOs: 437-443, or a sequence or a partial sequence thereof that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to any one of SEQ ID NOs: 437-443.

[0069] Embodiment 60: The fusion polypeptide according to any one of Embodiments 1 to 58, wherein a plurality of polypeptide segments comprise or consist of one or more segments of one or more viral proteins encoded by the HIV-1 Pol gene.

[0070] Embodiment 61: The fusion polypeptide according to Embodiment 60, wherein one or more viral proteins encoded by the HIV-1 Pol gene are selected from one or more of protease (PR), reverse transcriptase (RT), and integrase (INT).

[0071] Embodiment 62: The plurality of polypeptide segments are · SEQ ID NOs: 174 to 337 and 343 to 344, · SEQ ID NOs: 174, 175, 178, 179, 180, 181, 182, 183, 184, 185, 193, 194, 195, 196, 197, 198, 199, 200, 203, 204, 205, 206, 207, 208, 213, 214, 221, 222, 236, 237, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 263, 264, 266, 267, 268, 269, 270, 271, 272, 273, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 305, 306, 307, 308, 309, 310, 313, 314, 315, 316, 317, 318, 321 and 322, · SEQ ID NOs: 180, 181, 182, 183, 184, 185, 186, 187, 190, 191, 192, 193, 194, 195, 196, 221, 222, 294, 295, 296, 297, 298, 299, 300, 301, 305, 306, 307, 308, 311, 312, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336 and 337, · Sequence numbers 180, 181, 186, 187, 221, 222, 294, 295, 307, 308, 321 and 322, · Sequence numbers 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 282, 283, 294, 295, 296, 297, 298, 299, 300, 301, 302, 305, 306, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336 and 337, · Sequence numbers 176, 177, 188, 189, 213, 214, 223, 224, 259, 260, 282, 283, 294, 295, 305, 306, 319 and 320, · Sequence numbers 180, 181, 186, 187, 221, 222, 294, 295, 321 and 322, · Sequence numbers 182 to 202, 292 to 302, 305 and 306, · Sequence numbers 188, 189, 294, 295, 305 and 306, · Array numbers 176, 177, 178, 179, 180, 181, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 282, 283, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336 and 337, · Array numbers 176, 177, 213, 214, 223, 224, 259, 260, 282, 283, 319 and 320, · Array numbers 192, 201, 202, 215, 216, 217, 218, 219, 220, 229, 230, 231, 240, 241, 242, 243, 244, 265, 276, 277, 298, 299, 302, 311, 312, 327, 328, 331, 332, 333, 336 and 337, · Array numbers 192, 201, 215, 217, 219, 229, 230, 240, 241, 243, 265, 276, 298, 302, 311, 327, 331, 333 and 336, · Array numbers 190, 191, 192, 197, 198, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 238, 239, 261, 262, 274, 275, 276, 277, 296, 297, 298, 299, 300, 301, 302, 303, 304, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 343, 344, 375 and 376, · Array numbers 190, 197, 209, 210, 211, 225, 227, 234, 238, 261, 296, 300, 303, 323, 325, 329 and 334, and · At least two polypeptide segments comprising or consisting of an amino acid sequence selected from SEQ ID NOs: 192, 215, 217, 219, 229, 230, 276, 298, 302, 327, 331, 333, and 336, for example, at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, or more segments, of the fusion polypeptide according to Embodiment 60 or 61.

[0072] Embodiment 63: A plurality of polypeptide segments are · SEQ ID NOs: 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 28, 29, 30, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 282, 283, 294, 295, 296, 297, 298, 299, 300, 301, 302, 305, 306, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, and 338, · SEQ ID NOs: 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 28, 29, 30, 37, 38, 41, 42, 176, 177, 188, 189, 213, 214, 223, 224, 259, 260, 282, 283, 294, 295, 305, 306, 319, and 320, · SEQ ID NOs: 28, 29, 30, 41-56, 182-202, 292-302, 305 and 306, · SEQ ID NOs: 28, 29, 41, 42, 188, 189, 294, 295, 305 and 306, · SEQ ID NOs: 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 37, 38, 176, 177, 178, 179, 180, 181, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 282, 283, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336 and 337, and · at least two polypeptide segments comprising, or consisting of, an amino acid sequence selected from SEQ ID NOs: 4, 5, 11, 12, 37, 38, 176, 177, 213, 214, 223, 224, 259, 260, 282, 283, 319 and 320, e.g., at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40 or more segments, of the fusion polypeptide according to any one of embodiments 54-62.

[0073] Embodiment 64: In the order from the N-terminus to the C-terminus, optionally linked or connected by one or more linkers, · SEQ ID NOs: 188, 305, 28, 41, 294, 4, 176, 11, 319, 259, 282, 223, 213 and 37, · SEQ ID NOs: 188, 305, 28, 41 and 294, · SEQ ID NOs: 4, 176, 11, 319, 259, 282, 223, 213 and 37, · SEQ ID NOs: 189, 306, 29, 42, 295, 5, 177, 12, 320, 260, 283, 224, 214, and 38, · SEQ ID NOs: 189, 306, 29, 42, and 295, · SEQ ID NOs: 5, 177, 12, 320, 260, 283, 224, 214, and 38, · SEQ ID NOs: 305, 319, 259, 282, 223, 213, 294, 176, and 188, · SEQ ID NOs: 306, 320, 260, 283, 224, 214, 295, 177, and 189, · SEQ ID NOs: 305, 294, 223, 213, 176, 259, 319, 188, and 282, · SEQ ID NOs: 306, 295, 224, 214, 177, 260, 320, 189, and 283, · SEQ ID NOs: 305, 294, 319, 259, 282, 223, 176, and 188, · SEQ ID NOs: 306, 295, 320, 260, 283, 224, 177, and 189, · SEQ ID NOs: 305, 223, 294, 176, 259, 319, 188, and 282, or · a fusion polypeptide according to any one of embodiments 1, 6, 9 - 38, and 54 - 63, comprising or consisting of a polypeptide segment of SEQ ID NOs: 306, 224, 295, 177, 260, 320, 189, and 283.

[0074] Embodiment 65: At least two polypeptide segments, for example, at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or more segments, comprising or consisting of HIV-1 Pol amino acid sequences corresponding to amino acid residue positions selected from 144 - 168, 152 - 160, 291 - 315, 326 - 350, 328 - 352, 330 - 354, 333 - 354, 334 - 342, 336 - 344, 338 - 346, 374 - 398, 380 - 404, 382 - 390, 388 - 396, 399 - 423, 400 - 424, 406 - 430, 553 - 577, 642 - 666, 650 - 658, 759 - 783, 767 - 775, 768 - 792, 776 - 784, 834 - 858, 940 - 964, 947 - 971, 948 - 956, 948 - 972, 955 - 963, 956 - 964, 980 - 1003, and 988 - 996, and having amino acid positions with reference to SEQ ID NO: 406, the fusion polypeptide according to any one of Embodiments 60 - 64.

[0075] Embodiment 66: One, two, three, four, five, six, seven, eight, nine, ten, or more polypeptide segments, not comprising HIV-1 Pol amino acid sequences or partial sequences thereof corresponding to amino acid residue positions selected from 1 - 55, 118 - 128, 321 - 325, 355 - 366, 432 - 541, 607 - 641, 667 - 682, 709 - 746, 828 - 833, 921 - 930, and having amino acid positions with reference to SEQ ID NO: 406, the fusion polypeptide according to any one of Embodiments 60 - 65.

[0076] Embodiment 67: The fusion polypeptide according to any one of Embodiments 60 to 66, which does not contain 1, 2, 3, 4, 5, or more polypeptide segments, wherein the plurality of polypeptide segments include, or consist of, an HIV-1 Pol amino acid sequence of any one of SEQ ID NOs: 452 to 461, or a sequence or a partial sequence thereof that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to any one of SEQ ID NOs: 452 to 461.

[0077] Embodiment 68: The fusion polypeptide according to any one of Embodiments 1, 6 to 38, and 54 to 67, wherein the plurality of polypeptide segments include, or consist of, an amino acid sequence of any one of SEQ ID NOs: 357 to 366 and 407 to 410, or a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to any one of SEQ ID NOs: 357 to 366 and 407 to 410.

[0078] Embodiment 69: The fusion polypeptide according to any one of Embodiments 1, 3, and 8 to 68, wherein the plurality of polypeptide segments include, or consist of, segments of viral proteins encoded by the Gag, Nef, and Pol genes.

[0079] Embodiment 70: The plurality of polypeptide segments are · SEQ ID NOs: 76, 77, 86, 87, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 149, 150, 151, 152, 180, 181, 182, 183, 184, 185, 186, 187, 190, 191, 192, 193, 194, 195, 196, 221, 222, 294, 295, 296, 297, 298, 299, 300, 301, 305, 306, 307, 308, 311, 312, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 339, 340, 341 and 342, and · at least two polypeptide segments comprising, or consisting of, an amino acid sequence selected from SEQ ID NOs: 76, 77, 86, 87, 94, 95, 151, 152, 181, 182, 186, 187, 221, 222, 294, 195, 307, 308, 321, 322, for example, at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40 or more segments, of the fusion polypeptide according to embodiment 69.

[0080] Embodiment 71: In the order from the N-terminus to the C-terminus, optionally joined or connected by one or more linkers, · SEQ ID NOs: 76, 86, 94, 180, 186, 221, 294, 307, 321 and 151, or · the fusion polypeptide according to embodiment 69 or 70, comprising, or consisting of, polypeptide segments of SEQ ID NOs: 77, 87, 95, 181, 187, 222, 295, 308, 322 and 152.

[0081] Embodiment 72: The fusion polypeptide according to any one of Embodiments 69 to 71, wherein a plurality of polypeptide segments comprise, or consist of, any one amino acid sequence among SEQ ID NOs: 345 to 350, the sequences in Table 1, and SEQ ID NOs: 422 to 424, or a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one among SEQ ID NOs: 345 to 350, the sequences in Table 1, and SEQ ID NOs: 422 to 424.

[0082] Embodiment 73: The fusion polypeptide according to any one of Embodiments 1 to 72, wherein a plurality of polypeptide segments comprise, or consist of, segments of viral proteins encoded by the Gag, Pol, Env, and Nef genes, and each of the plurality of polypeptide segments can bind to, or be presented by, human HLA allele A * 0201.

[0083] Embodiment 74: The fusion polypeptide according to Embodiment 73, wherein each of the plurality of polypeptide segments is 8 to 35 amino acids in length, for example, 9 to 34 amino acids in length, for example, 9 to 25 amino acids in length.

[0084] Embodiment 75: A plurality of polypeptide segments are · SEQ ID NOs: 6, 7, 15, 16, 21, 22, 30, 60, 61, 78, 79, 96, 99, 100, 107, 108, 113, 114, 121, 122, 123, 124, 137, 138, 153, 154, 172, 173, 192, 201, 202, 215, 216, 217, 218, 219, 220, 229, 230, 231, 240, 241, 242, 243, 244, 265, 276, 277, 298, 299, 302, 311, 312, 327, 328, 331, 332, 333, 336 and 337, · SEQ ID NOs: 6, 15, 21, 30, 60, 78, 99, 107, 113, 121, 123, 137, 153, 172, 192, 201, 215, 217, 219, 229, 230, 240, 241, 243, 265, 276, 298, 302, 311, 327, 331, 333 and 336, · SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 10, 11, 12, 13, 14, 15, 16, 19, 20, 27, 55, 56, 57, 58, 59, 60, 61, 78, 79, 90, 91, 97, 98, 99, 100, 105, 106, 107, 108, 111, 112, 113, 114, 117, 118, 119, 120, 121, 122, 123, 124, 137, 138, 153, 154, 155, 156, 157, 158, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 190, 191, 192, 197, 198, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 238, 239, 261, 262, 274, 275, 276, 277, 296, 297, 298, 299, 300, 301, 302, 303, 304, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 343 and 344, · At least two polypeptide segments comprising, or consisting of, an amino acid sequence selected from SEQ ID NOs: 1, 10, 19, 27, 55, 56, 57, 78, 90, 97, 105, 111, 117, 119, 137, 153, 165, 190, 197, 209, 210, 211, 225, 227, 234, 238, 261, 296, 300, 303, 323, 325, 329 and 334, for example, at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40 or more segments, of the fusion polypeptide according to embodiment 73 or 74.

[0085] Embodiment 76: In the order from the N-terminus to the C-terminus, optionally linked or connected by one or more linkers, · SEQ ID NO: 201, 78, 107, 96, 229, 172, 327, 6, 333, 243, 331, 192, 265, 311, 137, 15, 123, 30, 336, 302, 153, 219, 298, 121, 230, 240, 60, 241, 276, 113, 99, 21, 217 and 215, · SEQ ID NO: 78, 296, 1, 339, 197, 329, 232, 323, 303, 234, 90, 261, 274, 238, 211, 325, 137, 227, 209, 190, 341, 57, 225, 27, 210, 119, 19, 165, 334, 117, 153, 10, 97 and 300, or · A fusion polypeptide according to any one of Embodiments 73 to 75, comprising or consisting of polypeptide segments of SEQ ID NO: 296, 1, 78, 197, 339, 227, 261, 274, 238, 325, 137, 329, 303, 234, 90, 232, 27, 57, 225, 323, 190, 341, 119, 19, 165, 334, 117, 153, 10, 97 and 300.

[0086] Embodiment 77: A fusion polypeptide according to any one of Embodiments 73 to 76, wherein the plurality of polypeptide segments comprises or consists of an amino acid sequence of any one of SEQ ID NOs: 367 to 377, 411, 431 to 435, or a sequence that is 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one of SEQ ID NOs: 367 to 377, 411, 431 to 435.

[0087] Embodiment 78: A fusion polypeptide according to any one of Embodiments 1 to 77, wherein the fusion polypeptide does not contain the amino acid sequence YMDD (SEQ ID NO: 462) or YVDD (SEQ ID NO: 463).

[0088] Embodiment 79: The fusion polypeptide according to embodiment 78, which does not contain one or more amino acid sequences selected from SEQ ID NOs: 215, 216, 217, 218, 219, and 220.

[0089] Embodiment 80: The fusion polypeptide according to embodiment 78 or 79, which does not contain one or more amino acid sequences selected from SEQ ID NOs: 209, 210, 211, 212, 213, 214, 343, and 344.

[0090] Embodiment 81: A fusion polypeptide comprising the amino acid sequence of SEQ ID NOs: 345 to 352, 357 to 362, 367, 373, 407 to 411, or 422 to 424, or a sequence that is at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to any one of SEQ ID NOs: 345 to 352, 357 to 362, 367, 373, 407 to 411, 422 to 424, and 431 to 435.

[0091] Embodiment 82: The fusion polypeptide according to any one of embodiments 1 to 81, comprising an N-terminal signal peptide or leader sequence.

[0092] Embodiment 83: The fusion polypeptide according to embodiment 82, wherein the signal peptide or leader sequence is derived from a source protein selected from serum proteins, cytokines, chemokines, chaperone proteins, invariant proteins, and proteins that target proteins to the lysosomal compartment.

[0093] Embodiment 84: The signal peptide or leader sequence is derived from a source protein selected from the group consisting of colony-stimulating factor 2 (CSF2, GM-CSF), tissue-type plasminogen activator (PLAT, t-PA), C-C motif chemokine ligand 7 (CCL7, MCP-3), C-X-C motif chemokine ligand 10 (CXCL10, IP-10), catenin beta 1 (CTNNB1), CD74 (p33; DHLAG; HLADG; Ia-gamma, invariant chain), serum albumin (ALB), polyubiquitin B / C (UBB / UBC), calreticulin (CALR), vesicular stomatitis virus G protein (VSV-G), lysosome-associated membrane protein 1 (LAMP-1), and lysosome-associated membrane protein 2 (LAMP-2), and is the fusion polypeptide according to Embodiment 82 or 83.

[0094] Embodiment 85: The signal peptide or leader sequence is selected from the amino acid sequences of any one of SEQ ID NOs: 393 to 402 and 412 to 413, or sequences that are at least 95%, 96%, 97%, 98%, or 99% identical to any one of SEQ ID NOs: 393 to 402 and 412 to 413, and is the fusion polypeptide according to any one of Embodiments 82 to 84.

[0095] Embodiment 86: The fusion polypeptide is recombinantly produced or chemically synthesized, and is the fusion polypeptide according to any one of Embodiments 1 to 85.

[0096] Embodiment 87: The fusion polypeptide can induce, promote, or stimulate an immune response in humans, and is the fusion polypeptide according to any one of Embodiments 1 to 86.

[0097] Embodiment 88: The fusion polypeptide can induce, promote, or stimulate an immune response against HIV-1 in humans, and is the fusion polypeptide according to any one of Embodiments 1 to 87.

[0098] Embodiment 89: The fusion polypeptide according to any one of Embodiments 1 to 88, which can induce, promote, or stimulate the proliferation and / or activation of one or more cell types selected from monocytes-derived dendritic cells (DCs), CD8+ T cells, and CD4+ T cells. Polynucleotide, lipoplex, expression cassette, vector, host cell

[0099] Embodiment 90: A polynucleotide encoding one or more fusion polypeptides according to any one of Embodiments 1 to 89.

[0100] Embodiment 91: The polynucleotide according to Embodiment 90, wherein the polynucleotide comprises or is in the form of cDNA, mRNA, self-amplifying RNA (SAM), self-replicating RNA, or self-amplifying replicon RNA (RepRNA).

[0101] Embodiment 92: The polynucleotide according to Embodiment 91, wherein the polynucleotide comprises one or more self-replicating or self-amplifying alphavirus replicons.

[0102] Embodiment 93: The polynucleotide according to any one of Embodiments 90 to 92, comprising a nucleic acid sequence of any one of SEQ ID NOs: 414 to 418, or a nucleic acid sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to any one of SEQ ID NOs: 414 to 418.

[0103] Embodiment 94: A lipoplex, such as a lipid nanoparticle (LNP), comprising the polynucleotide according to any one of Embodiments 90 to 93.

[0104] Embodiment 95: An expression cassette comprising the polynucleotide according to any one of Embodiments 90 to 93 operably linked to one or more regulatory sequences.

[0105] Embodiment 96: The expression cassette according to Embodiment 95, wherein the polynucleotide is operably linked to a constitutive promoter and is under its control.

[0106] Embodiment 97: The expression cassette according to Embodiment 95 or 96, wherein the promoter is selected from the CMV promoter, the CAG promoter, and the EF1a promoter.

[0107] Embodiment 98: A vector comprising one or more polynucleotides according to any one of Embodiments 90 to 93, or an expression cassette according to any one of Embodiments 95 to 97.

[0108] Embodiment 99: The vector according to Embodiment 98, wherein the vector is a plasmid vector, a bacterial vector, or a viral vector.

[0109] Embodiment 100: The vector according to Embodiment 98 or 99, wherein the vector is a viral vector or a viral expression vector.

[0110] Embodiment 101: The vector according to any one of Embodiments 98 to 100, wherein the viral vector or the viral expression vector is derived from a DNA virus or an RNA virus.

[0111] Embodiment 102: The vector according to any one of Embodiments 98 to 101, wherein the viral vector or the viral expression vector is derived from a virus selected from the group consisting of adenovirus, adeno-associated virus, arenavirus, alphavirus, poxvirus, cytomegalovirus, rhabdovirus, vesicular stomatitis virus, flavivirus, Maraba virus, and vaccinia virus.

[0112] Embodiment 103: The viral vector or viral expression vector is derived from a virus from a taxonomic family selected from the Adenoviridae, Arenaviridae, Herpesviridae (e.g., cytomegalovirus), Poxviridae (e.g., vaccinia virus, e.g., modified vaccinia Ankara (MVA)), Paramyxoviridae (e.g., measles virus), Flaviviridae (e.g., yellow fever virus), Rhabdoviridae (e.g., vesiculovirus, e.g., Maraba vesiculovirus), Togaviridae (e.g., alphavirus), the vector according to any one of Embodiments 98 to 102.

[0113] Embodiment 104: The viral vector or viral expression vector is an arenavirus vector selected from lymphocytic choriomeningitis mammarenavirus (LCMV), Calomys callosus mammarenavirus (synonym, Pichinde mammarenavirus or Pichinde arenavirus), Guanarito virus (GTOV), Junin virus (JUNV), Lassa virus (LASV), Lujo virus (LUJV), Machupo virus (MACV), Sabia virus (SABV), and Whitewater Arroyo virus (WWAV), the vector according to any one of Embodiments 98 to 103.

[0114] Embodiment 105: The viral vector or viral expression vector is an arenavirus vector selected from lymphocytic choriomeningitis mammarenavirus (LCMV) or Calomys callosus mammarenavirus (synonym, Pichinde mammarenavirus or Pichinde arenavirus), the vector according to Embodiment 104.

[0115] Embodiment 106: The viral vector or viral expression vector is a human adenovirus or a simian adenovirus (e.g., chimpanzee adenovirus, gorilla adenovirus, or rhesus adenovirus), the vector according to any one of Embodiments 98 to 103.

[0116] Embodiment 107: The viral vector or viral expression vector is an adenoviral vector selected from adenovirus serotype 5 (Ad5), adenovirus serotype 26 (Ad26), adenovirus serotype 34 (Ad34), adenovirus serotype 35 (Ad35), adenovirus serotype 48 (Ad48), chimpanzee adenovirus (e.g., ChAd3 (AdC3), ChAd5 (AdC5), ChAd6 (AdC6), ChAd7 (AdC7), ChAd8 (AdC8), ChAd9 (AdC9), ChAd10 (AdC10), ChAd11 (AdC11), ChAd17 (AdC17), ChAd16 (AdC16), ChAd19 (AdC19), ChAd20 (AdC20), ChAd22 (AdC22), ChAd24 (AdC24), ChAdY25, ChAd26 (AdC26), ChAd28 (AdC28), ChAd30 (AdC30), ChAd31 (AdC31), ChAd37 (AdC37), ChAd38 (AdC38), ChAd43 (AdC43), ChAd44 (AdC44), ChAd55 (AdC55), ChAd63 (AdC63), ChAdV63, ChAd68 (AdC68), ChAd73 (AdC73), ChAd82 (AdC82), ChAd83 (AdC83), ChAd143 (AdC143), ChAd144 (AdC144), ChAd145 (AdC145), ChAd147 (AdC147)), gorilla adenovirus (e.g., GC44, GC45, GC46) and rhesus adenovirus (e.g., RhAd51, RhAd52, RhAd53, RhAd54, RhAd55, RhAd56, RhAd57, RhAd58, RhAd59, RhAd60, RhAd61, RhAd62, RhAd63, RhAd64, RhAd65, RhAd66), the vector according to Embodiment 106.

[0117] Embodiment 108: The viral vector or viral expression vector is replication-deficient, replication-impaired, replication-attenuated or replication-competent, the vector according to any one of Embodiments 98 to 107.

[0118] Embodiment 109: The vector according to any one of Embodiments 98 to 108, wherein the viral vector or viral expression vector is an adenovirus vector containing one or more polynucleotides encoding one or more fusion proteins containing any one amino acid sequence of SEQ ID NOs: 345 to 377, 407 to 411, 422 to 424, 430 to 435, or a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one of SEQ ID NOs: 345 to 377, 407 to 411, 422 to 424, 430 to 435.

[0119] Embodiment 110: The vector contains two or more polynucleotides encoding two or more fusion proteins that are at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identical, or 100% identical to the amino acid sequences of SEQ ID NO: 345 and 346, SEQ ID NO: 347 and 348, SEQ ID NO: 349 and 350, SEQ ID NO: 351 and 352, SEQ ID NO: 430 and 352, SEQ ID NO: 357 and 358, SEQ ID NO: 360 and 362, SEQ ID NO: 359 and 361, SEQ ID NO: 351 and 357, SEQ ID NO: 351 and 358, SEQ ID NO: 351 and 359, SEQ ID NO: 351 and 360, SEQ ID NO: 351 and 361, SEQ ID NO: 351 and 362, SEQ ID NO: 351 and 407, SEQ ID NO: 351 and 408, SEQ ID NO: 351 and 409, SEQ ID NO: 351 and 410, SEQ ID NO: 352 and 357, SEQ ID NO: 352 and 358, SEQ ID NO: 352 and 359, SEQ ID NO: 352 and 360, SEQ ID NO: 352 and 361, SEQ ID NO: 352 and 362, SEQ ID NO: 352 and 407, SEQ ID NO: 352 and 408, SEQ ID NO: 352 and 409, SEQ ID NO: 352 and 410, SEQ ID NO: 430 and 357, SEQ ID NO: 430 and 358, SEQ ID NO: 430 and 359, SEQ ID NO: 430 and 360, SEQ ID NO: 430 and 361, SEQ ID NO: 430 and 362, SEQ ID NO: 407 and 409, SEQ ID NO: 407 and 408, SEQ ID NO: 408 and 410, or SEQ ID NO: 409 and 410. The vector according to any one of Embodiments 98 to 109.

[0120] Embodiment 111: A host cell comprising one or more polynucleotides according to any one of Embodiments 90 to 93, or one or more vectors according to any one of Embodiments 98 to 110.

[0121] Embodiment 112: The host cell according to Embodiment 111, wherein one or more polynucleotides are not integrated into the host cell genome, for example, are episomal.

