WO2010096561A1

WO2010096561A1 - Synthetic hiv/siv gag proteins and uses thereof

Info

Publication number: WO2010096561A1
Application number: PCT/US2010/024591
Authority: WO
Inventors: Gary J. Nabel; Zhi-Yong Yang; Wei Shi; Dan H. Barouch
Original assignee: The United States Of America, As Represented By The Secretary, Department Of Health And Human Services; Beth Israel Deaconess Medical Center
Priority date: 2009-02-18
Filing date: 2010-02-18
Publication date: 2010-08-26

Abstract

The invention provides a composition comprising a nucleic acid sequence encoding a polypeptide which comprises a HIV-1 Gag amino acid sequence, except that amino acids 358-411 or amino acids 355-408 of the HIV-1 Gag amino acid sequence have been replaced with amino acids 359-412 of a SIV Gag polypeptide. The invention also provides a nucleic acid sequence encoding the above-described polypeptide. Also provided is a method of inducing an immune response against HIV-1 in a mammal comprising administering two or more nucleic acid sequences encoding HIV and SIV amino acid sequences.

Description

SYNTHETIC HIV/SIV GAG PROTEINS AND USES THEREOF CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This patent application claims the benefit of U.S. Provisional Patent Application No. 61/153,622, filed February 18, 2009, which is incorporated by reference.

INCORPORATION-BY-REFERENCE OF MATERIAL SUBMITTED ELECTRONICALLY

[0002] Incorporated by reference in its entirety herein is a computer-readable nucleotide/amino acid sequence listing submitted concurrently herewith and identified as follows: One 789,517 Byte ASCII (Text) file named "SeqListing_ST25.TXT," created on February 16, 2010.

BACKGROUND OF THE INVENTION

[0003] Synthetic HIV-I Gag polypeptides comprising an immunogenic amino acid sequence from the SIV Gag polypeptide are disclosed. Such synthetic polypeptides are referred to herein as synthetic HIV-1/SIV Gag polypeptides. Methods and compositions for using the nucleic acids and synthetic HIV-1/SIV Gag polypeptides to induce an immune response are also disclosed. [0004] AIDS is the fifth leading cause of death among persons between the ages of 25 and 44 in the United States. About 47 million people worldwide have been infected with HIV-I since the start of the epidemic. HIV-I infections continue to rise due to the increase of drug-resistant strains of the disease. Many of the existing drugs used for treating HIV have undesirable side effects.

[0005] Accordingly, it is desirable to develop new approaches to reducing the incidence of HIV-I infection or ameliorating the consequences of HIV-I infection. Vaccines are particularly desirable in this regard.

BRIEF SUMMARY OF THE INVENTION

[0006] Compositions and methods for inducing an immune response to HIV-I are described in the present application. In one embodiment, a nucleic acid encoding a synthetic HIV-1/SIV Gag polypeptide comprising at least a portion of a synthetic HIV-I Gag polypeptide and an immunogenic amino acid sequence from the SIV Gag polypeptide is provided. In one aspect of this embodiment, the synthetic HIV-I Gag polypeptide is a mosaic HIV-I Gag polypeptide. In some aspects, the synthetic HIV-I Gag polypeptide may comprise a plurality of T cell epitopes which are not present in said HIV-I Gag polypeptide in its naturally-occurring form. In other aspects, any of the foregoing nucleic acids may encode a synthetic HIV-I Gag polypeptide which comprises at least 5, at least 10, at least 20 or more than 20 T cell epitopes which are not present in a single HIV-I Gag polypeptide in its naturally-occurring form. In other aspects, any of the foregoing nucleic acids may encode a synthetic HIV-I /SIV Gag polypeptide which comprises amino acids 359-412 of the SIV Gag polypeptide or an immunogenic portion thereof. In additional aspects, any of the foregoing nucleic acids may encode a synthetic HIV-I /SIV Gag polypeptide which comprises amino acids 420-457 from the SIV Gag polypeptide or an immunogenic portion thereof. In further aspects, any of the foregoing nucleic acids may encode a synthetic HIV-I /SIV Gag polypeptide which comprises amino acids 333-510 from the SIV Gag polypeptide. In other aspects, any of the foregoing nucleic acids may encode an HIV-I /SIV Gag polypeptide which comprises amino acids 216-225 from the SIV Gag polypeptide or an immunogenic portion thereof. In still further aspects, any of the foregoing nucleic acids may encode a polypeptide in which one or more amino acids in the synthetic HIV-I Gag polypeptide have been replaced with one or more amino acids from the corresponding region in the SIV Gag polypeptide. In other aspects, any of the foregoing nucleic acids encode a synthetic HIV-I /SIV Gag polypeptide which comprises a sequence in which at least a portion of the 179 carboxy terminal amino acids of the synthetic HIV-I Gag polypeptide has been replaced with an amino acid sequence comprising the corresponding portion of the SIV Gag protein. In further aspects, any of the foregoing nucleic acids may encode a synthetic HIV-I /SIV Gag polypeptide which comprises a sequence in which the at least a portion of the 179 carboxy terminal amino acids of the synthetic HIV-I Gag polypeptide is at least about 5 contiguous amino acids in length, at least about 10 contiguous amino acids in length, at least about 20 contiguous amino acids in length, at least about 30 contiguous amino acids in length, at least about 40 contiguous amino acids in length, at least about 50 contiguous amino acids in length, at least about 60 contiguous amino acids in length or more than 60 contiguous amino acids in length. In additional aspects, any of the foregoing nucleic acids may encode a synthetic HIV-I /SIV Gag polypeptide which comprises a sequence in which amino acids 324-500 of the HIV-I Gag polypeptide have been replaced with amino acids 333-510 from the SIV Gag protein. In still other aspects, any of the foregoing nucleic acids may encode a synthetic HIV-I /SIV Gag polypeptide which comprises a sequence in which at least a portion of the amino acid sequence between amino acids 358-411 of the synthetic HIV-I Gag polypeptide has been replaced with at least a portion of the corresponding region of the SIV Gag protein. In other aspects, any of the foregoing nucleic acids may encode a synthetic HIV-I /SIV Gag polypeptide which comprises a sequence in which amino acids 358-411 of the HIV-I Gag polypeptide have been replaced with amino acids 359- 412 of the SIV Gag protein. In additional aspects any of the foregoing nucleic acids may encode a synthetic HIV 1/SIV Gag polypeptide which comprises a sequence in which at least a portion of the amino acid sequence between amino acids 419-454 of the synthetic HIV-I Gag polypeptide has been replaced with at least a portion of the corresponding region of the SIV Gag protein. In further aspects, any of the foregoing nucleic acids may encode a synthetic HIV- 1/SIV Gag polypeptide which comprises a sequence in which amino acids 419-454 of the synthetic HIV 1 Gag polypeptide have been replaced with amino acids 420-457 of the SIV Gag protein. In other aspects, any of the foregoing nucleic acids may encode a synthetic HIV 1/SIV Gag polypeptide which comprises a sequence in which at least a portion of the amino acid sequence between amino acids 214-225 or 332-500 of the synthetic HIV-I Gag polypeptide have been replaced with at least a portion of the corresponding region of the SIV Gag protein. In additional aspects, any of the foregoing nucleic acids may encode a synthetic HIV- 1/SIV Gag polypeptide which comprises a sequence in which amino acids 214-225 of the synthetic HIV-I Gag polypeptide have been replaced with amino acids 216-225 of the SIV Gag protein and amino acids 332-500 of the synthetic HIV-I Gag polypeptide have been replaced with amino acids 333- 510 of the SIV Gag protein. In further aspects, any of the foregoing nucleic acids may encode a synthetic HIV- 1/SIV Gag polypeptide which comprises a sequence in which at least a portion of the amino acid sequence between amino acids 214 254 or 332-500 of the synthetic HIV-I Gag polypeptide have been replaced with at least a portion of the corresponding region of the SIV Gag protein. In further aspects, any of the foregoing nucleic acids may encode a synthetic HIV- 1/SIV Gag polypeptide which comprises a sequence in which amino acids 214-254 of the synthetic HIV-I Gag polypeptide have been replaced with amino acids 216-255 of the SIV Gag protein and amino acids 332-510 of the synthetic HIV-I Gag polypeptide have been replaced with amino acids 333-510 of the SIV Gag protein. In some aspects, any of the foregoing nucleic acids may encode a synthetic HIV 1/SIV Gag polypeptide which comprises at least a portion of the SIV Gag protein of SEQ ID NO: 1. In some aspects, any of the foregoing nucleic acids may encode a synthetic HIV- 1/SIV Gag polypeptide which is shorter than the full length naturally- occurring form of the HIV-I Gag polypeptide. In another aspect, any of the foregoing nucleic acids may comprise a sequence having at least about 90%, at least about 80%, at least about 70%, at least about 60% or at least about 50% sequence identity to a sequence selected from the group consisting of SEQ ID NOs: 83, 86, 89 and 92.