[0122] Embodiment 113: The host cell according to Embodiment 111, wherein one or more polynucleotides are integrated into the host cell genome.

[0123] Embodiment 114: The host cell according to any one of Embodiments 111 to 113, wherein the host cell is a mammalian cell, such as a human cell, such as a cell line selected from BHK-21, A549, Vero, HEK293 (e.g., HEK293E, HEK293F, HEK293H, HEK293T, Expi293 (trademark)) cells, MDCK, Caco-2, and Calu-3.

[0124] Embodiment 115: The host cell according to any one of Embodiments 111 to 114, wherein the host cell is in vitro.

[0125] Embodiment 116: The host cell according to any one of Embodiments 111 to 114, wherein the host cell is in vivo. Composition

[0126] Embodiment 117: An immunogenic composition comprising one or more of the fusion polypeptides according to any one of Embodiments 1 to 89, or one or more polynucleotides according to any one of Embodiments 90 to 93, or one or more vectors according to any one of Embodiments 98 to 110, and a pharmaceutically acceptable carrier.

[0127] Embodiment 118: The immunogenic composition according to Embodiment 117, comprising two or more of the fusion polypeptides according to any one of Embodiments 1 to 89, or two or more polynucleotides according to any one of Embodiments 90 to 93, or two or more vectors according to any one of Embodiments 98 to 110.

[0128] Embodiment 119: The immunogenic composition according to any one of Embodiments 117 to 118, wherein one or more polynucleotides comprise or are in the form of DNA, cDNA, mRNA, or self-replicating RNA.

[0129] Embodiment 120: 1) One or more fusion polypeptides, optionally linked or connected by one or more linkers, in the order from the N-terminus to the C-terminus, · comprising or consisting of the polypeptide segments of SEQ ID NO: 70, 76, 94, 151 and 161, or · SEQ ID NO: 71, 77, 95, 152 and 162, and 2) One or more fusion polypeptides, optionally linked or connected by one or more linkers, in the order from the N-terminus to the C-terminus, · SEQ ID NO: 188, 305, 28, 41, 294, 4, 176, 11, 319, 259, 282, 223, 213 and 37, · SEQ ID NO: 188, 305, 28, 41 and 294, · SEQ ID NO: 4, 176, 11, 319, 259, 282, 223, 213 and 37, · SEQ ID NO: 189, 306, 29, 42, 295, 5, 177, 12, 320, 260, 283, 224, 214 and 38, · SEQ ID NO: 189, 306, 29, 42 and 295, · SEQ ID NO: 5, 177, 12, 320, 260, 283, 224, 214 and 38, · SEQ ID NO: 305, 319, 259, 282, 223, 213, 294, 176 and 188, · SEQ ID NO: 306, 320, 260, 283, 224, 214, 295, 177 and 189, · SEQ ID NO: 305, 294, 223, 213, 176, 259, 319, 188 and 282, · SEQ ID NO: 306, 295, 224, 214, 177, 260, 320, 189 and 283, · SEQ ID NO: 305, 294, 319, 259, 282, 223, 176 and 188, · SEQ ID NO: 306, 295, 320, 260, 283, 224, 177 and 189, · SEQ ID NO: 305, 223, 294, 176, 259, 319, 188 and 282, or The immunogenic composition according to embodiment 117 or 118, comprising one or more fusion polypeptides comprising or consisting of polypeptide segments of SEQ ID NOs: 306, 224, 295, 177, 260, 320, 189 and 283.

[0130] Embodiment 121: The immunogenic composition according to any one of embodiments 117 to 120, comprising one or more adenoviral vectors, each adenoviral vector comprising one or more polynucleotides encoding one or more fusion proteins comprising an amino acid sequence of any one of SEQ ID NOs: 345-377, 407-411, 422-424, 430-435, or a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one of SEQ ID NOs: 345-377, 407-411, 422-424, 430-435.

[0131] Embodiment 122: An immunogenic composition according to any one of Embodiments 117 to 121, comprising one or more viral vectors, each viral vector encoding two or more fusion proteins having an amino acid sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequences of SEQ ID NOs: 345 and 346, SEQ ID NOs: 347 and 348, SEQ ID NOs: 349 and 350, SEQ ID NOs: 351 and 352, SEQ ID NOs: 430 and 352, SEQ ID NOs: 357 and 358, SEQ ID NOs: 360 and 362, SEQ ID NOs: 359 and 361, SEQ ID NOs: 351 and 357, SEQ ID NOs: 351 and 358, SEQ ID NOs: 351 and 359, SEQ ID NOs: 351 and 360, SEQ ID NOs: 351 and 361, SEQ ID NOs: 351 and 362, SEQ ID NOs: 351 and 407, SEQ ID NOs: 351 and 408, SEQ ID NOs: 351 and 409, SEQ ID NOs: 351 and 410, SEQ ID NOs: 352 and 357, SEQ ID NOs: 352 and 358, SEQ ID NOs: 352 and 359, SEQ ID NOs: 352 and 360, SEQ ID NOs: 352 and 361, SEQ ID NOs: 352 and 362, SEQ ID NOs: 352 and 407, SEQ ID NOs: 352 and 408, SEQ ID NOs: 352 and 409, SEQ ID NOs: 352 and 410, SEQ ID NOs: 430 and 357, SEQ ID NOs: 430 and 358, SEQ ID NOs: 430 and 359, SEQ ID NOs: 430 and 360, SEQ ID NOs: 430 and 361, SEQ ID NOs: 430 and 362, SEQ ID NOs: 407 and 409, SEQ ID NOs: 407 and 408, SEQ ID NOs: 408 and 410, or SEQ ID NOs: 409 and 410, and one or more polynucleotides encoding the fusion proteins.

[0132] Embodiment 123: 1) one or more fusion polypeptides comprising the amino acid sequence of any one of SEQ ID NOs: 351 to 356 and 430, or a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one of SEQ ID NOs: 351 to 356 and 430, and 2) One amino acid sequence among SEQ ID NOs: 357 to 366 and 407 to 410, or one or more fusion polypeptides comprising a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one of SEQ ID NOs: 357 to 366 and 407 to 410, the immunogenic composition according to any one of Embodiments 117 to 122.

[0133] Embodiment 124: A pharmaceutical composition comprising one or more of the fusion polypeptides according to any one of Embodiments 1 to 89, or one or more polynucleotides according to any one of Embodiments 90 to 93, or one or more vectors according to any one of Embodiments 98 to 110, and a pharmaceutically acceptable carrier.

[0134] Embodiment 125: The pharmaceutical composition according to Embodiment 124, comprising two or more fusion polypeptides, two or more polynucleotides, or two or more vectors.

[0135] Embodiment 126: The pharmaceutical composition according to Embodiment 124 or 125, further comprising one or more of an adjuvant, an immunostimulant, a detergent, a micelle-forming agent, and an oil.

[0136] Embodiment 127: The pharmaceutical composition according to Embodiment 126, wherein the immunomodulator is selected from Toll-like receptor (TLR) agonists, cytokines (such as IL-2, IL-7, IL-12, IL-15, IL-18, IL-21, IFN-α, IFN-γ, GM-CSF, FLT3LG, and combinations and functional variants thereof), for example, pathogen-associated molecular patterns (PAMPs), cytosine-phosphate-guanosine (CpG) oligodeoxynucleotides, and inhibitors of inhibitory immune checkpoint proteins or stimulants of stimulatory immune checkpoint proteins such as immunostimulatory RNA (isRNA, such as CV8102).

[0137] Embodiment 128: The pharmaceutical composition according to any one of Embodiments 124 to 127, formulated for administration via a route selected from the group consisting of intravenous, intramuscular, intradermal, subcutaneous, and mucosal (e.g., intraoral, intranasal, rectal, vaginal).

[0138] Embodiment 129: The pharmaceutical composition according to any one of Embodiments 124 to 128, formulated as a liquid.

[0139] Embodiment 130: The pharmaceutical composition according to any one of Embodiments 124 to 128, wherein the composition is lyophilized. Kit

[0140] Embodiment 131: A kit comprising one or more unit doses of one or more of the fusion polypeptides according to any one of Embodiments 1 to 89, or one or more of the polynucleotides according to any one of Embodiments 90 to 93, or one or more of the vectors according to any one of Embodiments 98 to 110, or one or more of the immunogenic compositions according to any one of Embodiments 117 to 121, or one or more of the pharmaceutical compositions according to any one of Embodiments 124 to 130.

[0141] Embodiment 132: The kit according to Embodiment 131, wherein one or more unit doses are in a single container.

[0142] Embodiment 133: The kit according to Embodiment 131, wherein one or more unit doses are in two or more separate containers.

[0143] Embodiment 134: The kit according to any one of Embodiments 131 to 133, comprising one or more containers selected from the group consisting of vials, ampoules, and pre-filled syringes.

[0144] Embodiment 135: The kit according to any one of Embodiments 131 to 134, comprising one or more containers containing one or more fusion polypeptides, one or more polynucleotides, or one or more vectors in an aqueous solution.

[0145] Embodiment 136: The kit according to any one of Embodiments 131 to 135, wherein one or more unit doses are the same.

[0146] Embodiment 137: The kit according to any one of Embodiments 131 to 135, wherein one or more unit doses are different.

[0147] Embodiment 138: Comprising one or more unit doses of one or more viral vectors according to any one of Embodiments 98 to 110, wherein the unit dose is about 10 3 ~ about 10 15 viral focus forming units (FFU) or plaque forming units (PFU) or infectious units (IU) or viral particles (vp), for example, about 10 4 ~ about 10 7 viral FFU or PFU or IU or vp, for example, about 10 3 ~ about 10 4 , 10 5 , 10 6 , 10 7 , 10 8 , 10 9 , 10 10 , 10 11 , 10 12 , 10 13 , 10 14 or 10 15 within the range of viral FFU or PFU or IU or vp, the kit according to any one of Embodiments 131 to 137.

[0148] Embodiment 139: The kit according to any one of Embodiments 131 to 138, comprising two or more of the fusion polypeptides according to any one of Embodiments 1 to 89, or two or more polynucleotides according to any one of Embodiments 90 to 93, or two or more vectors according to any one of Embodiments 98 to 110.

[0149] Embodiment 140: Comprising two or more polynucleotides encoding a fusion polypeptide or two or more vectors expressing a fusion polypeptide, wherein the fusion polypeptide is 1) One or more fusion polypeptides, optionally linked or connected by one or more linkers, in order from the N-terminus to the C-terminus, comprising or consisting of: · SEQ ID NO: 70, 76, 94, 151 and 161, or · One or more polypeptide segments comprising or consisting of SEQ ID NO: 71, 77, 95, 152 and 162, 2) One or more fusion polypeptides, optionally linked or connected by one or more linkers, in order from the N-terminus to the C-terminus, comprising: · SEQ ID NO: 188, 305, 28, 41, 294, 4, 176, 11, 319, 259, 282, 223, 213 and 37, · SEQ ID NO: 188, 305, 28, 41 and 294, · SEQ ID NO: 4, 176, 11, 319, 259, 282, 223, 213 and 37, · SEQ ID NO: 189, 306, 29, 42, 295, 5, 177, 12, 320, 260, 283, 224, 214 and 38, · SEQ ID NO: 189, 306, 29, 42 and 295, · SEQ ID NO: 5, 177, 12, 320, 260, 283, 224, 214 and 38, · SEQ ID NO: 305, 319, 259, 282, 223, 213, 294, 176 and 188, · SEQ ID NO: 306, 320, 260, 283, 224, 214, 295, 177 and 189, · SEQ ID NO: 305, 294, 223, 213, 176, 259, 319, 188 and 282, · SEQ ID NO: 306, 295, 224, 214, 177, 260, 320, 189 and 283, · SEQ ID NO: 305, 294, 319, 259, 282, 223, 176 and 188, · SEQ ID NO: 306, 295, 320, 260, 283, 224, 177 and 189, · SEQ ID NO: 305, 223, 294, 176, 259, 319, 188 and 282, or The kit according to Embodiment 139, comprising one or more fusion polypeptides comprising or consisting of polypeptide segments of SEQ ID NOs: 306, 224, 295, 177, 260, 320, 189 and 283.

[0150] Embodiment 141: Comprising two or more polynucleotides encoding a fusion polypeptide or two or more vectors expressing a fusion polypeptide, wherein the fusion polypeptide 1) One or more fusion polypeptides comprising an amino acid sequence of any one of SEQ ID NOs: 351 to 356 and 430, or one or more polynucleotides encoding a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one of SEQ ID NOs: 351 to 356 and 430, or one or more vectors capable of expressing the same, and 2) One or more fusion polypeptides comprising an amino acid sequence of any one of SEQ ID NOs: 357 to 366 and 407 to 410, or one or more polynucleotides encoding a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one of SEQ ID NOs: 357 to 366 and 407 to 410, or one or more vectors capable of expressing the same, the kit according to Embodiment 139.

[0151] Embodiment 142: Comprising one or more polynucleotides encoding a fusion polypeptide or one or more vectors expressing a fusion polypeptide, wherein the fusion polypeptide is joined or connected by one or more linkers, optionally, in order from the N-terminus to the C-terminus · SEQ ID NOs: 201, 78, 107, 96, 229, 172, 327, 6, 333, 243, 331, 192, 265, 311, 137, 15, 123, 30, 336, 302, 153, 219, 298, 121, 230, 240, 60, 241, 276, 113, 99, 21, 217 and 215, · SEQ ID NOs: 78, 296, 1, 339, 197, 329, 232, 323, 303, 234, 90, 261, 274, 238, 211, 325, 137, 227, 209, 190, 341, 57, 225, 27, 210, 119, 19, 165, 334, 117, 153, 10, 97 and 300, or · The kit according to any one of Embodiments 131 to 141, comprising or consisting of a polypeptide segment of SEQ ID NOs: 296, 1, 78, 197, 339, 227, 261, 274, 238, 325, 137, 329, 303, 234, 90, 232, 27, 57, 225, 323, 190, 341, 119, 19, 165, 334, 117, 153, 10, 97 and 300.

[0152] Embodiment 143: The kit according to any one of Embodiments 131 to 142, comprising one or more polynucleotides encoding a fusion polypeptide or one or more vectors expressing a fusion polypeptide, wherein the fusion polypeptide comprises an amino acid sequence of any one of SEQ ID NOs: 345 to 377, 411, 422 to 424 and 430 to 435, or a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one of SEQ ID NOs: 345 to 377, 411, 422 to 424 and 430 to 435, or consisting of the same.

[0153] Embodiment 144: The kit according to any one of Embodiments 131 to 143, comprising one or more adenovirus vectors, each adenovirus vector comprising one or more polynucleotides encoding one or more fusion proteins comprising any one of the amino acid sequences of SEQ ID NOs: 345 to 377, 407 to 411, 422 to 424, 430 to 435, or a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one of SEQ ID NOs: 345 to 377, 407 to 411, 422 to 424, 430 to 435.

[0154] Embodiment 145: A kit according to any one of Embodiments 131 to 144, comprising one or more viral vectors, each viral vector encoding two or more fusion proteins having an amino acid sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence of any one of SEQ ID NO: 345 and 346, SEQ ID NO: 347 and 348, SEQ ID NO: 349 and 350, SEQ ID NO: 351 and 352, SEQ ID NO: 430 and 352, SEQ ID NO: 357 and 358, SEQ ID NO: 360 and 362, SEQ ID NO: 359 and 361, SEQ ID NO: 351 and 357, SEQ ID NO: 351 and 358, SEQ ID NO: 351 and 359, SEQ ID NO: 351 and 360, SEQ ID NO: 351 and 361, SEQ ID NO: 351 and 362, SEQ ID NO: 351 and 407, SEQ ID NO: 351 and 408, SEQ ID NO: 351 and 409, SEQ ID NO: 351 and 410, SEQ ID NO: 352 and 357, SEQ ID NO: 352 and 358, SEQ ID NO: 352 and 359, SEQ ID NO: 352 and 360, SEQ ID NO: 352 and 361, SEQ ID NO: 352 and 362, SEQ ID NO: 352 and 407, SEQ ID NO: 352 and 408, SEQ ID NO: 352 and 409, SEQ ID NO: 352 and 410, SEQ ID NO: 430 and 357, SEQ ID NO: 430 and 358, SEQ ID NO: 430 and 359, SEQ ID NO: 430 and 360, SEQ ID NO: 430 and 361, SEQ ID NO: 430 and 362, SEQ ID NO: 407 and 409, SEQ ID NO: 407 and 408, SEQ ID NO: 408 and 410, or SEQ ID NO: 409 and 410.

[0155] Embodiment 146: A kit according to any one of Embodiments 131 to 145, further comprising one or more unit doses of one or more additional therapeutic agents.

[0156] Embodiment 147: A kit according to Embodiment 146, comprising one or more agents that activate latent HIV, for example, one or more latency reversing agents (LRAs).

[0157] Embodiment 148: The kit according to Embodiment 146 or 147, comprising one or more LRAs selected from the group consisting of agonists or activators of one or more Toll-like receptors (TLRs), histone deacetylase (HDAC) inhibitors, proteasome inhibitors, protein kinase C (PKC) activators, Smyd2 inhibitors, BET-bromodomain 4 (BRD4) inhibitors, ionomycin, apoptosis protein inhibitor (IAP) antagonists, and second mitochondria-derived caspase activator (SMAC) mimetics.

[0158] Embodiment 149: The kit according to any one of Embodiments 146 to 148, comprising one or more agonists or activators of one or more Toll-like receptors (TLRs).

[0159] Embodiment 150: The kit according to Embodiment 149, wherein the TLR agonist or activator is selected from the group consisting of TLR2 agonists, TLR3 agonists, TLR4 agonists, TLR5 agonists, TLR7 agonists, TLR8 agonists, and TLR9 agonists.

[0160] Embodiment 151: The TLR7 agonist is selected from the group consisting of GS9620 (vesatolimod), R848 (resiquimod), DS-0509, LHC-165, and TMX-101 (imiquimod), and / or the TLR8 agonist is selected from the group consisting of GS-9688, R848 (resiquimod), CV8102 (dual TLR7 / TLR8 agonist), and NKTR-262 (dual TLR7 / TLR8 agonist). The kit according to Embodiment 149 or 150.

[0161] Embodiment 152: The kit according to any one of Embodiments 149 to 151, wherein the TLR9 agonist is selected from the group consisting of AST-008, cobitolimod, CMP-001, IMO-2055, IMO-2125, retifimod, MGN-1601, BB-001, BB-006, IMO-3100, IMO-8400, IR-103, IMO-9200, agatrimod, DIMS-9054, DV-1079, DV-1179, AZD-1419, lefitolimod (MGN-1703), CYT-003, CYT-003-QbG10, chilsonimod, and PUL-042.

[0162] Embodiment 153: The kit according to any one of Embodiments 146 to 152, comprising one or more interleukin receptor agonists of interleukin selected from IL-2, IL-7, IL-12, IL-15, IL-18, IL-21, IFN-α, IFN-γ, GM-CSF, FLT3LG.

[0163] Embodiment 154: The kit of Embodiment 153, comprising one or more cytokines selected from the group consisting of IL-2, IL-7, IL-12, IL-15, IL-18, IL-21, IFN-α, IFN-γ, GM-CSF, FLT3LG, and combinations and functional variants thereof.

[0164] Embodiment 155: The kit according to any one of Embodiments 146 to 154, comprising one or more natural immune activators.

[0165] Embodiment 156: The kit according to Embodiment 155, wherein the one or more innate immune activators include agonists of receptors selected from the group consisting of non-coding immunostimulatory polynucleotides (e.g., pathogen-associated molecular patterns (PAMPs), cytosine-phosphate-guanosine (CpG) oligodeoxynucleotides, and immunostimulatory RNAs (isRNAs, e.g., CV8102)), fms-related tyrosine kinase 3 (FLT3), interferon gene stimulator (STING) receptor, DExD / H box helicase 58 (DDX58; also known as RIG-I), and nucleotide-binding oligomerization domain-containing 2 (NOD2).

[0166] Embodiment 157: The kit according to any one of Embodiments 146 to 156, comprising one or more blockers, antagonists, or inhibitors of inhibitory immune checkpoint proteins or receptors, and / or one or more activators or agonists of stimulatory immune checkpoint proteins or receptors.

[0167] Embodiment 158: One or more immune checkpoint proteins or receptors include CD27, CD70, CD40, CD40LG, CD47, CD48 (SLAMF2), Transmembrane and Immunoglobulin Domain Containing 2 (TMIGD2, CD28H), CD84 (LY9B, SLAMF5), CD96, CD160, MS4A1 (CD20), CD244 (SLAMF4), CD276 (B7H3), V-set domain-containing T cell activation inhibitor 1 (VTCN1, B7H4), V-set immune regulatory receptor (VSIR, B7H5, VISTA), Immunoglobulin Superfamily Member 11 (IGSF11, VSIG3), Natural Killer Cell Cytotoxicity Receptor 3 Ligand 1 (NCR3LG1, B7H6), HERV-H LTR-associated 2 (HHLA2, B7H7), Inducible T cell co-stimulator (ICOS, CD278), Inducible T cell co-stimulator ligand (ICOSLG, B7H2), TNF Receptor Superfamily Member 4 (TNFRSF4, OX40), TNF Superfamily Member 4 (TNFSF4, OX40L), TNFRSF8 (CD30), TNFSF8 (CD30L), TNFRSF10A (CD261, DR4, TRAILR1), TNFRSF9 (CD137), TNFSF9 (CD137L), TNFRSF10B (CD262, DR5, TRAILR2), TNFRSF10 (TRAIL), TNFRSF14 (HVEM, CD270), TNFSF14 (HVEML), CD272 (B and T lymphocyte associated (BTLA)), TNFRSF17 (BCMA, CD269), TNFSF13B (BAFF), TNFRSF18 (GITR), TNFSF18 (GITRL), MHC Class I Polypeptide Related Sequence A (MICA), MHC Class I Polypeptide Related Sequence B (MICB), CD274 (CD274, PDL1, PD-L1), Programmed Cell Death 1 (PDCD1, PD1, PD-1), Cytotoxic T Lymphocyte-associated Protein 4 (CTLA4, CD152), CD80 (B7-1), CD28, nectin cell adhesion molecule 2 (NECTIN2, CD112), CD226 (DNAM-1), Poliovirus Receptor (PVR) Cell Adhesion Molecule (PVR, CD155), PVR-related Immunoglobulin Domain-containing (PVRIG, CD112R),A T cell immunoreceptor comprising Ig and ITIM domains (TIGIT), T cell immunoglobulin and mucin domain-containing 4 (TIMD4; TIM4), hepatitis A virus cellular receptor 2 (HAVCR2, TIMD3, TIM3), galectin 9 (LGALS9), lymphocyte activation 3 (LAG3, CD223), signaling lymphocyte activation molecule family member 1 (SLAMF1, SLAM, CD150), lymphocyte antigen 9 (LY9, CD229, SLAMF3), SLAM family member 6 (SLAMF6, CD352), SLAM family member 7 (SLAMF7, CD319), UL16-binding protein 1 (ULBP1), UL16-binding protein 2 (ULBP2), UL16-binding protein 3 (ULBP3), retinoic acid early transcript 1E (RAET1E; ULBP4), retinoic acid early transcript 1G (RAET1G; ULBP5), retinoic acid early transcript 1L (RAET1L; ULBP6), lymphocyte antigen 3 (CD223), killer cell immunoglobulin-like receptor, three Ig domains, and long cytoplasmic tail 1 (KIR, CD158E1), killer cell lectin-like receptor C1 (KLRC1, NKG2A, CD159A), killer cell lectin-like receptor K1 (KLRK1, NKG2D, CD314), killer cell lectin-like receptor C2 (KLRC2, CD159c, NKG2C), killer cell lectin-like receptor C3 (KLRC3, NKG2E), killer cell lectin-like receptor C4 (KLRC4, NKG2F), killer cell immunoglobulin-like receptor, two Ig domains, and long cytoplasmic tail 1 (KIR2DL1), killer cell immunoglobulin-like receptor, two Ig domains, and long cytoplasmic tail 2 (KIR2DL2), killer cell immunoglobulin-like receptor, two Ig domains, and long cytoplasmic tail 3 (KIR2DL3), killer cell immunoglobulin-like receptor, three Ig domains, and long cytoplasmic tail 1 (KIR3DL1), killer cell lectin-like receptor D1 (KLRD1), SLAM family member 7 (SLAMF7), the kit according to embodiment 157, selected from the group consisting of.,

[0168] Embodiment 159: The kit according to Embodiment 157 or 158, comprising one or more blockers, antagonists, or inhibitors of one or more T cell inhibitory immune checkpoint proteins or receptors.