[0007] In a second embodiment, a nucleic acid encoding a synthetic HIV- 1/SIV Gag polypeptide in which a plurality of amino acid sequences in the synthetic HIV-I Gag polypeptide have been replaced with a plurality of amino acid sequences from the SIV Gag protein is provided. In one aspect of the second embodiment, the nucleic acid comprises a sequence selected from the group consisting of SEQ ID NOs: 83, 86, 89 and 92.

[0008] In a third embodiment, a polypeptide encoded by any of the nucleic acids discussed above is provided. In one aspect of the third embodiment, the polypeptide comprises a sequence selected from the group consisting of SEQ ID NOs: 82, 85, 88 and 91. In another aspect, In another aspect, the polypeptide comprises a sequence having at least about 90%, at least about 80%, at least about 70%, at least about 60% or at least about 50% sequence identity to a sequence selected from the group consisting of SEQ ID NOs: 82, 85, 88 and 91. [0009] In a fourth embodiment, a vector comprising any of the nucleic acids described above, wherein the vector is suitable for expressing the synthetic HIV- 1/SIV Gag polypeptide is provided. In one aspect, the vector is a viral vector. In another aspect, the viral vector is an adenovirus vector. In a further aspect, the adenovirus vector is an adenovirus 5 vector. In another aspect, the adenovirus vector is an adenovirus 26 vector. In an additional aspect, the adenovirus vector is an adenovirus 28 vector. In another aspect, the vector is a plasmid. [0010] In a fifth embodiment, a host cell comprising any of the vectors discussed above, wherein the host cell is suitable for expressing said synthetic HIV- 1/SIV Gag polypeptide, is provided. [0011] In a sixth embodiment, a composition capable of eliciting an immune response against HIV-I comprising any of the nucleic acids or vectors described above and a pharmaceutically acceptable carrier is provided. In a seventh embodiment, a syringe comprising the foregoing composition is provided. In an eighth embodiment, a needless delivery device comprising the foregoing composition is provided.

[0012] In a ninth embodiment, a method of inducing an immune response against HIV-I comprising administering any of the nucleic acids discussed above to an individual is provided.

In one aspect, the nucleic acid may comprise any of the vectors discussed above.

[0013] In a tenth embodiment, a method of inducing an immune response against HIV-I comprising administering any of the polypeptides described above to an individual is provided.

[0014] In an eleventh embodiment, use of any of the nucleic acids or vectors discussed above to induce an immune response in an individual is provided.

[0015] In a twelfth embodiment, use of any of the polypeptides discussed above to induce an immune response in an individual is provided.

[0016] The invention also provides a composition capable of eliciting an immune response against HIV-I in a mammal. The composition comprises a nucleic acid sequence encoding a polypeptide, wherein the polypeptide comprises a HIV-I Gag amino acid sequence, except that amino acids 358-411 or amino acids 355-408 of the HIV-I Gag amino acid sequence have been replaced with amino acids 359-412 of a SIV Gag polypeptide, and a pharmaceutically acceptable carrier.

[0017] The invention further provides nucleic acid sequence encoding a polypeptide , wherein the polypeptide comprises a HIV-I Gag amino acid sequence, except that amino acids

358-411 or amino acids 355-408 of the HIV-I Gag amino acid sequence have been replaced with amino acids 359-412 of a SIV Gag polypeptide.

[0018] The invention also provides a method of inducing an immune response against HIV-I in a mammal. The method comprises administering two or more different nucleic acid sequences to a mammal, wherein each nucleic acid sequence encodes a polypeptide comprising a

HIV-I Gag amino acid sequence, except that amino acids 358-411 or amino acids 355-408 of the

HIV-I Gag amino acid sequence have been replaced with amino acids 359-412 of a SIV Gag polypeptide. BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS

[0019] Figure 1 is an alignment of the sequence of the SIV Gag protein (SEQ ID NO: 1) with the sequence of the HIV-I Gag protein (SEQ ID NO: 2).

[0020] Figure 2 is a diagram which shows the structure of VRC4701 (SEQ ID NO: 81). [0021] Figure 3 a diagram which shows the structure of VRC4705 (SEQ ID NO: 84) [0022] Figure 4 a diagram which shows the structure of CMVR Mosaic HIV-gagl-SIV-gag (420-457) (SEQ ID NO: 87).

[0023] Figure 5 a diagram which shows the structure of CMVR Mosaic HIV-gag 2-SIV-gag (420-457) (SEQ ID NO: 90).

[0024] Figures 6A-F are graphs depicting the results of ELISPOT assays using wild type HIV-I Gag (Fig. 6A), chimeric HIV-I Gag in which amino acids 359-412 of the SIV Gag polypeptide were substituted for the corresponding amino acids in the HIV-I Gag protein (Fig. 6B), chimeric HIV-I Gag in which amino acids 420-457 of the SIV Gag polypeptide were substituted for the corresponding amino acids in the HIV-I Gag protein (Fig. 6C), mosaic HIV-I Gag (Fig. 6D), mosaic HIV-1/SIV Gag in which amino acids 359-412 of the SIV Gag polypeptide were substituted for the corresponding amino acids in the mosaic HIV-I Gag protein (Fig. 6E) and mosaic HIV-1/SIV Gag in which amino acids 359-412 of the SIV Gag polypeptide were substituted for the corresponding amino acids in the mosaic HIV-I Gag protein (Fig. 6F). [0025] Figure 7 is a graph which compares the immune responses obtained with chimeric HIV-1/SIV constructs and synthetic HIV-1/SIV constructs.

[0026] Figures 8 A and 8B are graphs which depict the comparison of T Cell responses elicited by HIV-I clade B Gag versus mosaic HIV-I Gag immunogens determined with HIV Gag PTE peptides in B6C57 Mice by ELISpot. Figure 8A provides the results with Clade B Gag (WT)). Figure 8B provides the results with wild type informatic mosaic HIV Gag. [0027] Figures 9A-C are graphs which illustrate the results of an ELISPOT analysis of T cell responses elicited by mosaic Gag compared to chimeric HIV/SIV mosaic Gag measured with PTE peptide subpools. Figure 9A shows the results with wild type informatic mosaic HIV Gag (Mosaic Gag (WT). Figure 9B shows the results with N5H modified informatic mosaic HIV Gag (Mosaic Gag (N5H)) containing amino acids 359-412 of the SIV Gag polypeptide (VRC4701 and VRC4705). Figure 9C shows the results with N6H modified informatic mosaic HIV Gag (Mosaic Gag(N6H)) containing amino acids 420-457 of the SIV Gag polypeptide

(CMVR Mosaic HIV-gagl-SIV-gag (420-457) and CMVR Mosaic HIV-gag 2-SIV-gag).

[0028] Figures 1 OA and B are graphs which compare the T cell response to PTE peptides provided by synthetic HIV-I /SIV Gag relative to that provided by synthetic HIV-I Gag. Figure

1OA shows the response in CD4 cells, and Figure 1OB shows the response in CD8 cells.

[0029] Figure 11 A-C are graphs which depict intracellular cytokine staining (ICS) of CD8 T cell responses to three subdominant HIV Gag 15mer PTE peptides. Figure 1 IA shows the response to the peptide MHMLKETINEEAEW (SEQ ID NO: 93). Figure 1 IB shows the response to the peptide TACQGVGGPSHKARV (SEQ ID NO: 94). Figure 11C shows the response to the peptide GGPSHKARVLAEAMG (SEQ ID NO: 95).

[0030] Figure 12 is an image of a Western Blot demonstrating the expression of modified

HIV-I Gag polypeptides.

[0031] Figure 13 is a diagram which shows the structure of the CMVR gag #1 construct

(SEQ ID NO: 3).

[0032] Figure 14 is a diagram which shows the structure of the CMVR gag 2 construct (SEQ

ID NO: 5).

[0033] Figure 15 is a diagram which shows the structure of the CMVR gag 3 construct (SEQ

ID NO: 7).

[0034] Figure 16 is a diagram which shows the structure of the CMVR gag 4 construct (SEQ

ID NO: 9).

[0035] Figure 17 is a diagram which shows the structure of the CMVR gag 5 construct (SEQ

ID NO: 11).

[0036] Figure 18 is a diagram which shows the structure of the CMVR gag 6 construct (SEQ

ID NO: 13).

[0037] Figure 19 is a diagram which shows the structure of the CMVR SIV-gag-HIV-pol #7 construct (SEQ ID NO: 15).