[0169] Embodiment 160: The kit according to Embodiment 159, wherein the T cell inhibitory immune checkpoint protein or receptor is selected from the group consisting of CD274 (CD274, PDL1, PD-L1), programmed cell death 1 ligand 2 (PDCD1LG2, PD-L2, CD273), programmed cell death 1 (PDCD1, PD1, PD-1), cytotoxic T lymphocyte-associated protein 4 (CTLA4, CD152), CD276 (B7H3), V-set domain-containing T cell activation inhibitor 1 (VTCN1, B7H4), V-set immunoregulatory receptor (VSIR, B7H5, VISTA), immunoglobulin superfamily member 11 (IGSF11, VSIG3), TNFRSF14 (HVEM, CD270), TNFSF14 (HVEML), CD272 (B and T lymphocyte-associated (BTLA)), PVR-related immunoglobulin domain-containing (PVRIG, CD112R), T cell immunoreceptor containing Ig and ITIM domains (TIGIT), lymphocyte activation 3 (LAG3, CD223), hepatitis A virus cellular receptor 2 (HAVCR2, TIMD3, TIM3), galectin 9 (LGALS9), killer cell immunoglobulin-like receptor, three Ig domains, and long cytoplasmic tail 1 (KIR, CD158E1), killer cell immunoglobulin-like receptor, two Ig domains, and long cytoplasmic tail 1 (KIR2DL1), killer cell immunoglobulin-like receptor, two Ig domains, and long cytoplasmic tail 2 (KIR2DL2), killer cell immunoglobulin-like receptor, two Ig domains, and long cytoplasmic tail 3 (KIR2DL3), killer cell immunoglobulin-like receptor, three Ig domains, and long cytoplasmic tail 1 (KIR3DL1).

[0170] Embodiment 161: The kit according to any one of Embodiments 157 to 160, comprising one or more agonists or activators of one or more T cell-stimulating immune checkpoint proteins or receptors.

[0171] Embodiment 162: The kit according to Embodiment 161, wherein the T cell-stimulating immune checkpoint protein or receptor is selected from the group consisting of CD27, CD70, CD40, CD40LG, inducible T cell co-stimulator (ICOS, CD278), inducible T cell co-stimulator ligand (ICOSLG, B7H2), TNF receptor superfamily member 4 (TNFRSF4, OX40), TNF superfamily member 4 (TNFSF4, OX40L), TNFRSF9 (CD137), TNFSF9 (CD137L), TNFRSF18 (GITR), TNFSF18 (GITRL), CD80 (B7-1), CD28, nectin cell adhesion molecule 2 (NECTIN2, CD112), CD226 (DNAM-1), and poliovirus receptor (PVR) cell adhesion molecule (PVR, CD155).

[0172] Embodiment 163: The kit according to any one of Embodiments 157 to 162, comprising one or more blockers, antagonists, or inhibitors of one or more NK cell-inhibitory immune checkpoint proteins or receptors.

[0173] Embodiment 164: The kit embodiment 163, wherein the NK cell inhibitory immune checkpoint protein or receptor is selected from the group consisting of killer cell immunoglobulin-like receptor, three Ig domains, and long cytoplasmic tail 1 (KIR, CD158E1); killer cell immunoglobulin-like receptor, two Ig domains, and long cytoplasmic tail 1 (KIR2DL1); killer cell immunoglobulin-like receptor, two Ig domains, and long cytoplasmic tail 2 (KIR2DL2); killer cell immunoglobulin-like receptor, two Ig domains, and long cytoplasmic tail 3 (KIR2DL3); killer cell immunoglobulin-like receptor, three Ig domains, and long cytoplasmic tail 1 (KIR3DL1); killer cell lectin-like receptor C1 (KLRC1, NKG2A, CD159A); and killer cell lectin-like receptor D1 (KLRD1, CD94).

[0174] Embodiment 165: The kit according to any one of embodiments 157 to 164, comprising one or more agonists or activators of one or more NK cell-stimulating immune checkpoint proteins or receptors.

[0175] Embodiment 166: The kit according to embodiment 165, wherein the NK cell-stimulating immune checkpoint protein or receptor is selected from CD16, CD226 (DNAM-1); killer cell lectin-like receptor K1 (KLRK1, NKG2D, CD314); and SLAM family member 7 (SLAMF7).

[0176] Embodiment 167: The kit according to any one of embodiments 157 to 166, wherein the one or more immune checkpoint inhibitors comprise a proteinaceous inhibitor of PD-L1 (CD274), PD-1 (PDCD1), or CTLA4.

[0177] Embodiment 168: The protein inhibitor of CTLA4 is selected from the group consisting of ipilimumab, tremelimumab, BMS-986218, AGEN1181, AGEN1884 (zalifrelimab), BMS-986249, MK-1308, REGN-4659, ADU-1604, CS-1002, BCD-145, APL-509, JS-007, BA-3071, ONC-392, AGEN-2041, JHL-1155, KN-044, CG-0161, ATOR-1144, PBI-5D3H5, FPT-155 (CTLA4 / PD-L1 / CD28), PF-06936308 (PD-1 / CTLA4), MGD-019 (PD-1 / CTLA4), KN-046 (PD-1 / CTLA4), MEDI-5752 (CTLA4 / PD-1), XmAb-20717 (PD-1 / CTLA4), and AK-104 (CTLA4 / PD-1), and is the kit according to Embodiment 167.

[0178] Embodiment 169: The proteinaceous inhibitor of PD-L1 (CD274) or PD-1 (PDCD1) is pembrolizumab, nivolumab, semiprimab, pidilizumab, AB122 (zimberelimab), AMP-224, MEDI0680 (AMP-514), spartalizumab, atezolizumab, avelumab, durvalumab, BMS-936559, CK-301, PF-06801591, BGB-A317 (tislelizumab), GLS-010 (WBP-3055), AK-103 (HX-008), AK-105, CS-1003, HLX-10, MGA-012, BI-754091, AGEN-2034 (balstilimab), JS-001 (toripalimab), JNJ-63723283, genolimuzumab (CBT-501), LZM-009, BCD-100, LY-3300054, SHR-1201, SHR-1210 (camrelizumab), Sym-021, ABBV-181, PD1-PIK, BAT-1306, (MSB0010718C), CX-072, CBT-502, TSR-042 (dostarlimab), MSB-2311, JTX-4014, BGB-A333, SHR-1316, CS-1001 (WBP-3155, KN-035, IBI-308 (sintilimab), HLX-20, KL-A167, STI-A1014, STI-A1015 (IMC-001), BCD-135, FAZ-053, TQB-2450, MDX1105-01, FPT-155 (CTLA4 / PD-L1 / CD28), PF-06936308 (PD-1 / CTLA4), MGD-013 (PD-1 / LAG-3), FS-118 (LAG-3 / PD-L1) MGD-019 (PD-1 / CTLA4), KN-046 (PD-1 / CTLA4), MEDI-5752 (CTLA4 / PD-1), RO-7121661 (PD-1 / TIM-3), XmAb-20717 (PD-1 / CTLA4), AK-104 (CTLA4 / PD-1), M7824 (PD-L1 / TGFβ-EC domain), CA-170 (PD-L1 / VISTA), CDX-527 (CD27 / PD-L1), LY-3415244 (TIM3 / PDL1), and INBRX-105 (4-1BB / PDL1), and the kit according to Embodiment 167 selected from the group consisting of

[0179] Embodiment 170: The kit according to any one of Embodiments 157 to 169, wherein the one or more immune checkpoint inhibitors include small molecule inhibitors of CD274 (PDL1, PD-L1), programmed cell death 1 (PDCD1, PD1, PD-1), or CTLA4.

[0180] Embodiment 171: The kit according to Embodiment 170, wherein the small molecule inhibitor of CD274 or PDCD1 is selected from the group consisting of GS-4224, GS-4416, INCB086550, and MAX10181.

[0181] Embodiment 172: The kit according to Embodiment 170, wherein the small molecule inhibitor of CTLA4 includes BPI-002.

[0182] Embodiment 173: The kit according to any one of Embodiments 146 to 172, further comprising one or more antiviral agents.

[0183] Embodiment 174: The kit according to Embodiment 173, wherein the one or more antiviral agents are selected from the group consisting of HIV protease inhibitors, HIV reverse transcriptase inhibitors, HIV integrase inhibitors, HIV non-catalytic site (or allosteric) integrase inhibitors, HIV entry (fusion) inhibitors, HIV maturation inhibitors, and capsid inhibitors. Method for treating or preventing HIV

[0184] Embodiment 175: A method for inducing an immune response against human immunodeficiency virus (HIV) in a subject in need thereof, the method comprising administering the pharmaceutical composition according to any one of Embodiments 124 to 130, or the immunogenic composition according to any one of Embodiments 117 to 121.

[0185] Embodiment 176: A method for treating or preventing human immunodeficiency virus (HIV) in a subject in need thereof, the method comprising administering to the subject the pharmaceutical composition according to any one of Embodiments 124 to 130, or the immunogenic composition according to any one of Embodiments 117 to 121.

[0186] Embodiment 177: The method according to Embodiment 175 or 176, comprising administering a single fusion polypeptide, or a polynucleotide or viral expression vector encoding the fusion polypeptide, wherein the fusion polypeptide comprises two or more multivalent polypeptide segments, for example, divalent polypeptide segments.

[0187] Embodiment 178: The method according to Embodiment 175 or 176, wherein two or more fusion polypeptides, or two or more viral expression vectors encoding the fusion polypeptides, are administered to the subject simultaneously or in parallel.

[0188] Embodiment 179: The method according to any one of Embodiments 175 to 178, wherein two or more fusion polypeptides, or two or more polynucleotides, or two or more viral expression vectors encoding the fusion polypeptides, are in the form of a divalent antigen composition.

[0189] Embodiment 180: To the subject, 1) one or more fusion polypeptides, or a polynucleotide encoding the fusion polypeptide, or a viral expression vector expressing the fusion polypeptide, wherein the fusion polypeptide is linked or connected by one or more linkers, optionally, in the order from the N-terminus to the C-terminus, · comprising the polypeptide segments of SEQ ID NOs: 70, 76, 94, 151 and 161, or · consisting of the polypeptide segments of SEQ ID NOs: 71, 77, 95, 152 and 162, and 2) one or more fusion polypeptides, or a polynucleotide encoding the fusion polypeptide, or a viral expression vector expressing the fusion polypeptide, wherein the fusion polypeptide is linked or connected by one or more linkers, optionally, in the order from the N-terminus to the C-terminus, · SEQ ID NOs: 188, 305, 28, 41, 294, 4, 176, 11, 319, 259, 282, 223, 213 and 37, · SEQ ID NOs: 188, 305, 28, 41 and 294, · SEQ ID NOs: 4, 176, 11, 319, 259, 282, 223, 213 and 37, · SEQ ID NOs: 189, 306, 29, 42, 295, 5, 177, 12, 320, 260, 283, 224, 214 and 38, · SEQ ID NOs: 189, 306, 29, 42 and 295, · SEQ ID NOs: 5, 177, 12, 320, 260, 283, 224, 214 and 38, · SEQ ID NOs: 305, 319, 259, 282, 223, 213, 294, 176 and 188, · SEQ ID NOs: 306, 320, 260, 283, 224, 214, 295, 177 and 189, · SEQ ID NOs: 305, 294, 223, 213, 176, 259, 319, 188 and 282, · SEQ ID NOs: 306, 295, 224, 214, 177, 260, 320, 189 and 283, · SEQ ID NOs: 305, 294, 319, 259, 282, 223, 176 and 188, · SEQ ID NOs: 306, 295, 320, 260, 283, 224, 177 and 189, · SEQ ID NOs: 305, 223, 294, 176, 259, 319, 188 and 282, or · one or more fusion polypeptides comprising or consisting of polypeptide segments of SEQ ID NOs: 306, 224, 295, 177, 260, 320, 189 and 283, or a polynucleotide encoding a fusion polypeptide, or a viral expression vector expressing a fusion polypeptide, and administering the same, according to any one of embodiments 175 to 179.

[0190] Embodiment 181: To a subject, 1) One or more fusion polypeptides, polynucleotides encoding the fusion polypeptides, or viral expression vectors expressing the fusion polypeptides, wherein the fusion polypeptide comprises, or consists of, an amino acid sequence of any one of SEQ ID NOs: 351 to 356 and 430, or a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one of SEQ ID NOs: 351 to 356 and 430, 2) The method according to any one of embodiments 175 to 180, comprising administering one or more fusion polypeptides, polynucleotides encoding the fusion polypeptides, or viral expression vectors expressing the fusion polypeptides, wherein the fusion polypeptide comprises, or consists of, an amino acid sequence of any one of SEQ ID NOs: 357 to 366 and 407 to 410, or a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one of SEQ ID NOs: 357 to 366 and 407 to 410.

[0191] Embodiment 182: Comprising administering to a subject one or more fusion polypeptides, polynucleotides encoding the fusion polypeptides, or viral expression vectors expressing the fusion polypeptides, wherein the fusion polypeptides are linked or connected by optionally one or more linkers in order from the N-terminus to the C-terminus, · SEQ ID NOs: 201, 78, 107, 96, 229, 172, 327, 6, 333, 243, 331, 192, 265, 311, 137, 15, 123, 30, 336, 302, 153, 219, 298, 121, 230, 240, 60, 241, 276, 113, 99, 21, 217 and 215, · SEQ ID NO: 78, 296, 1, 339, 197, 329, 232, 323, 303, 234, 90, 261, 274, 238, 211, 325, 137, 227, 209, 190, 341, 57, 225, 27, 210, 119, 19, 165, 334, 117, 153, 10, 97, and 300, or · A method according to any one of embodiments 175 to 178, comprising or consisting of a polypeptide segment of SEQ ID NO: 296, 1, 78, 197, 339, 227, 261, 274, 238, 325, 137, 329, 303, 234, 90, 232, 27, 57, 225, 323, 190, 341, 119, 19, 165, 334, 117, 153, 10, 97, and 300.

[0192] Embodiment 183: A method according to any one of embodiments 175 to 182, comprising administering to a subject one or more fusion polypeptides, or polynucleotides encoding a fusion polypeptide, or a viral expression vector expressing a fusion polypeptide, wherein the fusion polypeptide comprises an amino acid sequence of any one of SEQ ID NO: 345 - 377, 407 - 411, 422 - 424, 430 - 435, or a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one of SEQ ID NO: 345 - 377, 407 - 411, 422 - 424, 430 - 435 and comprises or consists of the same.

[0193] Embodiment 184: The method according to any one of Embodiments 175 to 183, comprising administering to a subject one or more adenovirus vectors, each adenovirus vector comprising one or more polynucleotides encoding one or more fusion proteins comprising an amino acid sequence of any one of SEQ ID NOs: 345 to 377, 407 to 411, 422 to 424, 430 to 435, or a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one of SEQ ID NOs: 345 to 377, 407 to 411, 422 to 424, 430 to 435.

[0194] Embodiment 185: The method according to any one of Embodiments 175 to 183, comprising administering to one or more viral vectors, each viral vector encoding two or more fusion proteins having an amino acid sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO: 345 and 346, SEQ ID NO: 347 and 348, SEQ ID NO: 349 and 350, SEQ ID NO: 351 and 352, SEQ ID NO: 430 and 352, SEQ ID NO: 357 and 358, SEQ ID NO: 360 and 362, SEQ ID NO: 359 and 361, SEQ ID NO: 351 and 357, SEQ ID NO: 351 and 358, SEQ ID NO: 351 and 359, SEQ ID NO: 351 and 360, SEQ ID NO: 351 and 361, SEQ ID NO: 351 and 362, SEQ ID NO: 351 and 407, SEQ ID NO: 351 and 408, SEQ ID NO: 351 and 409, SEQ ID NO: 351 and 410, SEQ ID NO: 352 and 357, SEQ ID NO: 352 and 358, SEQ ID NO: 352 and 359, SEQ ID NO: 352 and 360, SEQ ID NO: 352 and 361, SEQ ID NO: 352 and 362, SEQ ID NO: 352 and 407, SEQ ID NO: 352 and 408, SEQ ID NO: 352 and 409, SEQ ID NO: 352 and 410, SEQ ID NO: 430 and 357, SEQ ID NO: 430 and 358, SEQ ID NO: 430 and 359, SEQ ID NO: 430 and 360, SEQ ID NO: 430 and 361, SEQ ID NO: 430 and 362, SEQ ID NO: 407 and 409, SEQ ID NO: 407 and 408, SEQ ID NO: 408 and 410, or SEQ ID NO: 409 and 410.

[0195] Embodiment 186: The method according to any one of Embodiments 175 to 185, wherein the subject is infected with HIV-1, suspected of being infected with HIV-1, or at risk of being infected with HIV-1.

[0196] Embodiment 187: The method according to any one of Embodiments 175 to 186, wherein the subject is chronically infected with HIV-1.

[0197] Embodiment 188: The method according to any one of Embodiments 175 to 187, wherein the subject is acutely infected with HIV-1.

[0198] Embodiment 189: The method according to any one of Embodiments 175 to 188, wherein the subject has HIV-1 infection at Fibonacci stage IV or earlier, for example, Fibonacci stage III, Fibonacci stage II or Fibonacci stage I.

[0199] Embodiment 190: The method according to any one of Embodiments 175 to 189, wherein the composition is administered via a route selected from intravenous, intramuscular, intradermal, subcutaneous, and mucosal (e.g., intraoral, intranasal, rectal, vaginal).

[0200] Embodiment 191: Per administration, about 10 3 ~ about 10 15 virus focus forming units (FFU) or plaque forming units (PFU) or infectious units (IU) or virus particles (vp), for example, about 10 4 ~ about 10 7 virus FFU or PFU or IU or vp, for example, about 10 3 ~ about 10 4 、10 5 、10 6 、10 7 、10 8 、10 9 、10 10 、10 11 、10 12 、10 13 、10 14 or 10 15 virus FFU or PFU or IU or vp is administered, the method according to any one of Embodiments 175 to 190.

[0201] Embodiment 192: A prime-boost regimen, (i) administering a priming composition at a first time point and administering one or more boosting compositions at one or more subsequent time points (e.g., prime-boost-boost-boost, etc.), or (ii) administering a priming composition at a first time point and a boosting composition at a second time point, the method according to any one of embodiments 175 to 191, comprising one or more repeats (e.g., prime-boost-prime-boost, etc.) of a prime-boost regimen.

[0202] Embodiment 193: The method according to embodiment 192, wherein the administration of the priming composition and the one or more boosting compositions is spaced apart by at least one week, two weeks, three weeks, or one month, for example, at least two, three, four, five, or six months.

[0203] Embodiment 194: The method according to embodiment 192 or 193, wherein the priming composition and the boosting composition comprise the same immunogenic composition.

[0204] Embodiment 195: The method according to embodiment 192 or 193, wherein the priming composition and the boosting composition comprise different immunogenic compositions.

[0205] Embodiment 196: The method according to embodiment 192 or 193, wherein the priming composition and the boosting composition comprise the same one or more fusion polypeptides and the same polynucleotide or viral expression vector.

[0206] Embodiment 197: The method according to embodiment 192 or 193, wherein the priming composition and the boosting composition comprise different fusion polypeptides and / or different polynucleotides or viral expression vectors.

[0207] Embodiment 198: The method according to embodiment 197, comprising priming with a first polynucleotide or viral expression vector and boosting with a second polynucleotide or viral expression vector.

[0208] Embodiment 199: The prime-boost regimen is a) Priming with a viral expression vector and boosting with a polynucleotide, wherein the polynucleotide is DNA, cDNA, mRNA, or self-replicating RNA, the priming and boosting, b) Priming with a polynucleotide that is DNA, cDNA, mRNA, or self-replicating RNA and boosting with a viral expression vector, c) Priming with a first viral expression vector and boosting with a second viral expression vector, wherein the first and second viral expression vectors are derived from the same, related, or unrelated taxonomic families, the priming and boosting, d) Priming with a first replication-deficient viral expression vector and boosting with a second replication-deficient viral expression vector, wherein the first and second replication-deficient viral expression vectors are derived from the same, related, or unrelated taxonomic families, the priming and boosting, e) Priming with a first attenuated replication-deficient viral expression vector and boosting with a second replication-attenuated viral expression vector, wherein the first and second replication-attenuated viral expression vectors are derived from the same, related, or unrelated taxonomic families, the priming and boosting, f) Priming with a replication-deficient viral expression vector and boosting with a replication-attenuated viral expression vector, g) Priming with a replication-attenuated viral expression vector and boosting with a replication-deficient viral expression vector, h) Priming with a viral expression vector of lymphocytic choriomeningitis mammarenavirus (LCMV) and boosting with a viral expression vector of Pichinde mammarenavirus, i) Priming with a viral expression vector of Pichinde mammarenavirus and boosting with a viral expression vector of lymphocytic choriomeningitis mammarenavirus (LCMV), j) Priming with a viral expression vector of arenavirus and boosting with a viral expression vector of adenovirus, or The method according to any one of embodiments 192 to 198, comprising priming with an adenovirus viral expression vector and boosting with an arenavirus viral expression vector.

[0209] Embodiment 200: The method according to any one of embodiments 175 to 199, wherein the subject has not received antiretroviral therapy (ART) or ART has been discontinued prior to administration of one or more compositions.

[0210] Embodiment 201: The method according to any one of embodiments 175 to 200, wherein ART is discontinued after one or more administrations of the composition.

[0211] Embodiment 202: The method according to any one of embodiments 175 to 201, further comprising administering to the subject one or more additional therapeutic agents, such as 2, 3, 4, or more additional therapeutic agents.

[0212] Embodiment 203: The method according to embodiment 202, comprising co-administering one or more agents that activate latent HIV, such as one or more latency reversing agents (LRAs).

[0213] Embodiment 204: The method according to embodiment 202 or 203, wherein one or more LRAs are selected from the group consisting of agonists or activators of one or more toll-like receptors (TLRs), histone deacetylase (HDAC) inhibitors, proteasome inhibitors, protein kinase C (PKC) activators, Smyd2 inhibitors, BET-bromodomain 4 (BRD4) inhibitors, ionomycin, apoptosis protein inhibitor (IAP) antagonists, and second mitochondria-derived activator of caspase (SMAC) mimetics.

[0214] Embodiment 205: The method according to any one of embodiments 202 to 204, comprising co-administering one or more agonists or activators of one or more toll-like receptors (TLRs).

[0215] Embodiment 206: The method according to Embodiment 205, wherein the TLR agonist or activator is selected from the group consisting of a TLR2 agonist, a TLR3 agonist, a TLR4 agonist, a TLR5 agonist, a TLR7 agonist, a TLR8 agonist, and a TLR9 agonist.

[0216] Embodiment 207: The method according to Embodiment 205 or 206, wherein the TLR7 agonist is selected from the group consisting of GS9620 (vesatolimod), R848 (resiquimod), DS-0509, LHC-165, and TMX-101 (imiquimod), and / or the TLR8 agonist is selected from the group consisting of GS-9688, R848 (resiquimod), CV8102 (dual TLR7 / TLR8 agonist), and NKTR-262 (dual TLR7 / TLR8 agonist).

[0217] Embodiment 208: The method according to any one of Embodiments 202 to 207, comprising co-administering one or more interleukin receptor agonists of interleukin selected from IL-2, IL-7, IL-12, IL-15, IL-18, IL-21, IFN-α, IFN-γ, GM-CSF, and FLT3LG.

[0218] Embodiment 209: The method according to Embodiment 208, comprising co-administering one or more cytokines selected from the group consisting of IL-2, IL-7, IL-12, IL-15, IL-18, IL-21, IFN-α, IFN-γ, GM-CSF, FLT3LG, and combinations and functional variants thereof.

[0219] Embodiment 210: The method according to any one of Embodiments 202 to 209, comprising co-administering one or more innate immune activators.

[0220] Embodiment 211: The method according to Embodiment 210, wherein one or more natural immune activators include agonists of receptors selected from the group consisting of non-coding immunostimulatory polynucleotides (e.g., pathogen-associated molecular patterns (PAMPs), cytosine-phosphate-guanine (CpG) oligodeoxynucleotides, and immunostimulatory RNAs (isRNAs, e.g., CV8102)), fms-related tyrosine kinase 3 (FLT3), interferon gene stimulator (STING) receptor, DExD / H box helicase 58 (DDX58; also known as RIG-I), and nucleotide-binding oligomerization domain-containing 2 (NOD2).

[0221] Embodiment 212: The method according to any one of Embodiments 202 to 211, comprising co-administering one or more antagonists or inhibitors of inhibitory immune checkpoint proteins or receptors and / or one or more activators or agonists of stimulatory immune checkpoint proteins or receptors.