[0038] Figure 20 is a diagram which shows the structure of the CMVR SIV gag #8 construct

(SEQ ID NO: 17).

[0039] Figure 21 is a diagram which shows the structure of the CMVR gag 9 construct (SEQ

ID NO: 19). [0040] Figure 22 is a diagram which shows the structure of the CMVR gag 10 construct

(SEQ ID NO: 21).

[0041] Figure 23 is a diagram which shows the structure of the CMVR gag 11 construct

(SEQ ID NO: 23).

[0042] Figure 24 is a diagram which shows the structure of the CMVR gag 12 construct

(SEQ ID NO: 25).

[0043] Figure 25 is a diagram which shows the structure of the CMVR gag 13 construct

(SEQ ID NO: 27).

[0044] Figure 26 is a diagram which shows the structure of the CMVR gag 14 construct

(SEQ ID NO: 29).

[0045] Figure 27 is a diagram which shows the structure of the CMVR gag new 2 construct

(SEQ ID NO: 31).

[0046] Figure 28 is a diagram which shows the structure of the CMVR gag new 3 construct

(SEQ ID NO: 33).

[0047] Figure 29 is a diagram which shows the structure of the CMVR gag new 4 construct

(SEQ ID NO: 35).

[0048] Figure 30 is a diagram which shows the structure of the CMVR gag new 5 construct

(SEQ ID NO: 37).

[0049] Figure 31 is a diagram which shows the structure of the CMVR gag new 6 construct

(SEQ ID NO: 39).

[0050] Figure 32 is a diagram which shows the structure of the CMVR gag new 7 construct

(SEQ ID NO: 41).

[0051] Figure 33 is a diagram which shows the structure of the CMVR gag new 8 construct

(SEQ ID NO: 43).

[0052] Figure 34 is a diagram which shows the structure of the CMVR gag new 9 construct

(SEQ ID NO: 45).

[0053] Figure 35 is a diagram which shows the structure of the CMVR gag new 10 construct

(SEQ ID NO: 47).

[0054] Figure 36 is a diagram which shows the structure of the CMVR gag new 11 construct

(SEQ ID NO: 49). [0055] Figure 37 is a diagram which shows the structure of the CMVR gag new 14 construct

(SEQ ID NO: 51).

[0056] Figure 38 is a diagram which illustrates the results of an immunogenicity assay with several constructs expressing modified HIV-I Gag polypeptides.

[0057] Figure 39 is a diagram which illustrates the results of an immunogenicity assay with several constructs expressing modified HIV-I Gag polypeptides.

[0058] Figure 40 is a diagram which illustrates the results of an immunogenicity assay with several constructs expressing modified HIV-I Gag polypeptides

[0059] Figure 41 is a diagram which shows the structure of the CMVR gag new 1 construct

(SEQ ID NO: 53).

[0060] Figure 42 is a diagram which shows the structure of the CMVR gag new 4-1 construct (SEQ ID NO: 55).

[0061] Figure 43 is a diagram which shows the structure of the CMVR gag new 5-1 construct (SEQ ID NO: 57).

[0062] Figure 44 is a diagram which shows the structure of the CMVR gag new 6-1 construct (SEQ ID NO: 59).

[0063] Figure 45 is a diagram which shows the structure of the CMVR gag new Pl construct

(SEQ ID NO: 61).

[0064] Figure 46 is a diagram which shows the structure of the CMVR gag new PlB construct (SEQ ID NO: 63).

[0065] Figure 47 is a diagram which shows the structure of the CMVR gag new 12 construct

(SEQ ID NO: 65).

[0066] Figure 48 is a diagram which shows the structure of the CMVR gag new 13 construct

(SEQ ID NO: 67).

[0067] Figure 49 is a diagram which shows the structure of the CMVR gag new 15 construct

(SEQ ID NO: 69).

[0068] Figure 50 is a diagram which shows the structure of the CMVR gag new 16 construct

(SEQ ID NO: 71).

[0069] Figure 51 is a diagram which shows the structure of the CMVR gag new 17 construct

(SEQ ID NO: 73). [0070] Figure 52 is a graphical representation of CMVR gag new 1, CMVR gag new 4-1,

CMVR gag new 5-1, CMVR gag new 6-1, CMVR gag new Pl, and CMVR gag new PlB.

[0071] Figure 53 is a table which contains additional information about the constructs discussed herein.

[0072] Figure 54 is a diagram which shows the structure of the CMVR gag new 5-lh construct (SEQ ID NO: 75).