[0222] Embodiment 213: One or more immune checkpoint proteins or receptors include CD27, CD70, CD40, CD40LG, CD47, CD48 (SLAMF2), Transmembrane and Immunoglobulin Domain Containing 2 (TMIGD2, CD28H), CD84 (LY9B, SLAMF5), CD96, CD160, MS4A1 (CD20), CD244 (SLAMF4), CD276 (B7H3), V-set domain-containing T cell activation inhibitor 1 (VTCN1, B7H4), V-set immunoregulatory receptor (VSIR, B7H5, VISTA), Immunoglobulin Superfamily Member 11 (IGSF11, VSIG3), Natural Killer Cell Cytotoxicity Receptor 3 Ligand 1 (NCR3LG1, B7H6), HERV-H LTR-related 2 (HHLA2, B7H7), Inducible T cell co-stimulator (ICOS, CD278), Inducible T cell co-stimulator ligand (ICOSLG, B7H2), TNF receptor superfamily member 4 (TNFRSF4, OX40), TNF superfamily member 4 (TNFSF4, OX40L), TNFRSF8 (CD30), TNFSF8 (CD30L), TNFRSF10A (CD261, DR4, TRAILR1), TNFRSF9 (CD137), TNFSF9 (CD137L), TNFRSF10B (CD262, DR5, TRAILR2), TNFRSF10 (TRAIL), TNFRSF14 (HVEM, CD270), TNFSF14 (HVEML), CD272 (B and T lymphocyte associated (BTLA)), TNFRSF17 (BCMA, CD269), TNFSF13B (BAFF), TNFRSF18 (GITR), TNFSF18 (GITRL), MHC class I polypeptide-related sequence A (MICA), MHC class I polypeptide-related sequence B (MICB), CD274 (CD274, PDL1, PD-L1), Programmed cell death 1 (PDCD1, PD1, PD-1), Cytotoxic T lymphocyte-associated protein 4 (CTLA4, CD152), CD80 (B7-1), CD28, nectin cell adhesion molecule 2 (NECTIN2, CD112), CD226 (DNAM-1), poliovirus receptor (PVR) cell adhesion molecule (PVR, CD155), PVR-related immunoglobulin domain-containing (PVRIG, CD112R),A T cell immunoreceptor comprising Ig and ITIM domains (TIGIT), T cell immunoglobulin and mucin domain-containing 4 (TIMD4; TIM4), hepatitis A virus cellular receptor 2 (HAVCR2, TIMD3, TIM3), galectin 9 (LGALS9), lymphocyte activation 3 (LAG3, CD223), signaling lymphocyte activation molecule family member 1 (SLAMF1, SLAM, CD150), lymphocyte antigen 9 (LY9, CD229, SLAMF3), SLAM family member 6 (SLAMF6, CD352), SLAM family member 7 (SLAMF7, CD319), UL16-binding protein 1 (ULBP1), UL16-binding protein 2 (ULBP2), UL16-binding protein 3 (ULBP3), retinoic acid early transcript 1E (RAET1E; ULBP4), retinoic acid early transcript 1G (RAET1G; ULBP5), retinoic acid early transcript 1L (RAET1L; ULBP6), lymphocyte antigen 3 (CD223), killer cell immunoglobulin-like receptor, three Ig domains, and long cytoplasmic tail 1 (KIR, CD158E1), killer cell lectin-like receptor C1 (KLRC1, NKG2A, CD159A), killer cell lectin-like receptor K1 (KLRK1, NKG2D, CD314), killer cell lectin-like receptor C2 (KLRC2, CD159c, NKG2C), killer cell lectin-like receptor C3 (KLRC3, NKG2E), killer cell lectin-like receptor C4 (KLRC4, NKG2F), killer cell immunoglobulin-like receptor, two Ig domains, and long cytoplasmic tail 1 (KIR2DL1), killer cell immunoglobulin-like receptor, two Ig domains, and long cytoplasmic tail 2 (KIR2DL2), killer cell immunoglobulin-like receptor, two Ig domains, and long cytoplasmic tail 3 (KIR2DL3), killer cell immunoglobulin-like receptor, three Ig domains, and long cytoplasmic tail 1 (KIR3DL1), killer cell lectin-like receptor D1 (KLRD1), SLAM family member 7 (SLAMF7), the method according to embodiment 212, selected from the group consisting of.,

[0223] Embodiment 214: The method according to embodiment 212 or 213, comprising co-administering one or more blockers, antagonists, or inhibitors of one or more T cell inhibitory immune checkpoint proteins or receptors.

[0224] Embodiment 215: The method according to embodiment 214, wherein the T cell inhibitory immune checkpoint protein or receptor is selected from the group consisting of CD274 (CD274, PDL1, PD-L1), programmed cell death 1 ligand 2 (PDCD1LG2, PD-L2, CD273), programmed cell death 1 (PDCD1, PD1, PD-1), cytotoxic T lymphocyte-associated protein 4 (CTLA4, CD152), CD276 (B7H3), V-set domain-containing T cell activation inhibitor 1 (VTCN1, B7H4), V-set immunoregulatory receptor (VSIR, B7H5, VISTA), immunoglobulin superfamily member 11 (IGSF11, VSIG3), TNFRSF14 (HVEM, CD270), TNFSF14 (HVEML), CD272 (B and T lymphocyte-associated (BTLA)), PVR-related immunoglobulin domain-containing (PVRIG, CD112R), T cell immunoreceptor containing Ig and ITIM domains (TIGIT), lymphocyte activation 3 (LAG3, CD223), hepatitis A virus cellular receptor 2 (HAVCR2, TIMD3, TIM3), galectin 9 (LGALS9), killer cell immunoglobulin-like receptor, three Ig domains, and long cytoplasmic tail 1 (KIR, CD158E1), killer cell immunoglobulin-like receptor, two Ig domains, and long cytoplasmic tail 1 (KIR2DL1), killer cell immunoglobulin-like receptor, two Ig domains, and long cytoplasmic tail 2 (KIR2DL2), killer cell immunoglobulin-like receptor, two Ig domains, and long cytoplasmic tail 3 (KIR2DL3), killer cell immunoglobulin-like receptor, three Ig domains, and long cytoplasmic tail 1 (KIR3DL1).

[0225] Embodiment 216: The method according to embodiment 212 or 213, comprising co-administering one or more agonists or activators of one or more T cell-stimulating immune checkpoint proteins or receptors.

[0226] Embodiment 217: The method according to embodiment 216, wherein the T cell-stimulating immune checkpoint protein or receptor is selected from the group consisting of CD27, CD70, CD40, CD40LG, inducible T cell co-stimulator (ICOS, CD278), inducible T cell co-stimulator ligand (ICOSLG, B7H2), TNF receptor superfamily member 4 (TNFRSF4, OX40), TNF superfamily member 4 (TNFSF4, OX40L), TNFRSF9 (CD137), TNFSF9 (CD137L), TNFRSF18 (GITR), TNFSF18 (GITRL), CD80 (B7-1), CD28, nectin cell adhesion molecule 2 (NECTIN2, CD112), CD226 (DNAM-1), and poliovirus receptor (PVR) cell adhesion molecule (PVR, CD155).

[0227] Embodiment 218: The method according to embodiment 212 or 213, comprising co-administering one or more blockers, antagonists, or inhibitors of one or more NK cell-inhibiting immune checkpoint proteins or receptors.

[0228] Embodiment 219: The method according to embodiment 218, wherein the NK cell-inhibitory immune checkpoint protein or receptor is selected from the group consisting of killer cell immunoglobulin-like receptor, three Ig domains, and long cytoplasmic tail 1 (KIR, CD158E1), killer cell immunoglobulin-like receptor, two Ig domains, and long cytoplasmic tail 1 (KIR2DL1), killer cell immunoglobulin-like receptor, two Ig domains, and long cytoplasmic tail 2 (KIR2DL2), killer cell immunoglobulin-like receptor, two Ig domains, and long cytoplasmic tail 3 (KIR2DL3), killer cell immunoglobulin-like receptor, three Ig domains, and long cytoplasmic tail 1 (KIR3DL1), killer cell lectin-like receptor C1 (KLRC1, NKG2A, CD159A), and killer cell lectin-like receptor D1 (KLRD1, CD94).

[0229] Embodiment 220: The method according to embodiment 212 or 213, comprising co-administering one or more agonists or activators of one or more NK cell-stimulatory immune checkpoint proteins or receptors.

[0230] Embodiment 221: The method according to embodiment 220, wherein the NK cell-stimulatory immune checkpoint protein or receptor is selected from CD16, CD226 (DNAM-1), killer cell lectin-like receptor K1 (KLRK1, NKG2D, CD314), and SLAM family member 7 (SLAMF7).

[0231] Embodiment 222: The method according to any one of embodiments 212 to 215, wherein the one or more immune checkpoint inhibitors comprise a proteinaceous inhibitor of PD-L1 (CD274), PD-1 (PDCD1), or CTLA4.

[0232] Embodiment 223: The method according to Embodiment 222, wherein the protein inhibitor of CTLA4 is selected from the group consisting of ipilimumab, tremelimumab, BMS-986218, AGEN1181, AGEN1884 (zalifrelimab), BMS-986249, MK-1308, REGN-4659, ADU-1604, CS-1002, BCD-145, APL-509, JS-007, BA-3071, ONC-392, AGEN-2041, JHL-1155, KN-044, CG-0161, ATOR-1144, PBI-5D3H5, FPT-155 (CTLA4 / PD-L1 / CD28), PF-06936308 (PD-1 / CTLA4), MGD-019 (PD-1 / CTLA4), KN-046 (PD-1 / CTLA4), MEDI-5752 (CTLA4 / PD-1), XmAb-20717 (PD-1 / CTLA4), and AK-104 (CTLA4 / PD-1).

[0233] Embodiment 224: The method according to Embodiment 222, wherein the proteinaceous inhibitor of PD-L1 (CD274) or PD-1 (PDCD1) is selected from the group consisting of pembrolizumab, nivolumab, semiprimab, pidilizumab, AB122 (zimberelimab), AMP-224, MEDI0680 (AMP-514), spartalizumab, atezolizumab, avelumab, durvalumab, BMS-936559, CK-301, PF-06801591, BGB-A317 (tislelizumab), GLS-010 (WBP-3055), AK-103 (HX-008), AK-105, CS-1003, HLX-10, MGA-012, BI-754091, AGEN-2034 (balstilimab), JS-001 (toripalimab), JNJ-63723283, genolimuzumab (CBT-501), LZM-009, BCD-100, LY-3300054, SHR-1201, SHR-1210 (camrelizumab), Sym-021, ABBV-181, PD1-PIK, BAT-1306, (MSB0010718C), CX-072, CBT-502, TSR-042 (dostarlimab), MSB-2311, JTX-4014, BGB-A333, SHR-1316, CS-1001 (WBP-3155, KN-035, IBI-308 (sintilimab), HLX-20, KL-A167, STI-A1014, STI-A1015 (IMC-001), BCD-135, FAZ-053, TQB-2450, MDX1105-01, FPT-155 (CTLA4 / PD-L1 / CD28), PF-06936308 (PD-1 / CTLA4), MGD-013 (PD-1 / LAG-3), FS-118 (LAG-3 / PD-L1) MGD-019 (PD-1 / CTLA4), KN-046 (PD-1 / CTLA4), MEDI-5752 (CTLA4 / PD-1), RO-7121661 (PD-1 / TIM-3), XmAb-20717 (PD-1 / CTLA4), AK-104 (CTLA4 / PD-1), M7824 (PD-L1 / TGFβ-EC domain), CA-170 (PD-L1 / VISTA), CDX-527 (CD27 / PD-L1), LY-3415244 (TIM3 / PDL1), and INBRX-105 (4-1BB / PDL1).

[0234] Embodiment 225: The method according to any one of Embodiments 212 to 215, wherein the one or more immune checkpoint inhibitors comprise a small molecule inhibitor of CD274 (PDL1, PD-L1), programmed cell death 1 (PDCD1, PD1, PD-1), or CTLA4.

[0235] Embodiment 226: The method according to Embodiment 225, wherein the small molecule inhibitor of CD274 or PDCD1 is selected from the group consisting of GS-4224, GS-4416, INCB086550, and MAX10181.

[0236] Embodiment 227: The method according to Embodiment 225, wherein the small molecule inhibitor of CTLA4 comprises BPI-002.

[0237] Embodiment 228: The method according to any one of Embodiments 202 to 227, further comprising administering to the subject one or more antiviral agents.

[0238] Embodiment 229: The method according to Embodiment 228, wherein the one or more antiviral agents are selected from the group consisting of an HIV protease inhibitor, an HIV reverse transcriptase inhibitor, an HIV integrase inhibitor, an HIV non-catalytic site (or allosteric) integrase inhibitor, an HIV entry (fusion) inhibitor, an HIV maturation inhibitor, and a capsid inhibitor.

[0239] Embodiment 230: The method according to any one of Embodiments 202 to 229, further comprising administering to the subject one or more anti-HIV antibodies or antigen-binding fragments thereof.

[0240] Embodiment 231: The method according to Embodiment 230, wherein the one or more anti-HIV antibodies or antigen-binding fragments thereof bind to HIV gp120.

[0241] Embodiment 232: The method according to Embodiment 230 or 231, wherein the anti-HIV antibody or antigen-binding fragment thereof comprises a broadly neutralizing antibody.

[0242] Embodiment 233: The method according to any one of Embodiments 230 to 232, which is one or more anti-HIV antibodies or antigen-binding fragments thereof that bind to, inhibit, and / or neutralize HIV, and compete with or comprise the VH and VL variable domains of a broadly neutralizing antibody (bNAb) against HIV.

[0243] Embodiment 234: One or more anti-HIV antibodies or antigen-binding fragments thereof that bind to, inhibit, and / or neutralize HIV are i. comprising a third variable loop (V3) and / or a high-mannose patch comprising an N332 oligomannose glycan, ii. a CD4 binding site (CD4bs), iii. a second variable loop (V2) and / or an Env trimer apex, iv. a gp120 / gp41 interface, or v. bind to an epitope or region of gp120 selected from the group consisting of the silent face of gp120, the method according to any one of Embodiments 230 to 233.

[0244] Embodiment 235: An antibody or antigen-binding fragment thereof that binds to, inhibits, and / or neutralizes HIV binds to an epitope or region of gp120 within the third variable loop (V3) and / or a high-mannose patch comprising an N332 oligomannose glycan, and competes with or comprises the VH and VL regions derived from an antibody selected from the group consisting of GS-9722, PGT-121, PGT-122, PGT-123, PGT-124, PGT-125, PGT-126, PGT-128, PGT-130, PGT-133, PGT-134, PGT-135, PGT-136, PGT-137, PGT-138, PGT-139, 10-1074, VRC24, 2G12, BG18, 354BG8, 354BG18, 354BG42, 354BG33, 354BG129, 354BG188, 354BG411, 354BG426, DH270.1, DH270.6, PGDM12, VRC41.01, PGDM21, PCDN-33A, BF520.1, and VRC29.03, the method according to any one of Embodiments 230 to 234.

[0245] Embodiment 236: The method according to any one of Embodiments 230 to 235, wherein the antibody or antigen-binding fragment thereof binds to an epitope or region of gp120 in the CD4 binding site (CD4bs) and competes with or comprises VH and VL regions derived from an antibody selected from the group consisting of b12, F105, VRC01, VRC07, VRC07-523, VRC03, VRC06, VRC06b01, VRC08, VRC0801, NIH45-46, GS-9723, 3BNC117, 3BNC60, VRC-PG04, PGV04, CH103, 44-VRC13.01, 1NC9, 12A12, N6, N49-P7, NC-Cow1, IOMA, CH235 and CH235.12, N49P6, N49P7, N49P11, N49P9, and N60P25.

[0246] Embodiment 237: The method according to any one of Embodiments 230 to 236, wherein the antibody or antigen-binding fragment thereof that binds, inhibits, and / or neutralizes HIV binds to an epitope or region of gp120 in the second variable loop (V2) and / or the Env trimer apex and competes with or comprises VH and VL regions derived from an antibody selected from the group consisting of PG9, PG16, PGC14, PGG14, PGT-142, PGT-143, PGT-144, PGT-145, CH01, CH59, PGDM1400, CAP256, CAP256-VRC26.08, CAP256-VRC26.09, CAP256-VRC26.25, PCT64-24E, and VRC38.01.

[0247] Embodiment 238: The method according to any one of Embodiments 230 to 237, wherein the antibody or antigen-binding fragment binds to an epitope or region of gp120 at the gp120 / gp41 interface and competes with or comprises VH and VL regions derived from an antibody selected from the group consisting of PGT-151, CAP248-2B, 35O22, 8ANC195, ACS202, VRC34, and VRC34.01.

[0248] Embodiment 239: The method according to any one of Embodiments 230 to 238, wherein an antibody or an antigen-binding fragment thereof that binds to, inhibits, and / or neutralizes HIV binds to an epitope or region on the silent face of gp120 and competes with or comprises VH and VL regions derived from an antibody selected from the group consisting of VRC-PG05 and SF12.

[0249] Embodiment 240: The method according to any one of Embodiments 230 to 239, wherein an antibody or an antigen-binding fragment thereof that binds to, inhibits, and / or neutralizes HIV binds to an epitope or region of gp41 within the membrane-proximal region (MPER).

[0250] Embodiment 241: The method according to any one of Embodiments 230 to 240, wherein an antibody or an antigen-binding fragment thereof that binds to, inhibits, and / or neutralizes HIV binds to an epitope or region of gp41 within the membrane-proximal region (MPER) and competes with or comprises VH and VL regions derived from an antibody selected from the group consisting of 10E8, 10E8v4, 10E8-5R-100cF, 4E10, DH511.11P, 2F5, 7b2, and LN01.

[0251] Embodiment 242: The method according to any one of Embodiments 230 to 241, wherein an antibody or an antigen-binding fragment thereof that binds to, inhibits, and / or neutralizes HIV binds to an epitope or region of the gp41 fusion peptide and competes with or comprises VH and VL regions derived from an antibody selected from the group consisting of VRC34 and ACS202.

[0252] Embodiment 243: After administering one or more of the compositions in combination with one or more additional therapeutic agents optionally one or more times, the subject does not exhibit symptoms of HIV or AIDS for at least 6 months, at least 1 year, at least 2 years, at least 3 years, or more in the absence of antiretroviral therapy (ART), according to the method of any one of Embodiments 175 to 242.

[0253] Embodiment 244: After administering one or more of the compositions in combination with one or more additional therapeutic agents one or more times, the subject has a viral load of less than 500, e.g., less than 400, less than 300, less than 200, less than 100, less than 50 viral copies / ml of blood for at least 6 months, at least 1 year, at least 2 years, at least 3 years, or more in the absence of antiretroviral therapy (ART), according to any one of Embodiments 175 to 243. Method for immunogen design

[0254] Embodiment 245: A method for designing a fusion polypeptide capable of inducing an immune response against one or more viral target antigens, a) in silico identifying one or more regions of sequence conservation in a population of polypeptide sequences encoded by viral genes, the population being derived from an inter-patient viral population; b) in silico identifying the two most common polypeptide sequences from the one or more conserved regions identified in step a) and generating a multivalent polypeptide segment from the conserved regions.

[0255] Embodiment 246: The method according to Embodiment 245, wherein the multivalent polypeptide segment is a bivalent polypeptide segment.

[0256] Embodiment 247: Further comprising step c) of arranging the polypeptide segments in one or more continuous fusion polypeptides such that the creation of epitopes capable of binding to human MHC class I molecules or human MHC class II molecules is reduced or avoided, e.g., with a predicted binding affinity IC50 value of less than about 1000 nM or with a percentile rank within the top 5% in the population of polypeptide segments, according to the method of Embodiment 245 or 246.

[0257] Embodiment 248: The method according to any one of Embodiments 245 to 247, further comprising the step of inserting a linker between polypeptide segment junctions that are predicted to create epitopes capable of binding to human MHC class I or human MHC class II molecules.

[0258] Embodiment 249: After step b) and before step c), d) in silico identifying polypeptide segments that bind to human MHC class I molecules with an IC50 value of less than about 1000 nM or having a percentile rank within the top 5% in a population of polypeptide segments in one or more regions of sequence conservation identified in step a); e) generating polypeptide segments comprising one or more regions of sequence conservation that are identified in step a) and are predicted to bind to human MHC class I molecules with an IC50 value of less than about 1000 nM or having a percentile rank within the top 5% in a population of polypeptide segments. The method according to any one of Embodiments 245 to 248.

[0259] Embodiment 250: After step b) and before step c), further comprising the step of reducing or removing viral polypeptide 9mers having at least 55% (5 out of 9 amino acid residues), for example, at least 65% (6 out of 9 amino acid residues), for example, at least 75% (7 out of 9 amino acid residues), for example, at least 85% (8 out of 9 amino acid residues) amino acid sequence identity to human proteins. The method according to any one of Embodiments 245 to 249.

[0260] Embodiment 251: After step b) and before step c), further comprising the step of providing one or more polypeptide segments that are known or predicted to bind to human MHC class II molecules, for example, with a predicted binding affinity IC50 value of less than about 1000 nM or having a percentile rank within the top 5% in a population of polypeptide segments. The method according to any one of Embodiments 245 to 250.

[0261] Embodiment 252: After step b) and before step c), within one or more regions of sequence conservation identified in step a), identifying sequence divergence in a second population of polypeptide sequences encoded by a viral gene, wherein the second population is derived from the viral population within the patient, the method according to any one of embodiments 245 to 251 further comprising the step of identifying.

[0262] Embodiment 253: The method according to embodiment 252, wherein the sequence divergence from the viral population within the patient is determined by deep sequencing or next-generation sequencing.

[0263] Embodiment 254: A method of designing a fusion polypeptide capable of inducing an immune response against one or more viral target antigens, a) in silico identifying one or more regions of sequence conservation in a first population of polypeptide sequences encoded by a viral gene, wherein the first population is derived from the viral population among patients, the identifying; b) in silico identifying the two most common polypeptide sequences from the one or more conserved regions identified in step a); c) in silico identifying a polypeptide segment that binds to human MHC class I molecules with an IC50 value of less than about 1000 nM or having a percentile rank within the top 5% in a population of polypeptide segments within one or more regions of sequence conservation identified in step a); d) generating a polypeptide segment comprising one or more regions of sequence conservation that are identified in step a), have an IC50 value of less than about 1000 nM, or have a percentile rank within the top 5% in a population of polypeptide segments and are predicted to bind to human MHC class I molecules; e) Removing the viral polypeptide 9mer segment generated in step d) that was determined to have at least 55% (5 out of 9 amino acid residues), for example, at least 65% (6 out of 9 amino acid residues), for example, at least 75% (7 out of 9 amino acid residues), for example, at least 85% (8 out of 9 amino acid residues) amino acid sequence identity to a human protein, to obtain a retained viral polypeptide segment; f) Placing the retained polypeptide segments into one or more contiguous fusion polypeptides such that epitopes that can bind to human MHC class I molecules or human MHC class II molecules are avoided or reduced, for example, with a predicted binding affinity IC50 value of less than about 1000 nM, or having a percentile rank within the top 5% in a population of polypeptide segments, by a junction that connects the polypeptide segments; a method comprising.

[0264] Embodiment 255: A method of designing a fusion polypeptide capable of inducing an immune response against one or more viral target antigens, a) Identifying in silico one or more regions of sequence conservation in a first population of polypeptide sequences encoded by a viral gene, wherein the first population is derived from an inter-patient viral population; identifying; b) Optionally, identifying in silico the two most common polypeptide sequences from one or more conserved regions identified in step a); c) Identifying in silico the sequence divergence in a second population of polypeptide sequences encoded by a viral gene within one or more regions of sequence conservation identified in step a), wherein the second population is derived from an intra-patient viral population; identifying; d) Identifying in silico polypeptide segments that are predicted to bind to human MHC class I molecules with an IC50 value of less than about 1000 nM or having a percentile rank within the top 5% in a population of polypeptide segments within one or more regions of sequence conservation identified in step a); e) generating a polypeptide segment comprising one or more sequence conserved regions that are identified in step a) and predicted to bind to human MHC class I molecules with an IC50 value of less than about 1000 nM or having a percentile rank within the top 5% in a population of polypeptide segments f) removing the viral polypeptide 9mer segments generated in step e) that are determined to have at least 55% (5 out of 9 amino acid residues), for example, at least 65% (6 out of 9 amino acid residues), for example, at least 75% (7 out of 9 amino acid residues), for example, at least 85% (8 out of 9 amino acid residues) amino acid sequence identity to a human protein to obtain the retained viral polypeptide segments g) arranging the retained polypeptide segments into one or more contiguous fusion polypeptides such that the creation of epitopes that can bind to human MHC class I or human MHC class II molecules is avoided or reduced, for example, with a predicted binding affinity IC50 value of less than about 1000 nM or having a percentile rank within the top 5% in a population of polypeptide segments, by junctions that connect the polypeptide segments, a method comprising.

[0265] Embodiment 256: The method according to Embodiment 255, wherein the sequence dispersion from the viral population in the patient is determined by deep sequencing or next-generation sequencing.

[0266] Embodiment 257: The method according to any one of Embodiments 254 - 256, further comprising providing one or more polypeptide segments known or predicted to bind to human MHC class II molecules, for example, with a predicted binding affinity IC50 value of less than about 1000 nM or having a percentile rank within the top 5% in a population of polypeptide segments.

[0267] Embodiment 258: The method according to any one of Embodiments 254 to 257, further comprising the step of inserting a linker between polypeptide segment junctions predicted to be able to create epitopes that can bind to human MHC class I or human MHC class II molecules.

[0268] Embodiment 259: A method for producing a multivalent antigen, the method comprising: (a) aligning a population of viral proteome sequences; (b) for each sequence in the alignment, creating a set of 9 - amino acid partial sequences ( "9mers") starting from the N - terminal amino acid, each partial sequence overlapping the preceding partial sequence by 8 amino acids, such that each sequence of length l in the alignment contains (l - 8) 9mers; (c) calculating the frequency of each unique 9mer starting at position i in each sequence of the alignment and identifying the two or more most common 9mers at each position, where (c)(1) the frequency is calculated as the number of times the unique 9mer divides the total number of sequences in the alignment at position i; (d) calculating the multivalent conservation at each position by summing the proportion of sequences in the alignment that contain any of the two or more most common 9mers; (e) creating an alignment of conserved regions by extracting sequences in the alignment that have a multivalent conservation greater than 80% or greater than 90%; (f) determining the frequency of each pair of unique 9mers at each position in the alignment of conserved regions; (g) connecting 9mer pairs at adjacent positions in the alignment of conserved regions that share an 8 - amino acid overlap; (h) creating a directed acyclic graph where each 9mer pair is a node, the edges between adjacent nodes are formed from the connected 9mer pairs at adjacent positions, and the weight of each edge is equal to the frequency of the downstream 9mer pair; · adding a source node and connecting it to all nodes at the first position; · adding a sink node and connecting it to all nodes at the last position, and · invalidating all weights, and (i) finding an optimal path of a directed acyclic graph from a source node to the sink node, wherein the optimal path is defined with respect to the sum of the frequencies of all 9mer pairs within the directed acyclic graph, finding; and (j) connecting two or more 9mers that are adjacent in the optimal multivalent 9mer path when they share an overlap of eight amino acids, thereby creating two or more sequences of connected 9mers that together form a multivalent antigen, constructing a multivalent antigen; and (k) optionally, rearranging polypeptide segments to reduce or avoid the creation of harmful epitopes at the junctions between polypeptide segments, constructing, by a method comprising, in silico, a set of multivalent amino acid sequences within a structurally conserved region of a population of viral proteome sequences.

[0269] Embodiment 260: The method according to embodiment 259, wherein the multivalent conservation is bivalent conservation and the multivalent antigen is a bivalent antigen.

[0270] Embodiment 261: In step (a), the conserved region is (i) removing segments less than 35 amino acids in length, such as segments 9, 10, 15, 20, 25, 30, or 35 amino acids in length, (ii) removing segments determined to have less than 90% multivalent (e.g., bivalent) conservation, (iii) removing segments determined to be weakly immunogenic or non-immunogenic, as demonstrated, for example, in vitro or in vivo, and / or (iv) including additional segments determined to be immunogenic, as demonstrated, for example, in vitro or in vivo, further defined by performing one or more of: the method according to embodiment 259 or 260.

[0271] Embodiment 262: The method according to any one of Embodiments 259 to 261, wherein the step of rearranging peptide segments to reduce or avoid the creation of harmful epitopes is performed by a method including one or more of in-silico HLA binding analysis and human proteome cross-recognition analysis.

[0272] Embodiment 263: The method according to any one of Embodiments 259 to 262, further including inserting a linker sequence between one or more adjacent segments.

[0273] Embodiment 264: The method according to any one of Embodiments 259 to 263, further including improving the multivalent (e.g., bivalent) antigen produced in step (h) by removing junction 9mers that bind to specific HLA alleles with a predicted IC50 value of less than about 1000 nM or having a percentile rank within the top 5% in a population of polypeptide segments.

[0274] Embodiment 265: The method according to any one of Embodiments 259 to 264, further including improving the multivalent (e.g., bivalent) antigen produced in step (h) by removing 9mers having at least 55% (5 out of 9 amino acid residues), e.g., at least 65% (6 out of 9 amino acid residues), e.g., at least 75% (7 out of 9 amino acid residues), e.g., at least 85% (8 out of 9 amino acid residues) amino acid sequence identity with human peptides or having residues facing the same T cell receptor (TCR) as human proteins.

[0275] Embodiment 266: Further including improving the multivalent (e.g., bivalent) antigen produced in step (h) to generate T cell epitopes sufficient to cover intra-patient viral diversity, the method comprising: a) identifying viral quasispecies variants in a biological sample obtained from a subject; and b) (i) Determining, at each 9mer position in a multivalent (e.g., bivalent) antigen, the corresponding 9mer subsequences from a plurality of sequencing reads that fully cover that position; (ii) Extracting the 9mer subsequences; (iii) Aligning the extracted 9mer subsequences to the sequence of the multivalent (e.g., bivalent) antigen and determining the presence of any mismatches, and determining patient amino acid variants from the sequence of the multivalent (e.g., bivalent) antigen produced in step (h), by a method comprising:

[0276] Embodiment 267: The method according to embodiment 266, wherein the viral quasispecies is identified by a method comprising sequencing viral DNA, assembling a plurality of sequence reads to create a target consensus sequence, aligning each read within the plurality of reads to the target consensus sequence, and mapping the aligned reads of interest to a reference sequence to obtain sequence coordinates.

[0277] Embodiment 268: The method according to embodiment 266 or 267, wherein the biological sample is selected from blood, peripheral blood mononuclear cells (PBMC), serum, plasma, semen, or lymph nodes.

[0278] Embodiment 269: The method according to any one of embodiments 266 - 268, wherein the subject is acutely infected with HIV-1.

[0279] Embodiment 270: The method according to any one of embodiments 266 - 269, wherein the subject has HIV-1 infection at a febrile stage IV or earlier, e.g., febrile stage III, febrile stage II, or febrile stage I.

[0280] Embodiment 271: The method according to any one of embodiments 266 - 268, wherein the subject is chronically infected with HIV-1.

[0281] Embodiment 272: The method according to any one of Embodiments 266 to 271, wherein the subject is receiving antiretroviral therapy (ART).

[0282] Embodiment 273: The method according to any one of Embodiments 266 to 271, wherein the subject is not receiving antiretroviral therapy (ART).

[0283] Embodiment 274: The method according to any one of Embodiments 266 to 273, further comprising excluding sequences having existing escape variants.

[0284] Embodiment 275: The method according to any one of Embodiments 259 to 274, further comprising rearranging polypeptide segments to reduce or avoid the creation of harmful epitopes at the junctions between the polypeptide segments.

[0285] Embodiment 276: The method according to Embodiment 275, wherein the step of rearranging the peptide segments to reduce or avoid the creation of harmful epitopes is performed by a method comprising one or more of in silico HLA binding analysis and human proteome cross-recognition analysis.

[0286] Embodiment 277: The method according to any one of Embodiments 245 to 276, wherein one or more viral target antigens are derived from mammalian viruses, for example, human viruses.

[0287] Embodiment 278: The method according to any one of Embodiments 245 to 277, wherein one or more viral target antigens are derived from a virus selected from the group consisting of human immunodeficiency virus (HIV), hepatitis B virus (HBV), human papillomavirus (HPV), herpes simplex virus (HSV), Ebola virus, Zika virus, and chikungunya virus.

[0288] Embodiment 279: The method according to any one of Embodiments 245 to 278, wherein the inter-patient virus population is derived from a population of patients not receiving antiretroviral therapy (ART).

[0289] Embodiment 280: The method according to any one of Embodiments 245 to 278, wherein the inter-patient virus population is derived from a population of patients receiving antiretroviral therapy (ART).

[0290] Embodiment 281: The method according to any one of Embodiments 252 to 280, wherein the intra-patient virus population is derived from a patient not receiving antiretroviral therapy (ART).

[0291] Embodiment 282: The method according to any one of Embodiments 252 to 280, wherein the intra-patient virus population is derived from a patient receiving antiretroviral therapy (ART).