[0073] Figure 55 is a diagram which shows the structure of the CMVR gag new 5-h construct (SEQ ID NO: 77).

[0074] Figure 56 is a diagram which shows the structure of the CMVR gag new 6-h construct (SEQ ID NO: 79).

DETAILED DESCRIPTION OF THE INVENTION

[0075] A vaccine that includes highly immunogenic Gag will be an important component of an effective HIV vaccine. HIV Gag has been included in nearly all ongoing trials because of its importance in SIV models and its correlation with protection in HIV-infected long-term non- progressors and elite controllers. However, SIV Gag appears to elicit stronger immune response than HIV Gag in animal models, and Gag is much less immunogenic than Env gene vaccines in phase I human clinical trials.

[0076] The magnitude of HIV-I specific CD8 T-cell responses correlates with lower viremia in HIV-infected individuals, suggesting that containment of HIV-I infection in humans is mediated by antigen-specific T-cells. Genetic vaccine studies in SIV and SHIV monkey models have also demonstrated the efficacy of HIV specific T-cells in controlling lentiviral infection and preventing disease progression. However, SIV Gag appears to elicit stronger immune responses than HIV Gag in animal models, and Gag is much less immunogenic than Env gene vaccines in phase I human clinical trials.

[0077] Through sequence comparison, regions in HIV-I Gag have been identified as contributing to the decreased immunogenicity observed for HIV-I Gag. Replacement of these regions with corresponding SIV sequences significantly increased the resulting T-cell response to HIV Gag in mice. Figure 1 shows an alignment of the sequence of the SIV Gag protein (SEQ ID NO: 1) with the sequence of the HIV-I Gag protein (SEQ ID NO: 2). HIV-1/SIV chimeras may be utilized in an HIV vaccine to significantly enhance the overall immunogenicity of the vaccine. Such chimeras are described in PCT Application PCT/US2008/073395, filed August 15, 2008 and U.S. Provisional Patent Application Serial No. 60/965268, the disclosures of which are incorporated herein by reference in their entireties.

[0078] Incorporation of the immunogenic SIV Gag sequences into synthetic HIV-I Gag protein provided enhanced immunogenicity relative to synthetic HIV-I Gag proteins lacking the SIV sequences. This was measured both by the increase in the number of peptides to which a response was elicited with the synthetic HIV-I /SIV Gag polypeptides and the magnitude of the responses. These enhancements significantly improve the potential of synthetic HIV-I Gag proteins as effective vaccine candidates. Thus, inclusion of immune stimulatory SIV sequences or deletion of immune inhibitory regions and disruption of the endogenous HIV Gag trafficking pathways in synthetic HIV-I /SIV Gag polypeptides may help in the development of improved prophylactic and therapeutic vaccines against HIV.

[0079] As used herein "synthetic HIV-I Gag sequences" include consensus HIV-I Gag sequences, mosaic HIV-I Gag sequences, and other bioinformatically generated sequences. "Consensus HIV-I Gag sequences" are generated by comparing the sequences of a plurality of naturally-occurring HIV-I Gag sequences to identify common sequences within them and generating a synthetic HIV-I Gag sequences in which every amino acid is present in a plurality of sequences. An exemplary discussion of methods for the generation of a "consensus" sequences for the HIV-I Env protein is provided in Weaver E.A. et al., J. Virol. 80, 6745-6756 (2006).

[0080] "Mosaic HIV-I Gag sequences" are generated using natural sequences as input to algorithms, such as genetic algorithms, which maximize the diversity of potential T-cell epitopes present in the natural sequences. The genetic algorithm identifies potential T-cell epitopes within the input sequences, generates potential recombinants between the input sequences, and identifies those recombinants which have the greatest diversity of T cell epitopes. Epitopes which occur infrequently may be omitted from the mosaic sequences while those which provide enhanced coverage relative to a sequence lacking that epitope may be incorporated into the mosaic sequence. Preferably, the T cell epitopes are 9 amino acids in length, but they may have other lengths as well. For example, in some embodiments, the T cell epitopes are 10-12 amino acids in length. Methods for generating mosaic sequences have been described in Fischer et al., Nature Medicine, Vol. 13, Number 1, January 2007, pages 100-106 and PCT publication WO 2007/024941, the disclosures of which are incorporated by reference herein in their entireties. Programs for generating synthetic sequences are available at, for example, www.hiv.lanl.gov/content/sequence/SYNTHETIC/makeVaccine.html. [0081] It will be appreciated that other bioinformatic algorithms may also be applied to generate HIV-I Gag sequences having enhanced immunogenicity relative to naturally-occurring sequences and such bioinformatically identified sequences are included within the definition of "synthetic HIV-I Gag sequences."