[0292] Embodiment 283: A fusion polypeptide produced according to the method according to any one of Embodiments 245 to 282, wherein the fusion polypeptide induces an immune response against a virus in a mammal, such as a human. In embodiments of the present invention, for example, the following items are provided. (Item 1) A fusion polypeptide comprising an amino acid sequence of any one of SEQ ID NOs: 345 to 352, 357 to 362, 367, 373, 407 to 411, or 422 to 424, or a sequence that is at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to any one of SEQ ID NOs: 345 to 352, 357 to 362, 367, 373, 407 to 411, 422 to 424, and 431 to 435. (Item 2) The fusion polypeptide according to Item 1, wherein the fusion protein does not contain a polypeptide segment encoded by the HIV-1 Tat, Rev, Vif, Vpr, and / or Vpu gene. (Item 3) The fusion protein is (i) An HIV-1 Gag amino acid sequence or a partial sequence thereof corresponding to amino acid residue positions selected from 1 to 30, 54 to 127, 138 to 146, 370 to 428, and 445 to 500, wherein the amino acid positions are based on SEQ ID NO: 404, the HIV-1 Gag amino acid sequence, (ii) An HIV-1 Nef amino acid sequence or a partial sequence thereof corresponding to amino acid residue positions selected from 1 to 63, 103 to 116, and 155 to 206, wherein the amino acid positions are based on SEQ ID NO: 405, the HIV-1 Nef amino acid sequence, (iii) An HIV-1 Env amino acid sequence or a partial sequence thereof corresponding to amino acid residue positions selected from 1 to 27, 53 to 58, 84 to 112, 138 to 234, 269 to 474, 490 to 501, 611 to 856, wherein the amino acid positions are based on SEQ ID NO: 403, the HIV-1 Env amino acid sequence, and / or (iv) An HIV-1 Pol amino acid sequence or a partial sequence thereof corresponding to amino acid residue positions selected from 1 to 55, 118 to 128, 321 to 325, 355 to 366, 432 to 541, 607 to 641, 667 to 682, 709 to 746, 828 to 833, 921 to 930, wherein the amino acid positions are based on SEQ ID NO: 406, the HIV-1 Pol amino acid sequence, and comprising, or consisting of, one, two, three, four, five, or more polypeptide segments, the fusion polypeptide according to item 1 or 2 not containing. (Item 4) The fusion polypeptide according to any one of items 1 to 3, wherein the fusion polypeptide comprises, or consists of, an HIV-1 amino acid sequence of SEQ ID NOs: 437 to 461, or a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the amino acid sequence of SEQ ID NOs: 437 to 461, or a partial sequence thereof, and comprising, or consisting of, one, two, three, four, five, or more polypeptide segments. (Item 5) The fusion polypeptide according to any one of items 1 to 4, wherein the fusion polypeptide does not contain an HIV-1 Pol polypeptide segment containing the amino acid sequence YMDD (SEQ ID NO: 462) or YVDD (SEQ ID NO: 463). (Item 6) The fusion polypeptide according to item 5, wherein the fusion polypeptide does not contain one or more amino acid sequences selected from SEQ ID NOs: 215, 216, 217, 218, 219, and 220. (Item 7) The fusion polypeptide according to item 5 or 6, wherein the fusion polypeptide does not contain one or more amino acid sequences selected from SEQ ID NOs: 209, 210, 211, 212, 213, 214, 343, and 344. (Item 8) The fusion polypeptide according to any one of items 1 to 7, comprising an N-terminal signal peptide or leader sequence. (Item 9) The fusion polypeptide according to item 8, wherein the signal peptide or leader sequence is derived from a source protein selected from the group consisting of colony stimulating factor 2 (CSF2, GM-CSF), tissue-type plasminogen activator (PLAT, t-PA), C-C motif chemokine ligand 7 (CCL7, MCP-3), C-X-C motif chemokine ligand 10 (CXCL10, IP-10), catenin beta 1 (CTNNB1), CD74 (p33; DHLAG; HLADG; Ia-gamma, invariant chain), serum albumin (ALB), polyubiquitin B / C (UBB / UBC), calreticulin (CALR), vesicular stomatitis virus G protein (VSV-G), lysosome-associated membrane protein 1 (LAMP-1), and lysosome-associated membrane protein 2 (LAMP-2). (Item 10) A polynucleotide encoding one or more fusion polypeptides according to any one of items 1 to 9. (Item 11) The polynucleotide according to item 10, wherein the polynucleotide comprises cDNA, mRNA, self-amplifying RNA (SAM), self-replicating RNA, or self-amplifying replicon RNA (RepRNA). (Item 12) The polynucleotide according to item 11, wherein the polynucleotide comprises a self-replicating or self-amplifying alphavirus replicon. (Item 13) The polynucleotide according to any one of items 10 to 12, comprising a nucleic acid sequence of any one of SEQ ID NOs: 414 to 418, or a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one of SEQ ID NOs: 414 to 418. (Item 14) A lipid nanoparticle (LNP) comprising the polynucleotide according to any one of items 10 to 13. (Item 15) An expression cassette comprising the polynucleotide according to any one of items 10 to 13 operably linked to one or more regulatory sequences. (Item 16) The expression cassette according to item 15, wherein the polynucleotide is operably linked to and under the control of a constitutive promoter. (Item 17) The expression cassette according to item 15 or 16, wherein the promoter is selected from a CMV promoter, a CAG promoter, and an EF1a promoter. (Item 18) A vector comprising one or more polynucleotides according to any one of items 10 to 13, or an expression cassette according to any one of items 15 to 17. (Item 19) The vector according to item 18, wherein the vector is a plasmid vector, a bacterial vector, or a viral vector. (Item 20) The vector according to item 18 or 19, wherein the vector is a viral vector. (Item 21) The vector according to any one of items 18 to 20, wherein the viral vector is derived from a DNA virus or an RNA virus. (Item 22) The vector according to any one of items 18 to 21, wherein the viral vector is derived from a virus selected from the group consisting of an adenovirus, an adeno-associated virus, an arenavirus, an alphavirus, a poxvirus, a cytomegalovirus, a rhabdovirus, a vesicular stomatitis virus, a flavivirus, a maraba virus, and a vaccinia virus. (Item 23) The vector according to any one of items 18 to 22, wherein the viral vector is derived from a virus from a taxonomic family selected from the group consisting of Adenoviridae, Arenaviridae, Herpesviridae (e.g., cytomegalovirus), Poxviridae (e.g., vaccinia virus, e.g., modified vaccinia Ankara (MVA)), Paramyxoviridae (e.g., measles virus), Flaviviridae (e.g., yellow fever virus), Rhabdoviridae (e.g., vesiculovirus, e.g., maraba vesiculovirus), Togaviridae (e.g., alphavirus). (Item 24) The vector according to any one of items 18 to 23, wherein the viral vector is an arenavirus vector selected from the group consisting of lymphocytic choriomeningitis mammarenavirus (LCMV), Calomys callosus mammarenavirus (synonym, Pichinde mammarenavirus or Pichinde arenavirus), Guanarito virus (GTOV), Junin virus (JUNV), Lassa virus (LASV), Lujo virus (LUJV), Machupo virus (MACV), Sabia virus (SABV), and Whitewater Arroyo virus (WWAV). (Item 25) The vector according to item 24, wherein the viral vector is an arenavirus vector selected from the group consisting of lymphocytic choriomeningitis mammarenavirus (LCMV) or Calomys callosus mammarenavirus (synonym, Pichinde mammarenavirus or Pichinde arenavirus). (Item 26) The vector according to any one of items 18 to 23, wherein the viral vector is a human adenovirus or a simian adenovirus (for example, chimpanzee adenovirus, gorilla adenovirus, or rhesus adenovirus). (Item 27) The vector according to item 26, wherein the viral vector is an adenovirus vector selected from adenovirus serotype 5 (Ad5), adenovirus serotype 26 (Ad26), adenovirus serotype 34 (Ad34), adenovirus serotype 35 (Ad35), adenovirus serotype 48 (Ad48), chimpanzee adenovirus (for example, ChAd3 (AdC3), ChAd5 (AdC5), ChAd6 (AdC6), ChAd7 (AdC7), ChAd8 (AdC8), ChAd9 (AdC9), ChAd10 (AdC10), ChAd11 (AdC11), ChAd17 (AdC17), ChAd16 (AdC16), ChAd19 (AdC19), ChAd20 (AdC20), ChAd22 (AdC22), ChAd24 (AdC24), ChAdY25, ChAd26 (AdC26), ChAd28 (AdC28), ChAd30 (AdC30), ChAd31 (AdC31), ChAd37 (AdC37), ChAd38 (AdC38), ChAd43 (AdC43), ChAd44 (AdC44), ChAd55 (AdC55), ChAd63 (AdC63), ChAdV63, ChAd68 (AdC68), ChAd73 (AdC73), ChAd82 (AdC82), ChAd83 (AdC83), ChAd143 (AdC143), ChAd144 (AdC144), ChAd145 (AdC145), ChAd147 (AdC147)), gorilla adenovirus (for example, GC44, GC45, GC46), and rhesus adenovirus (for example, RhAd51, RhAd52, RhAd53, RhAd54, RhAd55, RhAd56, RhAd57, RhAd58, RhAd59, RhAd60, RhAd61, RhAd62, RhAd63, RhAd64, RhAd65, RhAd66). (Item 28) The vector according to any one of items 18 to 27, wherein the viral vector is replication-defective, replication-impaired, replication-attenuated or replication-competent. (Item 29) The adenoviral vector according to any one of items 18 to 28, wherein the viral vector comprises one or more polynucleotides encoding one or more fusion proteins comprising an amino acid sequence of any one of SEQ ID NOs: 345 to 377, 407 to 411, 422 to 424, 430 to 435, or a sequence having at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity with any one of SEQ ID NOs: 345 to 377, 407 to 411, 422 to 424, 430 to 435. (Item 30) The vector is · SEQ ID NO: 345 and 346, · SEQ ID NO: 347 and 348, · SEQ ID NO: 349 and 350, · SEQ ID NO: 351 and 352, · SEQ ID NO: 430 and 352, · SEQ ID NO: 357 and 358, · SEQ ID NO: 360 and 362, · SEQ ID NO: 359 and 361, · SEQ ID NO: 351 and 357, · SEQ ID NO: 351 and 358, · SEQ ID NO: 351 and 359, · SEQ ID NO: 351 and 360, · SEQ ID NO: 351 and 361, · SEQ ID NO: 351 and 362, · SEQ ID NO: 351 and 407, · SEQ ID NO: 351 and 408, · SEQ ID NO: 351 and 409, · SEQ ID NO: 351 and 410, · SEQ ID NO: 352 and 357, · SEQ ID NO: 352 and 358, · SEQ ID NO: 352 and 359, · SEQ ID NOs: 352 and 360, · SEQ ID NOs: 352 and 361, · SEQ ID NOs: 352 and 362, · SEQ ID NOs: 352 and 407, · SEQ ID NOs: 352 and 408, · SEQ ID NOs: 352 and 409, · SEQ ID NOs: 352 and 410, · SEQ ID NOs: 430 and 357, · SEQ ID NOs: 430 and 358, · SEQ ID NOs: 430 and 359, · SEQ ID NOs: 430 and 360, · SEQ ID NOs: 430 and 361, · SEQ ID NOs: 430 and 362, · SEQ ID NOs: 407 and 409, · SEQ ID NOs: 407 and 408, · SEQ ID NOs: 408 and 410, or · two or more polynucleotides encoding two or more fusion proteins that are at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequences of SEQ ID NOs: 409 and 410, the vector according to any one of items 18 - 29. (Item 31) The vector according to any one of items 18 - 30, further comprising a polynucleotide encoding a cytokine or a functional variant thereof, or a non - coding immunostimulatory polynucleotide. (Item 32) The vector according to item 31, comprising a polynucleotide encoding a cytokine selected from the group consisting of IL - 2, IL - 7, IL - 12, IL - 15, IL - 18, IL - 21, IFN - α, IFN - γ, GM - CSF, fms - related receptor tyrosine kinase 3 ligand (FLT3LG), and combinations and functional variants thereof. (Item 33) The vector according to item 31, comprising a non-coding immunostimulatory polynucleotide selected from pathogen-associated molecular patterns (PAMPs), cytosine-phosphate-guanosine (CpG) oligodeoxynucleotides, and immunostimulatory RNAs (isRNAs, e.g., CV8102). (Item 34) A host cell comprising one or more polynucleotides according to any one of items 10 to 13, or one or more vectors according to any one of items 18 to 33. (Item 35) The host cell according to item 34, wherein the one or more polynucleotides are not integrated into the host cell genome, e.g., are episomal. (Item 36) The host cell according to item 34, wherein the one or more polynucleotides are integrated into the host cell genome. (Item 37) The host cell according to any one of items 34 to 36, wherein the host cell is a mammalian cell, e.g., a human cell. (Item 38) The host cell according to any one of items 34 to 37, wherein the host cell is in vitro. (Item 39) The host cell according to any one of items 34 to 37, wherein the host cell is in vivo. (Item 40) An immunogenic composition comprising one or more of the fusion polypeptides according to any one of items 1 to 9, or one or more polynucleotides according to any one of items 10 to 13, or one or more vectors according to any one of items 18 to 33, and a pharmaceutically acceptable carrier. (Item 41) The immunogenic composition according to item 40, comprising two or more of the fusion polypeptides according to any one of items 1 to 9, or two or more polynucleotides according to any one of items 10 to 13, or two or more vectors according to any one of items 18 to 33. (Item 42) The immunogenic composition according to item 40 or 41, wherein the one or more polynucleotides are DNA, cDNA, mRNA, or self-replicating RNA. (Item 43) The immunogenic composition according to any one of items 40 to 42, comprising one or more adenovirus vectors, each adenovirus vector encoding one or more fusion proteins comprising an amino acid sequence of any one of SEQ ID NOs: 345 to 377, 407 to 411, 422 to 424, 430 to 435, or a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one of SEQ ID NOs: 345 to 377, 407 to 411, 422 to 424, 430 to 435. (Item 44) Comprising one or more viral vectors, each viral vector · SEQ ID NOs: 345 and 346, · SEQ ID NOs: 347 and 348, · SEQ ID NOs: 349 and 350, · SEQ ID NOs: 351 and 352, · SEQ ID NOs: 430 and 352, · SEQ ID NOs: 357 and 358, · SEQ ID NOs: 360 and 362, · SEQ ID NOs: 359 and 361, · SEQ ID NOs: 351 and 357, · SEQ ID NOs: 351 and 358, · SEQ ID NOs: 351 and 359, · SEQ ID NOs: 351 and 360, · SEQ ID NOs: 351 and 361, · SEQ ID NOs: 351 and 362, · SEQ ID NOs: 351 and 407, · SEQ ID NOs: 351 and 408, · SEQ ID NOs: 351 and 409, · SEQ ID NOs: 351 and 410, · SEQ ID NOs: 352 and 357, · SEQ ID NOs: 352 and 358, · SEQ ID NO: 352 and 359, · SEQ ID NO: 352 and 360, · SEQ ID NO: 352 and 361, · SEQ ID NO: 352 and 362, · SEQ ID NO: 352 and 407, · SEQ ID NO: 352 and 408, · SEQ ID NO: 352 and 409, · SEQ ID NO: 352 and 410, · SEQ ID NO: 430 and 357, · SEQ ID NO: 430 and 358, · SEQ ID NO: 430 and 359, · SEQ ID NO: 430 and 360, · SEQ ID NO: 430 and 361, · SEQ ID NO: 430 and 362, · SEQ ID NO: 407 and 409, · SEQ ID NO: 407 and 408, · SEQ ID NO: 408 and 410, or · one or more polynucleotides encoding two or more fusion proteins having an amino acid sequence of SEQ ID NO: 409 and 410 that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical, or the immunogenic composition according to any one of items 40 to 43. (Item 45) 1) one or more fusion polypeptides comprising an amino acid sequence of any one of SEQ ID NO: 351 to 356 and 430, or one or more polynucleotides encoding a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one of SEQ ID NO: 351 to 356 and 430, or one or more vectors capable of expressing the same, 2) One or more fusion polypeptides comprising any one amino acid sequence among SEQ ID NOs: 357 to 366 and 407 to 410, or one or more polynucleotides encoding a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one among SEQ ID NOs: 357 to 366 and 407 to 410, or one or more vectors capable of expressing the same, and an immunogenic composition according to any one of items 40 to 43. (Item 46) A pharmaceutical composition comprising one or more of the fusion polypeptides according to any one of items 1 to 9, or one or more polynucleotides according to any one of items 10 to 13, or one or more vectors according to any one of items 18 to 33, and a pharmaceutically acceptable carrier. (Item 47) A pharmaceutical composition according to item 46, comprising two or more fusion polypeptides, two or more polynucleotides, or two or more vectors. (Item 48) A pharmaceutical composition according to item 46 or 47, further comprising one or more of an adjuvant, an immunostimulant, a detergent, a micelle-forming agent, and an oil. (Item 49) The pharmaceutical composition according to item 48, wherein the immunostimulant is selected from Toll-like receptor (TLR) agonists, cytokines, non-coding immunostimulatory polynucleotides, inhibitors of inhibitory immune checkpoint proteins, or stimulants of stimulatory immune checkpoint proteins. (Item 50) A pharmaceutical composition according to item 49, comprising a polynucleotide encoding a cytokine selected from the group consisting of IL-2, IL-7, IL-12, IL-15, IL-18, IL-21, IFN-α, IFN-γ, GM-CSF, FLT3LG, and combinations and functional variants thereof. (Item 51) The pharmaceutical composition according to item 49, comprising a non-coding immunostimulatory polynucleotide selected from pathogen-associated molecular patterns (PAMPs), cytosine-phosphate-guanosine (CpG) oligodeoxynucleotides, and immunostimulatory RNA (isRNA, for example, CV8102). (Item 52) The pharmaceutical composition according to any one of items 46 to 51, formulated for administration via a route selected from the group consisting of intravenous, intramuscular, intradermal, subcutaneous, and mucosal (e.g., intraoral, intranasal, rectal, vaginal). (Item 53) The pharmaceutical composition according to any one of items 46 to 52, formulated as a liquid. (Item 54) The pharmaceutical composition according to any one of items 46 to 52, wherein the composition is lyophilized. (Item 55) A kit comprising one or more unit doses of one or more of the fusion polypeptides according to any one of items 1 to 9, or one or more of the polynucleotides according to any one of items 10 to 13, or one or more of the vectors according to any one of items 18 to 33, or one or more of the immunogenic compositions according to any one of items 40 to 45, or one or more of the pharmaceutical compositions according to any one of items 46 to 54. (Item 56) The kit according to item 55, wherein the one or more unit doses are in a single container. (Item 57) The kit according to item 55, wherein the one or more unit doses are in two or more separate containers. (Item 58) The kit according to any one of items 55 to 57, comprising one or more containers selected from the group consisting of vials, ampoules, and pre-filled syringes. (Item 59) The kit according to any one of items 55 to 58, comprising one or more containers containing one or more of the fusion polypeptides, one or more of the polynucleotides, or one or more of the vectors in an aqueous solution. (Item 60) The kit according to any one of items 55 to 59, wherein the one or more unit doses are the same. (Item 61) The kit according to any one of items 55 to 59, wherein the one or more unit doses are different. (Item 62) Comprising one or more unit doses of one or more viral vectors according to any one of items 18 to 33, wherein the unit dose is about 10 3 ~ about 10 15 Viral focus forming units (FFU) or plaque forming units (PFU) or infectious units (IU) or viral particles (vp), for example, about 10 4 ~ about 10 7 Viral FFU or PFU or IU or vp, for example, about 10 3 ~ about 10 4 , 10 5 , 10 6 , 10 7 , 10 8 , 10 9 , 10 10 , 10 11 , 10 12 , 10 13 , 10 14 Or 10 15 The kit according to any one of items 55 to 61, which is within the range of viral FFU or PFU or IU or vp. (Item 63) The kit according to any one of items 55 to 62, comprising two or more of the fusion polypeptides according to any one of items 1 to 9, or two or more polynucleotides according to any one of items 10 to 13, or two or more vectors according to any one of items 18 to 33. (Item 64) One or more polynucleotides encoding the fusion polypeptide or one or more vectors expressing the fusion polypeptide, wherein the fusion polypeptide comprises an amino acid sequence of any one of SEQ ID NOs: 345 to 377, 411, 422 to 424, and 430 to 435, or a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one of SEQ ID NOs: 345 to 377, 411, 422 to 424, and 430 to 435, or consists of the same, the kit according to any one of items 55 to 63. (Item 65) Comprising one or more adenoviral vectors, each adenoviral vector comprising one or more polynucleotides encoding one or more fusion proteins, wherein the amino acid sequence of any one of SEQ ID NOs: 345 to 377, 407 to 411, 422 to 424, 430 to 435, or a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one of SEQ ID NOs: 345 to 377, 407 to 411, 422 to 424, 430 to 435, the kit according to any one of items 55 to 64. (Item 66) Comprising one or more viral vectors, each viral vector being · SEQ ID NOs: 345 and 346, · SEQ ID NOs: 347 and 348, · SEQ ID NOs: 349 and 350, · SEQ ID NOs: 351 and 352, · SEQ ID NOs: 430 and 352, · SEQ ID NOs: 357 and 358, · SEQ ID NOs: 360 and 362, · SEQ ID NOs: 359 and 361, · SEQ ID NOs: 351 and 357, · SEQ ID NOs: 351 and 358, · SEQ ID NOs: 351 and 359, · SEQ ID NOs: 351 and 360, · SEQ ID NO: 351 and 361, · SEQ ID NO: 351 and 362, · SEQ ID NO: 351 and 407, · SEQ ID NO: 351 and 408, · SEQ ID NO: 351 and 409, · SEQ ID NO: 351 and 410, · SEQ ID NO: 352 and 357, · SEQ ID NO: 352 and 358, · SEQ ID NO: 352 and 359, · SEQ ID NO: 352 and 360, · SEQ ID NO: 352 and 361, · SEQ ID NO: 352 and 362, · SEQ ID NO: 352 and 407, · SEQ ID NO: 352 and 408, · SEQ ID NO: 352 and 409, · SEQ ID NO: 352 and 410, · SEQ ID NO: 430 and 357, · SEQ ID NO: 430 and 358, · SEQ ID NO: 430 and 359, · SEQ ID NO: 430 and 360, · SEQ ID NO: 430 and 361, · SEQ ID NO: 430 and 362, · SEQ ID NO: 407 and 409, · SEQ ID NO: 407 and 408, · SEQ ID NO: 408 and 410, or · two or more polynucleotides encoding two or more fusion proteins that are at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequences of SEQ ID NO: 409 and 410, the kit according to any one of items 55 - 65. (Item 67) Comprising two or more polynucleotides encoding the fusion polypeptide or two or more vectors expressing the fusion polypeptide, wherein the fusion polypeptide is 1) Any one of the amino acid sequences of SEQ ID NOs: 351 to 356 and 430, or a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one of SEQ ID NOs: 351 to 356 and 430, 2) Any one of the amino acid sequences of SEQ ID NOs: 357 to 366 and 407 to 410, or a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one of SEQ ID NOs: 357 to 366 and 407 to 410, and the kit according to item 63. (Item 68) The kit according to any one of items 55 to 66, further comprising one or more unit doses of one or more additional therapeutic agents. (Item 69) The kit according to item 68, comprising one or more agents that activate latent HIV, for example, one or more latency reversing agents (LRAs). (Item 70) The kit according to item 68 or 69, comprising one or more LRAs selected from the group consisting of agonists or activators of one or more toll-like receptors (TLRs), histone deacetylase (HDAC) inhibitors, proteasome inhibitors, protein kinase C (PKC) activators, Smyd2 inhibitors, BET-bromodomain 4 (BRD4) inhibitors, ionomycin, apoptosis protein inhibitor (IAP) antagonists, and second mitochondrial-derived caspase activator (SMAC) mimetics. (Item 71) The kit according to any one of items 68 to 70, comprising one or more agonists or activators of one or more toll-like receptors (TLRs). (Item 72) The kit according to item 71, wherein the TLR agonist or activator is selected from the group consisting of a TLR2 agonist, a TLR3 agonist, a TLR4 agonist, a TLR5 agonist, a TLR7 agonist, a TLR8 agonist, and a TLR9 agonist. (Item 73) The kit according to item 71 or 72, wherein the TLR7 agonist is selected from the group consisting of GS9620 (vesatolimod), R848 (resiquimod), DS-0509, LHC-165, and TMX-101 (imiquimod), and / or the TLR8 agonist is selected from the group consisting of GS-9688, R848 (resiquimod), CV8102 (dual TLR7 / TLR8 agonist), and NKTR-262 (dual TLR7 / TLR8 agonist). (Item 74) The kit according to any one of items 71 to 73, wherein the TLR9 agonist is selected from the group consisting of AST-008, cobitolimod, CMP-001, IMO-2055, IMO-2125, retifimod, MGN-1601, BB-001, BB-006, IMO-3100, IMO-8400, IR-103, IMO-9200, agatolimod, DIMS-9054, DV-1079, DV-1179, AZD-1419, lefitolimod (MGN-1703), CYT-003, CYT-003-QbG10, tilsotolimod, and PUL-042. (Item 75) The kit according to any one of items 68 to 74, comprising one or more interleukin receptor agonists of interleukin selected from IL-2, IL-7, IL-12, IL-15, IL-18, IL-21, IFN-α, IFN-γ, GM-CSF, and FLT3LG. (Item 76) The kit according to item 75, comprising one or more cytokines selected from the group consisting of IL-2, IL-7, IL-12, IL-15, IL-18, IL-21, IFN-α, IFN-γ, GM-CSF, FLT3LG, and combinations and functional variants thereof. (Item 77) The kit according to any one of items 68 to 76, comprising an agonist of a receptor selected from the group consisting of fms-related tyrosine kinase 3 (FLT3), interferon gene stimulator (STING) receptor, DExD / H-box helicase 58 (DDX58; also known as RIG-I), and nucleotide-binding oligomerization domain-containing 2 (NOD2). (Item 78) (Item 78) The kit according to any one of items 68 to 77, comprising an inhibitor of a T cell inhibitory immune checkpoint protein or receptor selected from the group consisting of CD274 (CD274, PDL1, PD-L1), programmed cell death 1 ligand 2 (PDCD1LG2, PD-L2, CD273), programmed cell death 1 (PDCD1, PD1, PD-1), cytotoxic T lymphocyte-associated protein 4 (CTLA4, CD152), CD276 (B7H3), V-set domain-containing T cell activation inhibitor 1 (VTCN1, B7H4), V-set immunoregulatory receptor (VSIR, B7H5, VISTA), immunoglobulin superfamily member 11 (IGSF11, VSIG3), TNFRSF14 (HVEM, CD270), TNFSF14 (HVEML), CD272 (B and T lymphocyte-associated (BTLA)), PVR-related immunoglobulin domain-containing (PVRIG, CD112R), T cell immune receptor containing Ig and ITIM domains (TIGIT), lymphocyte activation 3 (LAG3, CD223), hepatitis A virus cell receptor 2 (HAVCR2, TIMD3, TIM3), galectin 9 (LGALS9), killer cell immunoglobulin-like receptor, three Ig domains, and long cytoplasmic tail 1 (KIR, CD158E1), killer cell immunoglobulin-like receptor, two Ig domains, and long cytoplasmic tail 1 (KIR2DL1), killer cell immunoglobulin-like receptor, two Ig domains, and long cytoplasmic tail 2 (KIR2DL2), killer cell immunoglobulin-like receptor, two Ig domains, and long cytoplasmic tail 3 (KIR2DL3), killer cell immunoglobulin-like receptor, three Ig domains, and long cytoplasmic tail 1 (KIR3DL1). (Item 79) An agonist, activator or stimulator of a T cell-stimulating immune checkpoint protein or receptor selected from the group consisting of CD27, CD70, CD40, CD40LG, inducible T cell co-stimulator (ICOS, CD278), inducible T cell co-stimulator ligand (ICOSLG, B7H2), TNF receptor superfamily member 4 (TNFRSF4, OX40), TNF superfamily member 4 (TNFSF4, OX40L), TNFRSF9 (CD137), TNFSF9 (CD137L), TNFRSF18 (GITR), TNFSF18 (GITRL), CD80 (B7-1), CD28, nectin cell adhesion molecule 2 (NECTIN2, CD112), CD226 (DNAM-1), and poliovirus receptor (PVR) cell adhesion molecule (PVR, CD155), the kit according to any one of items 68 to 78. (Item 80) The inhibitor of CTLA4 is selected from the group consisting of ipilimumab, tremelimumab, BMS-986218, AGEN1181, AGEN1884 (zalifrelimab), BMS-986249, MK-1308, REGN-4659, ADU-1604, CS-1002, BCD-145, APL-509, JS-007, BA-3071, ONC-392, AGEN-2041, JHL-1155, KN-044, CG-0161, ATOR-1144, PBI-5D3H5, FPT-155 (CTLA4 / PD-L1 / CD28), PF-06936308 (PD-1 / CTLA4), MGD-019 (PD-1 / CTLA4), KN-046 (PD-1 / CTLA4), MEDI-5752 (CTLA4 / PD-1), XmAb-20717 (PD-1 / CTLA4), AK-104 (CTLA4 / PD-1) and BPI-002, the kit according to item 78. (Item 81) The inhibitor of the aforementioned PD-L1 (CD274) or PD-1 (PDCD1) is pembrolizumab, nivolumab, semiprimab, pidilizumab, AB122 (zimberelimab), AMP-224, MEDI0680 (AMP-514), spartalizumab, atezolizumab, avelumab, durvalumab, BMS-936559, CK-301, PF-06801591, BGB-A317 (tislelizumab), GLS-010 (WBP-3055), AK-103 (HX-008), AK-105, CS-1003, HLX-10, MGA-012, BI-754091, AGEN-2034 (), JS-001 (toripalimab), JNJ-63723283, genolimuzumab (CBT-501), LZM-009, BCD-100, LY-3300054, SHR-1201, SHR-1210 (camrelizumab), Sym-021, ABBV-181, PD1-PIK, BAT-1306, (MSB0010718C), CX-072, CBT-502, TSR-042 (dostarlimab), MSB-2311, JTX-4014, BGB-A333, SHR-1316, CS-1001 (WBP-3155, KN-035, IBI-308 (sintilimab), HLX-20, KL-A167, STI-A1014, STI-A1015 (IMC-001), BCD-135, FAZ-053, TQB-2450, MDX1105-01, FPT-155 (CTLA4 / PD-L1 / CD28), PF-06936308 (PD-1 / CTLA4), MGD-013 (PD-1 / LAG-3), FS-118 (LAG-3 / PD-L1) MGD-019 (PD-1 / CTLA4), KN-046 (PD-1 / CTLA4), MEDI-5752 (CTLA4 / PD-1), RO-7121661 (PD-1 / TIM-3), XmAb-20717 (PD-1 / CTLA4), AK-104 (CTLA4 / PD-1), M7824 (PD-L1 / TGFβ-EC domain), CA-170 (PD-L1 / VISTA), CDX-527 (CD27 / PD-L1), LY-3415244 (TIM3 / PDL1), INBRX-105 (4-1BB / PDL1), GS-4224, GS-4416, INCB086550 and MAX10181, and the kit according to item 78 selected from the group consisting of the above. (Item 82) The kit according to any one of Items 68 to 81, further comprising administering an inhibitor of CD47 to the subject. (Item 83) The kit according to any one of Items 68 to 82, further comprising one or more antiviral agents. (Item 84) The kit according to Item 83, wherein the one or more antiviral agents are selected from the group consisting of an HIV protease inhibitor, an HIV reverse transcriptase inhibitor, an HIV integrase inhibitor, an HIV non-catalytic site (or allosteric) integrase inhibitor, an HIV entry (fusion) inhibitor, an HIV maturation inhibitor, and a capsid inhibitor. (Item 85) A method for inducing an immune response against human immunodeficiency virus (HIV) in a subject in need thereof, comprising administering to the subject one or more of the fusion polypeptides according to any one of Items 1 to 9, or one or more of the polynucleotides according to any one of Items 10 to 13, or one or more of the vectors according to any one of Items 18 to 33, or one or more of the immunogenic compositions according to any one of Items 40 to 45, or one or more of the pharmaceutical compositions according to any one of Items 46 to 54. (Item 86) A method for treating or preventing human immunodeficiency virus (HIV) in a subject in need thereof, comprising administering to the subject one or more of the fusion polypeptides according to any one of Items 1 to 9, or one or more of the polynucleotides according to any one of Items 10 to 13, or one or more of the vectors according to any one of Items 18 to 33, or one or more of the immunogenic compositions according to any one of Items 40 to 45, or one or more of the pharmaceutical compositions according to any one of Items 46 to 54. (Item 87) The method according to Item 85 or 86, comprising administering a single fusion polypeptide, or a polynucleotide or viral expression vector encoding the fusion polypeptide, wherein the fusion polypeptide comprises two or more multivalent polypeptide segments, such as divalent polypeptide segments. (Item 88) The method according to item 85 or 86, wherein two or more fusion polypeptides, or two or more viral expression vectors encoding said fusion polypeptides, are administered to said subject simultaneously or in parallel. (Item 89) The method according to any one of items 85 to 88, wherein two or more fusion polypeptides, or two or more polynucleotides, or two or more viral expression vectors encoding said fusion polypeptides are in the form of a bivalent antigen composition. (Item 90) Comprising administering to said subject one or more fusion polypeptides, or a polynucleotide encoding said fusion polypeptide, or a viral expression vector expressing said fusion polypeptide, wherein said fusion polypeptide comprises the amino acid sequence of any one of SEQ ID NOs: 345 - 377, 407 - 411, 422 - 424, 430 - 435, or a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one of SEQ ID NOs: 345 - 377, 407 - 411, 422 - 424, 430 - 435, or consists of the same; the method according to any one of items 85 - 89. (Item 91) Comprising administering to said subject one or more adenoviral vectors, each adenoviral vector comprising one or more polynucleotides encoding one or more fusion proteins comprising the amino acid sequence of any one of SEQ ID NOs: 345 - 377, 407 - 411, 422 - 424, 430 - 435, or a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one of SEQ ID NOs: 345 - 377, 407 - 411, 422 - 424, 430 - 435; the method according to any one of items 85 - 90. (Item 92) administering to the subject one or more viral vectors, each viral vector comprising · SEQ ID NOs: 345 and 346, · SEQ ID NOs: 347 and 348, · SEQ ID NOs: 349 and 350, · SEQ ID NOs: 351 and 352, · SEQ ID NOs: 430 and 352, · SEQ ID NOs: 357 and 358, · SEQ ID NOs: 360 and 362, · SEQ ID NOs: 359 and 361, · SEQ ID NOs: 351 and 357, · SEQ ID NOs: 351 and 358, · SEQ ID NOs: 351 and 359, · SEQ ID NOs: 351 and 360, · SEQ ID NOs: 351 and 361, · SEQ ID NOs: 351 and 362, · SEQ ID NOs: 351 and 407, · SEQ ID NOs: 351 and 408, · SEQ ID NOs: 351 and 409, · SEQ ID NOs: 351 and 410, · SEQ ID NOs: 352 and 357, · SEQ ID NOs: 352 and 358, · SEQ ID NOs: 352 and 359, · SEQ ID NOs: 352 and 360, · SEQ ID NOs: 352 and 361, · SEQ ID NOs: 352 and 362, · SEQ ID NOs: 352 and 407, · SEQ ID NOs: 352 and 408, · SEQ ID NOs: 352 and 409, · SEQ ID NOs: 352 and 410, · SEQ ID NOs: 430 and 357, · SEQ ID NOs: 430 and 358, · SEQ ID NOs: 430 and 359, · SEQ ID NOs: 430 and 360, · SEQ ID NOs: 430 and 361, · SEQ ID NOs: 430 and 362, · SEQ ID NOs: 407 and 409, · SEQ ID NOs: 407 and 408, · SEQ ID NOs: 408 and 410, or · Two or more polynucleotides encoding two or more fusion proteins that are at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequences of SEQ ID NOs: 409 and 410, the method according to any one of items 85-91. (Item 93) To the subject, 1) One or more fusion polypeptides, or a polynucleotide encoding the fusion polypeptide, or a viral expression vector expressing the fusion polypeptide, wherein the fusion polypeptide comprises an amino acid sequence of any one of SEQ ID NOs: 351-356 and 430, or a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one of SEQ ID NOs: 351-356 and 430, or consisting of the same, one or more fusion polypeptides, or a polynucleotide encoding the fusion polypeptide, or a viral expression vector expressing the fusion polypeptide, and 2) One or more fusion polypeptides, or a polynucleotide encoding the fusion polypeptide, or a viral expression vector expressing the fusion polypeptide, wherein the fusion polypeptide comprises an amino acid sequence of any one of SEQ ID NOs: 357-366 and 407-410, or a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one of SEQ ID NOs: 357-366 and 407-410, or consisting of the same, one or more fusion polypeptides, or a polynucleotide encoding the fusion polypeptide, or a viral expression vector expressing the fusion polypeptide, the method according to any one of items 85-91, comprising administering. (Item 94) The subject is a method according to any one of items 85 to 92 that is infected with HIV-1, suspected of being infected with HIV-1, or at risk of being infected with HIV-1. (Item 95) The subject is a method according to any one of items 85 to 94 that is chronically infected with HIV-1. (Item 96) The subject is a method according to any one of items 85 to 95 that is acutely infected with HIV-1. (Item 97) The subject is a method according to any one of items 85 to 96 that has an HIV-1 infection at the Virchow stage IV or earlier, for example, at the Virchow stage III, Virchow stage II, or Virchow stage I. (Item 98) The composition is administered via a route selected from intravenous, intramuscular, intradermal, subcutaneous, and mucosal (e.g., intraoral, intranasal, rectal, intravaginal) routes, and is a method according to any one of items 85 to 97. (Item 99) Per administration, about 10 3 ~about 10 15 virus focus forming units (FFU) or plaque forming units (PFU) or infectious units (IU) or virus particles (vp), for example, about 10 4 ~about 10 7 virus FFU or PFU or IU or vp, for example, about 10 3 ~about 10 4 、10 5 、10 6 、10 7 、10 8 、10 9 、10 10 、10 11 、10 12 、10 13 、10 14 or 10 15 administering virus FFU or PFU or IU or vp, and is a method according to any one of items 85 to 98. (Item 100) A prime-boost regimen, comprising: (i) administering a priming composition at a first time point and administering one or more boosting compositions at one or more subsequent time points (e.g., prime-boost-boost-boost, etc.), or (ii) administering a priming composition at a first time point and administering a boosting composition at a second time point, a prime-boost regimen comprising one or more repetitions (e.g., prime-boost-prime-boost, etc.), the method according to any one of items 85 to 99. (Item 101) The method according to item 100, wherein the administrations of the priming composition and the one or more boosting compositions are spaced apart by at least one week, two weeks, three weeks, or one month, e.g., at least two, three, four, five, or six months. (Item 102) The method according to item 100 or 101, wherein the priming composition and the boosting composition comprise the same immunogenic composition. (Item 103) The method according to item 100 or 101, wherein the priming composition and the boosting composition comprise different immunogenic compositions. (Item 104) The method according to item 100 or 101, wherein the priming composition and the boosting composition comprise the same one or more fusion polypeptides and the same polynucleotide or viral expression vector. (Item 105) The method according to item 100 or 101, wherein the priming composition and the boosting composition comprise different fusion polypeptides and / or different polynucleotides or viral expression vectors. (Item 106) The method according to item 105, comprising priming with a first polynucleotide or viral expression vector and boosting with a second polynucleotide or viral expression vector. (Item 107) The prime-boost regimen is a) Priming with a viral expression vector and boosting with a polynucleotide, wherein the polynucleotide is DNA, cDNA, mRNA, or self-replicating RNA, the priming and boosting, b) Priming with a polynucleotide that is DNA, cDNA, mRNA, or self-replicating RNA and boosting with a viral expression vector, c) Priming with a first viral expression vector and boosting with a second viral expression vector, wherein the first and second viral expression vectors are from the same, related, or unrelated taxonomic families, the priming and boosting, d) Priming with a first replication-deficient viral expression vector and boosting with a second replication-deficient viral expression vector, wherein the first and second replication-deficient viral expression vectors are from the same, related, or unrelated taxonomic families, the priming and boosting, e) Priming with a first attenuated replication-deficient viral expression vector and boosting with a second replication-attenuated viral expression vector, wherein the first and second replication-attenuated viral expression vectors are from the same, related, or unrelated taxonomic families, the priming and boosting, f) Priming with a replication-deficient viral expression vector and boosting with a replication-attenuated viral expression vector, g) Priming with a replication-attenuated viral expression vector and boosting with a replication-deficient viral expression vector, h) Priming with a viral expression vector of lymphocytic choriomeningitis mammarenavirus (LCMV) and boosting with a viral expression vector of Pichinde mammarenavirus, i) Priming with a viral expression vector of Pichinde mammarenavirus and boosting with a viral expression vector of lymphocytic choriomeningitis mammarenavirus (LCMV), j) Priming with a viral expression vector of arenavirus and boosting with a viral expression vector of adenovirus, or k) A method according to any one of items 100 to 106, comprising priming with an adenovirus viral expression vector and boosting with an arenavirus viral expression vector. (Item 108) A method according to any one of items 85 to 107, wherein the subject has not received antiretroviral therapy (ART) or ART has been discontinued prior to administration of the one or more compositions. (Item 109) A method according to any one of items 85 to 108, wherein ART is discontinued after one or more administrations of the composition. (Item 110) A method according to any one of items 85 to 109, further comprising administering to the subject one or more additional therapeutic agents, such as two, three, four, or more additional therapeutic agents. (Item 111) A method according to item 110, comprising co-administering one or more agents that activate latent HIV, such as one or more latency reversing agents (LRAs). (Item 112) The method according to item 110 or 111, wherein the one or more LRAs are selected from the group consisting of agonists or activators of one or more toll-like receptors (TLRs), histone deacetylase (HDAC) inhibitors, proteasome inhibitors, protein kinase C (PKC) activators, Smyd2 inhibitors, BET-bromodomain 4 (BRD4) inhibitors, ionomycin, apoptosis protein inhibitor (IAP) antagonists, and second mitochondrial-derived caspase activator (SMAC) mimetics. (Item 113) A method according to any one of items 110 to 112, comprising co-administering one or more agonists or activators of one or more toll-like receptors (TLRs). (Item 114) The method according to item 113, wherein the TLR agonist or activator is selected from the group consisting of TLR2 agonist, TLR3 agonist, TLR4 agonist, TLR5 agonist, TLR7 agonist, TLR8 agonist, and TLR9 agonist. (Item 115) The method according to item 113 or 114, wherein the TLR7 agonist is selected from the group consisting of GS9620 (vesatolimod), R848 (resiquimod), DS-0509, LHC-165, and TMX-101 (imiquimod), and / or the TLR8 agonist is selected from the group consisting of GS-9688, R848 (resiquimod), CV8102 (dual TLR7 / TLR8 agonist), and NKTR-262 (dual TLR7 / TLR8 agonist). (Item 116) The method according to any one of items 110 to 115, comprising co-administering one or more interleukin receptor agonists of interleukin selected from IL-2, IL-7, IL-12, IL-15, IL-18, IL-21, IFN-α, IFN-γ, GM-CSF, and FLT3LG. (Item 117) The method according to item 116, comprising co-administering one or more cytokines selected from the group consisting of IL-2, IL-7, IL-12, IL-15, IL-18, IL-21, IFN-α, IFN-γ, GM-CSF, FLT3LG, and combinations and functional variants thereof. (Item 118) The method according to any one of items 110 to 117, comprising co-administering an agonist of a receptor selected from the group consisting of fms-related tyrosine kinase 3 (FLT3), interferon gene stimulator (STING) receptor, DExD / H-box helicase 58 (DDX58; also known as RIG-I), and nucleotide-binding oligomerization domain-containing 2 (NOD2). (Item 119) An inhibitor of a T cell inhibitory immune checkpoint protein or receptor selected from the group consisting of CD274 (CD274, PDL1, PD-L1), programmed cell death 1 ligand 2 (PDCD1LG2, PD-L2, CD273), programmed cell death 1 (PDCD1, PD1, PD-1), cytotoxic T lymphocyte-associated protein 4 (CTLA4, CD152), CD276 (B7H3), V-set domain-containing T cell activation inhibitor 1 (VTCN1, B7H4), V-set immunoregulatory receptor (VSIR, B7H5, VISTA), immunoglobulin superfamily member 11 (IGSF11, VSIG3), TNFRSF14 (HVEM, CD270), TNFSF14 (HVEML), CD272 (B and T lymphocyte-associated (BTLA)), PVR-related immunoglobulin domain-containing (PVRIG, CD112R), T cell immunoreceptor containing Ig and ITIM domains (TIGIT), lymphocyte activation 3 (LAG3, CD223), hepatitis A virus cellular receptor 2 (HAVCR2, TIMD3, TIM3), galectin 9 (LGALS9), killer cell immunoglobulin-like receptor, three Ig domains, and long cytoplasmic tail 1 (KIR, CD158E1), killer cell immunoglobulin-like receptor, two Ig domains, and long cytoplasmic tail 1 (KIR2DL1), killer cell immunoglobulin-like receptor, two Ig domains, and long cytoplasmic tail 2 (KIR2DL2), killer cell immunoglobulin-like receptor, two Ig domains, and long cytoplasmic tail 3 (KIR2DL3), killer cell immunoglobulin-like receptor, three Ig domains, and long cytoplasmic tail 1 (KIR3DL1), is co-administered, the method according to any one of items 110 to 118. (Item 120) An agonist, activator or stimulator of a T cell-stimulatory immune checkpoint protein or receptor selected from the group consisting of CD27, CD70, CD40, CD40LG, inducible T cell co-stimulator (ICOS, CD278), inducible T cell co-stimulator ligand (ICOSLG, B7H2), TNF receptor superfamily member 4 (TNFRSF4, OX40), TNF superfamily member 4 (TNFSF4, OX40L), TNFRSF9 (CD137), TNFSF9 (CD137L), TNFRSF18 (GITR), TNFSF18 (GITRL), CD80 (B7-1), CD28, nectin cell adhesion molecule 2 (NECTIN2, CD112), CD226 (DNAM-1), and poliovirus receptor (PVR) cell adhesion molecule (PVR, CD155), the method according to any one of items 110 to 119, comprising co-administering. (Item 121) The method according to item 119, wherein the inhibitor of CTLA4 is selected from the group consisting of ipilimumab, tremelimumab, BMS-986218, AGEN1181, AGEN1884 (zalifrelimab), BMS-986249, MK-1308, REGN-4659, ADU-1604, CS-1002, BCD-145, APL-509, JS-007, BA-3071, ONC-392, AGEN-2041, JHL-1155, KN-044, CG-0161, ATOR-1144, PBI-5D3H5, FPT-155 (CTLA4 / PD-L1 / CD28), PF-06936308 (PD-1 / CTLA4), MGD-019 (PD-1 / CTLA4), KN-046 (PD-1 / CTLA4), MEDI-5752 (CTLA4 / PD-1), XmAb-20717 (PD-1 / CTLA4), AK-104 (CTLA4 / PD-1) and BPI-002. (Item 122) The inhibitor of the aforementioned PD-L1 (CD274) or PD-1 (PDCD1) is pembrolizumab, nivolumab, semiprimab, pidilizumab, AB122 (zimberelimab), AMP-224, MEDI0680 (AMP-514), spartalizumab, atezolizumab, avelumab, durvalumab, BMS-936559, CK-301, PF-06801591, BGB-A317 (tislelizumab), GLS-010 (WBP-3055), AK-103 (HX-008), AK-105, CS-1003, HLX-10, MGA-012, BI-754091, AGEN-2034 (balstilimab), JS-001 (toripalimab), JNJ-63723283, genolimuzumab (CBT-501), LZM-009, BCD-100, LY-3300054, SHR-1201, SHR-1210 (camrelizumab), Sym-021, ABBV-181, PD1-PIK, BAT-1306, (MSB0010718C), CX-072, CBT-502, TSR-042 (dostarlimab), MSB-2311, JTX-4014, BGB-A333, SHR-1316, CS-1001 (WBP-3155, KN-035, IBI-308 (sintilimab), HLX-20, KL-A167, STI-A1014, STI-A1015 (IMC-001), BCD-135, FAZ-053, TQB-2450, MDX1105-01, FPT-155 (CTLA4 / PD-L1 / CD28), PF-06936308 (PD-1 / CTLA4), MGD-013 (PD-1 / LAG-3), FS-118 (LAG-3 / PD-L1) MGD-019 (PD-1 / CTLA4), KN-046 (PD-1 / CTLA4), MEDI-5752 (CTLA4 / PD-1), RO-7121661 (PD-1 / TIM-3), XmAb-20717 (PD-1 / CTLA4), AK-104 (CTLA4 / PD-1), M7824 (PD-L1 / TGFβ-EC domain), CA-170 (PD-L1 / VISTA), CDX-527 (CD27 / PD-L1), LY-3415244 (TIM3 / PDL1), INBRX-105 (4-1BB / PDL1), GS-4224, GS-4416, INCB086550 and MAX10181, and the method according to item 119 selected from the group consisting of these substances. (Item 123) The method according to any one of Items 110 to 122, further comprising administering an inhibitor of CD47 to the subject. (Item 124) The method according to any one of Items 110 to 123, further comprising administering one or more antiviral agents to the subject. (Item 125) The method according to Item 124, wherein the one or more antiviral agents are selected from the group consisting of an HIV protease inhibitor, an HIV reverse transcriptase inhibitor, an HIV integrase inhibitor, an HIV non-catalytic site (or allosteric) integrase inhibitor, an HIV entry (fusion) inhibitor, an HIV maturation inhibitor, and a capsid inhibitor. (Item 126) After administering one or more of the compositions, optionally in combination with one or more additional therapeutic agents, one or more times, the subject does not exhibit symptoms of HIV or AIDS for at least 6 months, at least 1 year, at least 2 years, at least 3 years, or more in the absence of antiretroviral therapy (ART). The method according to any one of Items 85 to 125. (Item 127) After administering one or more of the compositions, optionally in combination with one or more additional therapeutic agents, one or more times, the subject has a viral load of less than 500, for example, less than 400, less than 300, less than 200, less than 100, less than 50 copies / ml of blood for at least 6 months, at least 1 year, at least 2 years, at least 3 years, or more in the absence of antiretroviral therapy (ART). The method according to any one of Items 85 to 126. (Item 128) For use in inducing an immune response against human immunodeficiency virus (HIV) in a subject in need thereof, one or more fusion polypeptides according to any one of items 1 to 9, or one or more polynucleotides according to any one of items 10 to 13, or one or more vectors according to any one of items 18 to 33, or one or more immunogenic compositions according to any one of items 40 to 45, or one or more pharmaceutical compositions according to any one of items 46 to 54. (Item 129) For use in treating or preventing human immunodeficiency virus (HIV) in a subject in need thereof, one or more fusion polypeptides according to any one of items 1 to 9, or one or more polynucleotides according to any one of items 10 to 13, or one or more vectors according to any one of items 18 to 33, or one or more immunogenic compositions according to any one of items 40 to 45, or one or more pharmaceutical compositions according to any one of items 46 to 54.

Brief Description of the Drawings

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Figure 4A

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Figure 5A

Figure 5B

Figure 5C

[0298]

Figure 6

[0299]

Figure 7

[0300]

Figure 8

[0301]

Figure 9

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Figure 10A

Figure 10B

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Figure 11

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Figure 12A

Figure 12B

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Figure 13

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Figure 14

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Figure 16

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Figure 17

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Figure 18

[0311]

Figure 19A

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Figure 19C

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Figure 21A

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Figure 21C

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Figure 22

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Figure 24A

Figure 24B

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Figure 25A

Figure 25B

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Figure 26A

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Figure 26B

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Figure 28C

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Figure 29A

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[0325]

Figure 33A

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[0326]

Figure 34A

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[0329]

Figure 37A

Figure 37B

Figure 37C

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Figure 37F

Mode for Carrying Out the Invention

[0330] 1 Introduction Provided herein are fusion polypeptides comprising a plurality of polypeptides or peptide segments, and related compositions including immunogenic and pharmaceutical compositions, and methods for making the fusion polypeptides, and methods for using them to induce an immunogenic response against human immunodeficiency virus (HIV-1) in a subject in need thereof. As used herein, an "immunogen" is a substance such as an antigen that induces or is capable of inducing an immune response. Also provided are polynucleotides encoding the fusion polypeptides described herein, and vectors containing the same.

[0331] Disclosed herein are fusion polypeptides designed to induce an antiviral immune response. The vaccine constructs described herein are designed to provide a mathematically determined improved coverage of predicted T cell epitopes (“PTEs”) using the most highly conserved predicted epitopes within a source set of viral proteome sequences. As a paradigm for methods of designing antiviral immunogens, fusion polypeptides encoded by one, two, three, or four of the HIV-1 Gag, Pol, Env, and Nef genes were used. The methods described herein retain the positional information of PTEs within the source set of sequences and construct a bivalent set of sequences to improve the coverage of conserved PTEs. The result is an initial bivalent vaccine construct that advantageously improves or increases highly conserved PTEs that are very likely to be highly similar to conserved epitopes in native sequences in proteins expressed by viral species in a population of patients and within an individual patient, due to both the retained positional information. Furthermore, by using only the highly conserved PTE sequences among HIV-1 species between and within patients, the likelihood of escape variants is reduced because the highly conserved sequences are likely to contribute to viral structure and function.

[0332] Furthermore, a computational approach is provided for designing antiviral vaccine immunogens for highly variable viruses such as HIV-1. The antiviral vaccine immunogen design method incorporates deep sequencing data from individual patient samples having variable sequences, analyzes sequence diversity in the context of host HLA diversity, and develops antiviral vaccines for therapeutic and prophylactic use. The antiviral immunogen can be designed to provide coverage at the individual level for a group of individuals having a defined set of HLA alleles or for broad population coverage. In the vaccine immunogen design methods described herein, the inventors define a computational approach for targeting conserved regions within the vaccine sequence using bulk population sequences (e.g., from publicly available databases and internally developed databases). Furthermore, deep sequence data from individual patients is used to define the sequence variability of each potential T cell epitope within the conserved region. Furthermore, based on the likelihood of presentation by the individual host set of HLA alleles, regions that can function as actual epitopes are identified. A deep learning model is developed that models peptide binding per allele using the likelihood of binding to host HLA defined by publicly available and internally developed databases. This can be combined with in silico, published and / or experimental in vitro T cell priming data that defines the potential impact of antigen variants in modulating TCR recognition or identifies peptides as escape variants. These data are used to design a set of peptide immunogens containing epitopes and related epitope variants. The epitope sequences are either directly fused or linked via a linker sequence and are ligated or serially connected in a single fusion polypeptide. The peptide segments are joined in a computationally determined sequential order from the N-terminus to the C-terminus that can mimic human self-antigens and reduce or eliminate the creation of junctional epitopes that can have undesired effects (e.g., inducing an autoimmune or tolerogenic response).

[0333] Unlike similar graph-based approaches to vaccine design, the approach described herein constructs segments of connected PTEs using only adjacent PTEs that are also adjacent to the native sequence. Further, the method first constructs a bivalent construct consisting of two polypeptides that match to improve or increase coverage at each PTE position within the viral proteome. The bivalent construct itself can be used as a vaccine, as in the constructs described in Examples 1 and 2 below, or it can function as a basis for further constructs (e.g., the HLA-restricted constructs described in Example 3 or the individualized constructs described in Examples 4 and 5 below). Bivalent constructs designed by analysis of population-based sequences (e.g., inter-patient diversity) identify population-based conserved sequences that can contribute to viral structure and function and can serve as templates for defining conservation within the patient's sequence, and this information can be applied to construct individualized vaccine constructs.

[0334] The method described herein can start with the identification of conserved region bivalent sequences using a process referred to herein as "conservation analysis" or "conservation algorithm". The method may further include constructing a bivalent vaccine construct with maximum epitope coverage while retaining the position information of the PTEs from the native sequence using a process referred to herein as "conservation walking algorithm" or "CWA".

[0335] Therapeutic vaccines based on the induction of T cell responses are readily evaluated and show efficacy in the context of cancer vaccines. These vaccines are typically epitope-based and can be tailored to the individual's HLA alleles as well as their specific tumor antigens (see, e.g., Tran, et al., Science, (2014) 344(6184):641-5). We have developed vaccine sequences that can target subpopulations based on the population prevalence of specific HLA alleles or that can be specifically tailored to the range of an individual's HLA alleles. 2. Fusion polypeptides useful for promoting an immune response against human immunodeficiency virus-1 (HIV-1)

[0336] This specification provides a fusion polypeptide comprising a plurality of polypeptides or peptide segments encoded by one or more HIV-1 genes. A "segment" of a fusion polypeptide described herein is a contiguous sequence of at least 8 amino acids with respect to a reference sequence (e.g., the HIV-1 HXB2 reference sequences for the Env, Gag, Nef, and Pol polypeptides, provided herein as SEQ ID NOs: 403-406, respectively). A polypeptide described herein is a "fusion" polypeptide in that it is assembled from two or more connected or linked polypeptides or peptide segments of HIV-1 proteins. With respect to the HIV-1 protein reference sequences, a polypeptide or peptide segment may correspond to discontinuous sequences of the same or different HIV-1 proteins. Generally, the fusion polypeptide is non-naturally occurring and can be synthetically or recombinantly produced. a. Polypeptide segment

[0337] Regarding the HIV-1 genes encoding polypeptide segments used to construct the fusion polypeptides described herein, in various embodiments, the fusion polypeptide comprises one or more (e.g., two or more, three or more, four or more) polypeptide segments of one or more human immunodeficiency virus-1 (HIV-1) proteins encoded by HIV-1 genes selected from Gag, Nef, Env, Pol, Vpu, Vpr, and Vif (e.g., two or more, three or more, four or more HIV-1 genes selected from Gag, Nef, Env, Pol, and Vif). In some embodiments, the plurality of polypeptide segments consists only of polypeptide segments encoded by the HIV-1 genes Env, Gag, Nef, and Pol, and for example, does not include polypeptide segments encoded by the HIV-1 Tat, Rev, Vif, Vpr, and / or Vpu genes. In some embodiments, the plurality of polypeptide segments consists only of polypeptide segments encoded by the HIV-1 genes Gag, Nef, and Pol, and for example, does not include polypeptide segments encoded by the HIV-1 Env, Tat, Rev, Vif, Vpr, and / or Vpu genes. In some embodiments, the plurality of polypeptide segments consists only of polypeptide segments encoded by the HIV-1 genes Gag and Nef, and for example, does not include polypeptide segments encoded by the HIV-1 Env, Pol, Tat, Rev, Vif, Vpr, and / or Vpu genes. In some embodiments, the plurality of polypeptide segments consists only of polypeptide segments encoded by the HIV-1 genes Pol and Nef, and for example, does not include polypeptide segments encoded by the HIV-1 Env, Gag, Tat, Rev, Vif, Vpr, and / or Vpu genes. In some embodiments, the plurality of polypeptide segments consists only of polypeptide segments encoded by the HIV-1 genes Pol and Env, and for example, does not include polypeptide segments encoded by the HIV-1 Gag, Nef, Tat, Rev, Vif, Vpr, and / or Vpu genes.In some embodiments, the plurality of polypeptide segments consists only of polypeptide segments encoded by the HIV-1 Pol gene and does not include, for example, polypeptide segments encoded by the HIV-1 Env, Gag, Nef, Tat, Rev, Vif, Vpr, and / or Vpu genes. In various embodiments, the plurality of polypeptide segments is HIV. Does not contain segments encoded by one, two, three, or four of the Tat, Rev, Vif, Vpr, and / or Vpu genes.

[0338] With respect to the number of polypeptide segments assembled, connected, linked, or joined to a single fusion polypeptide, in various embodiments, the fusion polypeptide consists of at least 5 and up to 40 polypeptide segments, for example, 5 polypeptide segments and up to 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, or 40 polypeptide segments. Optionally, the polypeptide segments can be arranged in the same order or in an order different from that of the naturally occurring protein.

[0339] Regarding regions of polypeptides encoded by HIV-1 genes selected as polypeptide segments comprising a fusion polypeptide, in various embodiments, the polypeptide segments are derived from conserved regions of a population of viral proteome sequences. In some embodiments, the conserved region is conserved at greater than 80%, e.g., 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% among HIV-1 species as determined, for example, among patients and / or within a patient population. As used herein, a conserved region in a polypeptide encoded by an HIV-1 gene refers to the percentage of sequences in a population of sequences comprising the same amino acid segment or subsequence (e.g., a segment 9 amino acids in length or a 9mer segment) as the most prevalent at a given amino acid segment or subsequence position, where the amino acid segment or subsequence position is determined with respect to a reference sequence (e.g., the HIV-1 HXB2 polypeptide sequence (e.g., SEQ ID NOs: 403 - 406)). In various embodiments, the conserved region is conserved among one or more of the HIV-1 clades within group M, e.g., one or more of HIV-1 clades A - K, e.g., one or more of clades A, B, C, D and G, e.g., among HIV-1 group M, clade B and its recombinant forms, e.g., CRF01_AE. In some embodiments, a plurality of polypeptide segments comprises at least 2 polypeptide segments, e.g., at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, or more polypeptide segments selected from SEQ ID NOs: 1 - 344, e.g., the polypeptide segments identified in Table B.In some embodiments, the plurality of polypeptide segments comprises at least two polypeptide segments selected from SEQ ID NOs: 2, 3, 8, 9, 13, 14, 17, 18, 23, 24, 25, 26, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 58, 59, 62, 63, 64, 65, 66, 67, 68, 69, 72, 73, 74, 75, 76, 77, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 92, 93, 101, 102, 103, 104, 109, 110, 115, 116, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 155, 156, 157, 158, 159, 160, 166, 167, 168, 169, 170, 171, 174, 175, 178, 179, 180, 181, 182, 183, 184, 185, 193, 194, 195, 196, 197, 198, 199, 200, 203, 204, 205, 206, 207, 208, 213, 214, 221, 222, 236, 237, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 263, 264, 266, 267, 268, 269, 270, 271, 272, 273, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 305, 306, 307, 308, 309, 310, 313, 314, 315, 316, 317, 318, 321 and 322, e.g., at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, or more polypeptide segments, e.g., the polypeptide segments identified in Table C.The starting and ending positions are with respect to the HIV-1 HXB2 reference polypeptide, GenBank accession number K03455 (ncbi.nlm.nih.gov / nuccore / K03455), provided herein as SEQ ID NOs: 403 - 406, and specified in Table A. [Table 1] [Table 2-1] [Table 2-2] [Table 2-3] [Table 2-4] [Table 2-5] [Table 2-6] [Table 2-7] [Table 2-8] [Table 2-9] [Table 2-10] [Table 2-11] [Table 2-12] [Table 2-13] [Table 3-1]

Table 3-2

Table 3-3

Table 3-4

Table 3-5

Table 3-6

Table 3-7

Table 3-8

[0340] Regarding the length ranges of individual polypeptides or peptide segments, in various embodiments, each peptide segment is at least 8 amino acids in length and up to about 250 amino acids in length, for example, from at least 8 amino acids in length up to a maximum of 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, or 250 amino acids in length. In various embodiments, each peptide segment is at least 8 amino acids in length and up to about 35 amino acids in length, for example, from at least 8 amino acids in length up to a maximum of 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, or 35 amino acids in length. In various embodiments, each peptide segment is at least 15 amino acids in length and up to about 30 amino acids in length, for example, from at least 15 amino acids in length up to a maximum of 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 amino acids in length.

[0341] Regarding the length of the full-length fusion polypeptide, in various embodiments, in some embodiments, the full length of the fusion polypeptide is at least about 350 amino acids and at most about 1000 amino acids, for example, at least about 350 amino acids and at most about 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, or 1000 amino acids. Regarding the length of the full-length fusion polypeptide, in various embodiments, in some embodiments, the full length of the fusion polypeptide is at least about 350 amino acids and at most about 800 amino acids, for example, at least about 350 amino acids and at most about 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, or 800 amino acids. In some embodiments, the full length of the fusion polypeptide is 800 amino acids or less, for example, 795, 790, 785, 780, 775, 770, 765, 760, 755, 750, 745, 740, 735, 730, 725, 720, 715, 710, 705, or 700 amino acids.

[0342] Generally, the fusion polypeptide is immunogenic in that it can induce an immune response in humans, for example, against HIV-1. In some embodiments, the fusion polypeptide can optionally, for example, in combination with one or more additional therapeutic agents as described herein, induce a protective or therapeutically effective immune response against HIV-1 in humans, for example, prevent HIV-1 infection in uninfected individuals, or in a therapeutic setting, induce immune-mediated control of HIV-1 in infected individuals or induce an immune response sufficient to eradicate HIV-1. The immunogenicity of the fusion polypeptide can be evaluated and demonstrated in in vitro and in vivo assays as described herein. For example, the immunogenicity of the fusion polypeptide can be demonstrated by in vitro assays including CD4+ and / or CD8+ T cell activation (including cytokine expression and target killing assays) or proliferation assays. T cells can be activated by exposure to antigen-presenting cells (APCs) (such as dendritic cells, for example, monocyte-derived dendritic cells) transfected with a polynucleotide encoding the fusion polypeptide. Such assays are known in the art and are described herein. The immunogenicity of the fusion polypeptide can also be demonstrated in in vivo animal models, for example, by administering to mice that are transgenic for one or more human HLA molecules (available from Jackson Laboratories or Taconic), or non-human primates, and evaluating CD4+ and / or CD8+ T cell activation (including serum cytokine levels) or proliferation. In various embodiments, one, two, three, or more of each polypeptide segment includes or consists of one or more predicted T cell epitopes determined, for example, computationally or experimentally. In some embodiments, the fusion polypeptide includes one or more polypeptide segments that bind to or are presented by one or more human HLA class I and / or class II alleles (such as 1, 2, 3, 4, 5, or 6 alleles), for example, within a single subject or between multiple subjects. In some embodiments, the fusion polypeptide is at least human A* It comprises one or more polypeptide segments that bind to or are presented by HLA class I molecules. In some embodiments, the fusion polypeptide binds to or is presented by, for example, one or more human HLA class I and / or class II alleles (e.g., 1, 2, 3, 4, 5, or 6 alleles) within a single subject, and includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or more 8mer, 9mer, and / or 10mer polypeptide segments. In some embodiments, the fusion polypeptide is processed intracellularly and presented by one or more human HLA class I and / or class II alleles (e.g., 1, 2, 3, 4, 5, or 6 alleles) within a single subject, and includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or more polypeptide segments each 15 - 30 amino acids in length. Linker polypeptide segment

[0343] Optionally, one or more of the polypeptide segments may abut or fuse directly to an adjacent segment, or may be joined, connected, or linked to an adjacent segment by one or more peptide linkers. In various embodiments, one or more peptide linkers are selected from, for example, within the linker, or within the full-length fusion polypeptide, from one or more of polyalanine linkers, polyglycine linkers, cleavable linkers, flexible linkers, rigid linkers, Nef linker sequences, and combinations thereof. Exemplary fusion protein linkers that may be used in the fusion polypeptides of the invention to connect one or more polypeptide segments are described, for example, in Chen, et al., Adv Drug Deliv Rev. (2013) 65(10):1357-1369. In some embodiments, the polyalanine linker is two or three contiguous alanine residues, for example, AA, AAA (SEQ ID NO: 378), AAY (SEQ ID NO: 379) or AAX (X is any amino acid (e.g., A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, Y) (SEQ ID NO: 380) and includes or consists of them. In some embodiments, polyglycine linkers such as GGS (SEQ ID NO: 419), GSG (SEQ ID NO: 420) or GGGS (SEQ ID NO: 421) are used.

[0344] In some embodiments, the cleavable linker is selected from 2A cleavable peptides. Exemplary 2A cleavable peptides that may be used in the fusion polypeptides of the invention to connect one or more polypeptide segments are described, for example, in Donnelly, et al., J. Gen. Virol (2001), 82, 1027-1041 and Chng, et It is described in al., mAbs (2015) 7:2, 403 - 412. Exemplary cleavable peptides that can be used to link one or more polypeptide segments include 2A cleavage sequences (e.g., Foot-and-Mouth Disease Virus (F2A), Equine rhinitis A virus (E2A), Porcine teschovirus-1 (P2A), and Thosea asigna virus (T2A)), and furin recognition / cleavage sequences (e.g., REKR (SEQ ID NO: 382), RRKR (SEQ ID NO: 383), RAKR (SEQ ID NO: 381)), but are not limited thereto. In certain embodiments, furin recognition / cleavage sequences (e.g., REKR (SEQ ID NO: 382), RRKR (SEQ ID NO: 383), RAKR (SEQ ID NO: 381)) are combined or fused with a 2A cleavable peptide (e.g., Foot-and-Mouth Disease Virus (F2A), Equine rhinitis A virus (E2A), Porcine teschovirus-1 (P2A), and Thosea asigna virus (T2A)) in a single linker. See, for example, Chng, et al., mAbs (2015) 7:2, 403 - 412. In various embodiments, the 2A cleavable linker comprises, or consists of, an amino acid sequence that is at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least 99% identical to ATNFSLLKQAGDVEENPGP (SEQ ID NO: 384), APVKQTLNFDLLKLAGDVESNPGP (SEQ ID NO: 385), RAKRAPVKQTLNFDLLKLAGDVESNPGP (SEQ ID NO: 386), QCTNYALLKLAGDVESNPGP (SEQ ID NO: 387), or EGRGSLLTCGDVEENPGP (SEQ ID NO: 388), or comprises, or consists of, the amino acid sequence of ATNFSLLKQAGDVEENPGP (SEQ ID NO: 384), APVKQTLNFDLLKLAGDVESNPGP (SEQ ID NO: 385), RAKRAPVKQTLNFDLLKLAGDVESNPGP (SEQ ID NO: 386), QCTNYALLKLAGDVESNPGP (SEQ ID NO: 387), or EGRGSLLTCGDVEENPGP (SEQ ID NO: 388). Optionally, in certain embodiments, the furin recognition / cleavage sequence can be positioned at either the N-terminus or the C-terminus of the 2A linker.In some embodiments, the cleavable linker comprises or consists of a furin recognition / cleavage site selected from the group consisting of RAKR (SEQ ID NO: 381), REKR (SEQ ID NO: 382), and RRKR (SEQ ID NO: 383). REKR (SEQ ID NO: 382) is a cleavable linker that naturally occurs in the HIV and SIV envelope glycoprotein precursors (Bahbouhi, et al., Biochem. J. (2002) 366, 863-872). In some embodiments, one or more Nef-linker sequences comprise or consist of an amino acid sequence that is at least 95%, 96%, 97%, 98%, or 99% identical to VHAGPIA (SEQ ID NO: 389), VHAGPVA (SEQ ID NO: 390), or GALDI (SEQ ID NO: 391), or comprise or consist of an amino acid sequence selected from VHAGPIA (SEQ ID NO: 389), VHAGPVA (SEQ ID NO: 390), and GALDI (SEQ ID NO: 391). Exemplary linkers that can be used to link or connect one or more polypeptide segments in the fusion polypeptide are provided in Table D.

Table 4

[0345] In various embodiments, the fusion polypeptide comprises one or more segments of one or more viral proteins encoded by the HIV-1 Gag gene, or fragments or subsequences thereof. In some embodiments, the one or more viral proteins encoded by the HIV-1 Gag gene are selected from p17 (N-terminal matrix), p24 (capsid), p7 (nucleocapsid), and p6 (C-terminal). In some embodiments, the one or more viral proteins encoded by the HIV-1 Gag gene do not include any p6 component.In some embodiments, the plurality of polypeptide segments comprise, or consist of, amino acid sequences selected from SEQ ID NOs: 68-146 and 339-342, SEQ ID NOs: 68, 69, 72, 73, 74, 75, 76, 77, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 92, 93, 101, 102, 103, 104, 109, 110, 115, 116, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 139, 140, 141, 142, 143, 144, 145 and 146, SEQ ID NOs: 76, 77, 86, 87 and 92-124, SEQ ID NOs: 76, 77, 86, 87, 94 and 95, SEQ ID NOs: 76, 86 and 94, SEQ ID NOs: 77, 87 and 95, SEQ ID NOs: 68-79 and 92-124, SEQ ID NOs: 70-71, 76-77 and 94-95, SEQ ID NOs: 78, 79, 96, 99, 100, 107, 108, 113, 114, 121, 122, 123, 124, 137 and 138, SEQ ID NOs: 78, 99, 107, 113, 121, 123 and 137, SEQ ID NOs: 78, 79, 90, 91, 97, 98, 99, 100, 105, 106, 107, 108, 111, 112, 113, 114, 117, 118, 119, 120, 121, 122, 123, 124, 137 and 138, SEQ ID NOs: 78, 90, 97, 105, 111, 117, 119 and 137, and SEQ ID NO: 78, 137, and include at least two polypeptide segments, e.g., at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, or more segments.

[0346] In some embodiments, the fusion polypeptide comprises, or consists of, at least two polypeptide segments corresponding to HIV-1 Gag amino acid sequences at amino acid residue positions selected from 31 - 53, 37 - 51, 142 - 166, 175 - 199, 183 - 191, 257 - 282, 257 - 290, 265 - 282, 288 - 313, 288 - 321, 296 - 313, 333 - 357, 337 - 361, 341 - 349, 345 - 353, and 429 - 444, for example, at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more segments, with the amino acid positions based on SEQ ID NO: 404. In certain embodiments, the fusion polypeptide does not comprise one, two, three, four, five, or more polypeptide segments corresponding to an HIV-1 Gag amino acid sequence or a partial sequence thereof at amino acid residue positions selected from 1 - 30, 54 - 127, 138 - 146, 370 - 428, and 445 - 500, with the amino acid positions based on SEQ ID NO: 404. In some embodiments, the plurality of polypeptide segments does not comprise one, two, three, four, five, or more polypeptide segments comprising, or consisting of, an HIV-1 Gag amino acid sequence of any one of SEQ ID NOs: 444 - 448, or a sequence or partial sequence thereof that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to any one of SEQ ID NOs: 444 - 448 (Table K), or the fusion proteins described herein do not comprise them. HIV-1 An exemplary polypeptide segment encoded by the Gag gene and incorporated into the fusion polypeptides described herein (e.g., determined to be from a conserved region, human HLA A *(Predicted to bind to 0201 and / or known to be immunogenic) is shown as aligned to the HIV-1 HXB2 Gag reference polypeptide of FIG. 18. As used herein, the numbering of a given amino acid polymer or nucleic acid polymer refers to the position of any given polymer component (e.g., amino acid, nucleotide, commonly also referred to as a "residue") not by the actual numerical position of the component in the given polymer, but by reference to the same or equivalent position in a selected amino acid or nucleic acid polymer (e.g., based on an optimal alignment or consensus sequence), such that the numbering of the selected or reference amino acid polymer or nucleic acid polymer is "corresponding", "corresponds", or is "relative" to the numbering of the given polymer. Polypeptide segment encoded by the HIV-1 Nef gene

[0347] In some embodiments, the fusion polypeptide comprises one or more segments of a viral protein encoded by the HIV-1 Nef gene. In some embodiments, the plurality of polypeptide segments are amino acid sequences selected from SEQ ID NO: 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171 and 172; SEQ ID NO: 147, 148, 149, 150, 155, 156, 157, 158, 159, 160, 166, 167, 168, 169, 170 and 171; SEQ ID NO: 149-152; SEQ ID NO: 151-152; SEQ ID NO: 149, 150, 151, 152, 159, 160, 161, 162, 163, 164, 166, 167, 168, 169, 170, 171, 172, 173 and 174; SEQ ID NO: 151, 152, 161 and 162; SEQ ID NO: 151 and 152; SEQ ID NO: 153, 154, 172 and 173; SEQ ID NO: 153 and 172; SEQ ID NO: 153, 154, 155, 156, 157, 158, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172 and 173; SEQ ID NO: 153 and 165; and SEQ ID NO: 153, and comprise, or consist of, at least one polypeptide segment, e.g., at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or more segments.

[0348] In some embodiments, the fusion polypeptide comprises, or consists of, at least two polypeptide segments corresponding to HIV-1 Nef amino acid sequences at amino acid residue positions selected from 64-102, 81-102, 88-97, 91-99, 130-148, 130-154, 134-142, 134-148, 136-148, 137-145, 137-145, and 117-154, for example, at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or more segments, with the amino acid positions being based on SEQ ID NO: 405. In certain embodiments, the fusion polypeptide does not comprise one, two, three, or more polypeptide segments corresponding to, or consisting of, an HIV-1 Nef amino acid sequence or a subsequence thereof at amino acid residue positions selected from 1-63, 103-116, and 155-206, with the amino acid positions being based on SEQ ID NO: 405. In some embodiments, the plurality of polypeptide segments do not comprise one, two, three, or more polypeptide segments comprising, or consisting of, an HIV-1 Nef amino acid sequence of any one of SEQ ID NOs: 449-451, or a sequence or subsequence thereof that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to any one of SEQ ID NOs: 449-451 (Table K), or the fusion proteins described herein do not contain them. Exemplary polypeptide segments encoded by the HIV-1 Nef gene and incorporated into the fusion polypeptides described herein (e.g., determined to be from a conserved region and predicted to bind to human HLA A * 0201 and / or known to be immunogenic) are shown aligned to the HIV-1 HXB2 Nef reference polypeptide of FIG. 19. Fusion polypeptide having polypeptide segments encoded by the HIV-1 Gag and Nef genes

[0349] In some embodiments, the fusion polypeptide comprises or consists of one or more segments of viral proteins encoded by the HIV-1 Gag and Nef genes, and does not, for example, comprise one or more polypeptide segments encoded by the HIV-1 Env, Pol, Tat, Rev, Vif, Vpr or Vpu genes. In some embodiments, the fusion polypeptide comprises or consists of at least two polypeptide segments, for example at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, or more segments, having amino acid sequences selected from SEQ ID NOs: 68-79 and 92-124, 149, 150, 151, 152, 159, 160, 161, 162, 163, 164, 166, 167, 168, 169, 170, 171, 172, 173 and 174, SEQ ID NOs: 70, 71, 76, 77, 94, 95, 151, 152, 161 and 162, SEQ ID NOs: 70, 76, 94, 151 and 161, and SEQ ID NOs: 71, 77, 95, 152 and 162. The polypeptide segments contained in the fusion polypeptide having polypeptide segments encoded by the HIV-1 Gag and Nef genes are listed in Table E.

Table 5-1

Table 5-2

Table 5-3

[0350] In some embodiments, the fusion polypeptide comprises or consists of polypeptide segments of SEQ ID NOs: 70, 76, 94, 151 and 161, or SEQ ID NOs: 71, 77, 95, 152 and 162, optionally joined or connected by one or more linkers, in order from the N-terminus to the C-terminus.

[0351] In some embodiments, the fusion polypeptide comprises, or consists of, the amino acid sequence of any one of SEQ ID NOs: 351-356 and 430, or a sequence that is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to any one of SEQ ID NOs: 351-356 and 430.

[0352] In the structure of the fusion polypeptides described herein and the polynucleotides encoding such fusion polypeptides, modifications may be made and still obtain a functional molecule encoding a variant or derivative polypeptide that still has the desired (e.g., immunogenic) properties. If it is desired to alter the amino acid sequence of the polypeptide to create an equivalent of the fusion polypeptide described herein, or a further improved variant or portion, one of ordinary skill in the art will typically alter one or more of the codons of the encoding DNA sequence.

[0353] For example, certain amino acids can be substituted for other amino acids in the protein structure without a recognizable loss of their ability to bind to other polypeptides (e.g., antigens) or cells. Since it is the binding ability and properties of the protein that define the biological functional activity of the protein, certain amino acid sequence substitutions are the protein sequence and, of course, the underlying DNA coding sequence, and yet a protein with similar properties can be obtained. Accordingly, it is contemplated that various changes can be made in the polypeptide sequence of the disclosed fusion polypeptide, or in the corresponding DNA sequence encoding such fusion polypeptide without an apparent loss of its biological utility or activity.

[0354] Often, polypeptide variants will contain one or more conservative substitutions. A "conservative substitution" is one in which an amino acid is replaced with another amino acid having similar properties, and one of ordinary skill in peptide chemistry would expect the secondary structure and hydrogen-bonding properties of the polypeptide to not substantially change.

[0355] When comparing polynucleotide and polypeptide sequences, two sequences are said to be "identical" if the nucleotide or amino acid sequences in the two sequences are the same when aligned for maximum correspondence as described below. The comparison between two sequences is typically performed by comparing the sequences in a comparison window in order to identify and compare local regions of sequence similarity. As used herein, a "comparison window" refers to a segment of at least about 20 contiguous positions, usually 30 to about 75, 40 to about 50, where the sequences can be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned.

[0356] Optimal alignment of arrays for comparison can be performed using the Megalign program of the Lasergene suite of bioinformatics software (DNASTAR, Inc., Madison, WI) using default parameters. This program embodies multiple alignment schemes described in the following references. Dayhoff, M.O. (1978) A model of evolutionary change in proteins - Matrices for detecting distant relationships. In Dayhoff, M.O. (ed.) Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, Washington DC Vol. 5, Suppl. 3, pp. 345 - 358, Hein J. (1990) Unified Approach to Alignment and Phylogenes pp. 626 - 645 Methods in Enzymology vol. 183, Academic Press, Inc., San Diego, CA, Higgins, D.G. and Sharp, P.M. (1989) CABIOS 5:151 - 153, Myers, E.W. and Muller W. (1988) CABIOS 4:11 - 17, Robinson, E.D. (1971) Comb. Theor 77:105; Santou, N. Nes, M. (1987) Mol. Biol. Evol. 4:406 - 425, Sneath, P.H.A. and Sokal, R.R. (1973) Numerical Taxonomy - the Principles and Practice of Numerical Taxonomy, Freeman Press, San Francisco, CA, Wilbur, W.J. and Lipman, D.J. (1983) Proc. Natl. Acad., Sci. USA 80:726 - 730.

[0357] Alternatively, the optimal alignment of arrays for comparison can be performed by the local identity algorithm of Smith and Waterman (1981) Add. APL. Math 2:482, by the identity alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443, by the search for similarity methods of Pearson and Lipman (1988) Proc. Natl. Acad. Sci. USA 85:2444, by computerized implementations of these algorithms (GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, WI), or by inspection.

[0358] An example of an algorithm suitable for determining percent sequence identity and sequence similarity is the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al. (1977) Nucl. Acids Res. 25:3389-3402 and Altschul et al. (1990) J. Mol. Biol. 215:403-410, respectively. BLAST and BLAST 2.0 can be used with, for example, the parameters described herein to determine the percent sequence identity of the polynucleotides and polypeptides described herein. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (blast.ncbi.nlm.nih.gov / Blast.cgi).

[0359] In one exemplary example, the cumulative score for a nucleotide sequence can be calculated using parameters M (reward score for a pair of matching residues, always >0) and N (penalty score for mismatching residues, always <0). The extension of the word hit in each direction stops when the cumulative alignment score drops by an amount X from its ...

Claims

1. A computer-implemented method for designing a fusion polypeptide capable of inducing an immune response against one or more viral target antigens, comprising: a) the following steps: 1) aligning a set of source virus proteome sequences to a reference sequence; 2) extracting all unique 9-mers from the virus proteome sequence, determining their frequency, and constructing a set of 9-mer pairs having the frequency; 3) connecting 9-mer pairs at adjacent positions of an alignment of conserved regions sharing an overlap of 8 amino acids; and 4) finding the path from the first 9-mer position to the last position with respect to the maximum sum of the frequencies of all the 9-mers in the path by executing an algorithm including, in silico identifying one or more sequence conserved regions in a population of polypeptide sequences encoded by viral genes, wherein the population is derived from an inter-patient virus population; b) in silico identifying two of the most common polypeptide sequences from the one or more conserved regions identified in step a), generating a bivalent polypeptide segment from the conserved regions, thereby constructing a bivalent vaccine sequence based on the bivalent 9-mer pair path of step a), and connecting two 9-mers at adjacent positions within the bivalent 9-mer pair path when they share an overlap of 8 amino acids; c) reducing or removing viral polypeptide 9-mers having at least 55% (5 out of 9 amino acid residues) amino acid sequence identity to human proteins; d) arranging the polypeptide segments in one or more contiguous fusion polypeptides such that the creation of epitopes capable of binding to human MHC class I or human MHC class II molecules is reduced or avoided with a predicted binding affinity IC50 value of less than about 1000 nM or having a percentile rank within the top 5% in a population of polypeptide segments, wherein the MHC binding affinity is predicted using one or more algorithms A method comprising the above steps.

2. The method according to claim 1, wherein the MHC binding affinity is predicted using one or more algorithms selected from NetMHC, MHCflurry, MAPPPP, PepVac, EpiSopt, BIMAS, Propred-1, EpiJen, IEDB-MHCI, NetMHCpan, nHLAPred, NetCTL, WAPP, EpiDOCK, PrediVac, EpiTOP, TEpITOPE, Propred, IEDB-MHCII, IL4pred, MHC2PRED, NetMHCII, NetMHCIIpan, MotifScan, Rankpep, SYFPEITHI, Vaxign, MHCpred, MULTIPRED2, SVMHC, and SVRMHC.

3. The method according to claim 1, further comprising the step of inserting a linker between polypeptide segment junctions predicted to create epitopes capable of binding to human MHC class I or human MHC class II molecules.

4. After step b) and before step d), e) in silico identifying a polypeptide segment predicted to bind to a human MHC class I molecule with an IC50 value of less than about 1000 nM or having a percentile rank within the top 5% in a population of polypeptide segments within the one or more sequence conservation regions identified in step a); f) generating a polypeptide segment comprising the one or more sequence conservation regions identified in step a) predicted to bind to a human MHC class I molecule with an IC50 value of less than about 1000 nM or having a percentile rank within the top 5% in a population of polypeptide segments The method according to claim 1, comprising, wherein the MHC binding affinity is predicted using one or more algorithms.

5. The method according to claim 4, wherein the polypeptide segment binds to one or more MHC class I HLA supertypes selected from A01, A02, A03, A24, B07, B08, B27, B44, B58, and B62.

6. After step b) and before step d), further comprising the step of providing one or more polypeptide segments that are known or predicted to bind to human MHC class II molecules with a predicted binding affinity IC50 value of less than about 1000 nM or having a percentile rank within the top 5% in a population of polypeptide segments, wherein the MHC binding affinity is predicted using one or more algorithms, the method of claim 1.

7. After step b) and before step d), identifying sequence variation in a second population of polypeptide sequences encoded by the viral gene within the one or more sequence conservation regions identified in step a), wherein the second population is derived from the intra-patient viral population, further comprising the step of identifying, wherein the sequence variation from the intra-patient viral population is determined by deep sequencing or next-generation sequencing, the method of claim 1.

8. A computer-implemented method of designing a fusion polypeptide capable of inducing an immune response against one or more viral target antigens, a) the following steps: 1) aligning a set of source viral proteome sequences to a reference sequence; 2) extracting all unique 9mers from the viral proteome sequences, identifying their frequencies, and constructing a set of 9mer pairs having frequencies; 3) connecting 9mer pairs at adjacent positions of an alignment of conserved regions sharing an overlap of 8 amino acids; and 4) finding the path from the first 9mer position to the last position with respect to the maximum sum of the frequencies of all said 9mers in the path by performing an algorithm comprising identifying in silico one or more sequence conservation regions in a first population of polypeptide sequences encoded by a viral gene, wherein the first population is derived from an inter-patient viral population; b) identifying in silico the two most common polypeptide sequences from the one or more conserved regions identified in step a), thereby constructing a bivalent vaccine sequence based on the bivalent 9mer pair path of step a), and connecting two 9mers at adjacent positions within the bivalent 9mer pair path when they share an overlap of 8 amino acids; c) In silico identifying polypeptide segments that bind to human MHC class I molecules with an IC50 value of less than about 1000 nM or having a percentile rank within the top 5% in a population of polypeptide segments within the one or more sequence conservation regions identified in step a); d) Generating polypeptide segments comprising the one or more sequence conservation regions identified in step a) that are predicted to bind to human MHC class I molecules with an IC50 value of less than about 1000 nM or having a percentile rank within the top 5% in a population of polypeptide segments; e) Removing viral polypeptide 9mer segments generated in step d) that are determined to have at least 55% (5 out of 9 amino acid residues) amino acid sequence identity to human proteins to obtain retained viral polypeptide segments; f) Placing the retained polypeptide segments into one or more contiguous fusion polypeptides such that creation of epitopes that can bind to human MHC class I or human MHC class II molecules with a predicted binding affinity IC50 value of less than about 1000 nM or having a percentile rank within the top 5% in a population of polypeptide segments is avoided or reduced at the junctions connecting the polypeptide segments; comprising, wherein the MHC binding affinity in steps c), d) and f) is predicted using one or more algorithms. **Claim 9** A computer-implemented method of designing a fusion polypeptide capable of inducing an immune response against one or more viral target antigens, a) the following steps: 1) Aligning a set of source viral proteome sequences to a reference sequence; 2) Extracting all unique 9mers from the viral proteome sequences, identifying their frequencies, and constructing a set of 9mer pairs having frequencies; 3) Connecting 9mer pairs at adjacent positions of an alignment of conserved regions sharing an overlap of 8 amino acids; and 4) Finding the path from the first 9mer position to the last position with respect to the maximum sum of the frequencies of all said 9mers in the path A step of in silico identifying one or more sequence conservation regions in a first population of polypeptide sequences encoded by a viral gene by executing an algorithm comprising, wherein the first population is derived from an inter-patient viral population; b) Optionally, in silico identifying two most common polypeptide sequences from the one or more conservation regions identified in step a), thereby constructing a bivalent vaccine sequence based on the bivalent 9mer pair pathway of step a), and connecting two 9mers at adjacent positions within the bivalent 9mer pair pathway when they share an overlap of eight amino acids; c) A step of identifying sequence dispersion in a second population of polypeptide sequences encoded by the viral gene within the one or more sequence conservation regions identified in step a), wherein the second population is derived from an intra-patient viral population, and the sequence dispersion from the intra-patient viral population is determined by deep sequencing or next-generation sequencing; d) In silico identifying polypeptide segments that are predicted to bind to human MHC class I molecules within the one or more sequence conservation regions identified in step a) with an IC50 value of less than about 1000 nM or having a percentile rank within the top 5% in a population of polypeptide segments; e) Generating polypeptide segments comprising the one or more sequence conservation regions identified in step a) that are predicted to bind to human MHC class I molecules with an IC50 value of less than about 1000 nM or having a percentile rank within the top 5% in a population of polypeptide segments; f) Removing viral polypeptide 9mer segments generated in step e) that are determined to have at least 55% (5 out of 9 amino acid residues) amino acid sequence identity to human proteins to obtain retained viral polypeptide segments; g) The step of arranging the retained polypeptide segment in one or more contiguous fusion polypeptides such that creation of an epitope that can bind to human MHC class I or human MHC class II molecules is avoided or reduced, with a predicted binding affinity IC50 value of less than about 1000 nM or having a percentile rank within the top 5% in a population of polypeptide segments, by means of a junction connecting the polypeptide segments comprising steps d), e) and g), wherein the MHC binding affinity is predicted using one or more algorithms. **Claim 10** The method according to claim 8 or claim 9, wherein the polypeptide segment binds to one or more MHC class I HLA supertypes selected from A01, A02, A03, A24, B07, B08, B27, B44, B58, and B62. **Claim 11** The method according to claim 8 or 9, further comprising the step of incorporating one or more polypeptide segments known or predicted to bind to human MHC class II molecules with a predicted binding affinity IC50 value of less than about 1000 nM or having a percentile rank within the top 5% in a population of polypeptide segments, wherein the MHC binding affinity is predicted using one or more algorithms. **Claim 12** The method according to claim 8 or 9, further comprising the step of inserting a linker between polypeptide segments at a polypeptide segment junction predicted to create an epitope that can bind to human MHC class I or human MHC class II molecules. **Claim 13** The method according to claim 1, further comprising rearranging the polypeptide segments to reduce or avoid creation of a harmful epitope at the junction between the polypeptide segments. **Claim 14** The method according to claim 13, wherein the step of rearranging the peptide segments to reduce or avoid creation of a harmful epitope is performed by a method comprising one or more of in silico HLA binding analysis and human proteome cross-recognition analysis. **Claim 15** The method according to claim 1, wherein the one or more viral target antigens are derived from mammalian viruses. **Claim 16** The method according to claim 1, wherein the one or more viral target antigens are derived from a virus selected from the group consisting of human immunodeficiency virus (HIV), hepatitis B virus (HBV), human papillomavirus (HPV), herpes simplex virus (HSV), Ebola virus, Zika virus, and chikungunya virus.

17. The method according to claim 1, wherein the inter-patient virus population is derived from a population of patients who have not received antiretroviral therapy (ART).

18. The method according to claim 1, wherein the inter-patient virus population is derived from a population of patients who have received antiretroviral therapy (ART).

19. The method according to claim 7, wherein the intra-patient virus population is derived from a patient who has not received antiretroviral therapy (ART).

20. The method according to claim 7, wherein the intra-patient virus population is derived from a patient who has received antiretroviral therapy (ART).

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