[0082] The present application describes synthetic HIV-1/SIV Gag polypeptides which comprise an immunogenic amino acid sequence from the SIV Gag polypeptide and nucleic acids encoding these synthetic HIV-1/SIV Gag polypeptides. The immunogenic amino acid sequence from the SIV Gag polypeptide may be located anywhere in the synthetic HIV-1/SIV Gag polypeptide. In some embodiments, the synthetic HIV-1/SIV Gag polypeptides comprise an amino acid sequence in which one or more amino acids in the synthetic HIV-I Gag polypeptide have been replaced with one or more amino acids from the corresponding region in the SIV Gag protein. In some embodiments, the synthetic HIV-1/SIV Gag polypeptides may have a length at least about 95%, at least about 90%, at least about 85%, at least about 80%, at least about 75%, at least about 70%, at least about 65%. at least about 60%, at least about 50%, at least about 40%, at least about 30%, at least about 20%, or at least about 10% of the length of the full length HIV-I Gag protein (502 amino acids). In some embodiments, the synthetic HIV-1/SIV Gag polypeptide is at least about 10, at least about 20, at least about 30, at least about 40, at least about 60, at least about 80, at least about 100, at least about 150, at least about 200, at least about 250, at least about 300, at least about 350, at least about 400, at least about 450, at least about 460, at least about 470, at least about 480, at least about 490, or at least about 500 amino acids in length and includes a sequence in which one or more amino acids of the synthetic HIV-I Gag amino acid sequence has been replaced by one or more amino acids from the corresponding region of the SIV Gag protein. In some embodiments, the foregoing synthetic HIV-1/SIV Gag proteins comprise one or more antigenic regions capable of inducing an immune response against HIV-I, wherein the at least one of the one or more antigenic regions comprises a sequence in which one or more amino acids from the synthetic HIV-I Gag polypeptide have been replaced with one or more amino acids from the corresponding region in the SIV Gag protein. In some embodiments, the synthetic HIV-I /SIV Gag polypeptides containing one or more amino acids from the SIV Gag protein are able to induce a greater or broader immune response than synthetic HIV-I Gag polypeptides lacking the one or more amino acids from the SIV Gag protein. For example, in some embodiments, the immune response against the synthetic HIV-I /SIV Gag protein containing one or more amino acids from the SIV Gag protein may be at least about 1.5 times greater, at least about 5 times greater, or at least about 10 times greater than the immune response against the synthetic HIV-I Gag polypeptides lacking the one or more amino acids from the SIV Gag protein. In some embodiments, the synthetic HIV-I /SIV Gag protein containing one or more amino acids from the SIV Gag protein induce a greater CD8 T-cell response than the synthetic HIV-I Gag polypeptides lacking the one or more amino acids from the SIV Gag protein. In some embodiments, at least about 5 contiguous amino acids, at least about 10 contiguous amino acids, at least about 20 contiguous amino acids, at least about 30 contiguous amino acids, at least about 40 contiguous amino acids, at least about 50 contiguous amino acids, at least about 60 contiguous amino acids or more than 60 contiguous amino acids of the synthetic HIV-I Gag polypeptide have been replaced by at least about 5 contiguous amino acids, at least about 10 contiguous amino acids, at least about 20 contiguous amino acids, at least about 30 contiguous amino acids, at least about 40 contiguous amino acids, at least about 50 contiguous amino acids, at least about 60 contiguous amino acids or more than 60 contiguous amino acids of the SIV Gag protein. In some embodiments, the synthetic HIV-I /SIV Gag polypeptide is a mosaic HIV-I Gag polypeptide in which one or more amino acids have been replaced with one or more amino acids from the SIV Gag polypeptide. [0083] In some embodiments, the synthetic HIV-I /SIV Gag polypeptide comprises a sequence in which at least a portion of the carboxy terminal region of the synthetic HIV-I Gag polypeptide has been replaced with a portion of the carboxy terminal region from the SIV Gag protein. For example, in some embodiments, at least a portion of the 179 carboxy terminal amino acids of the synthetic HIV-I Gag polypeptide has been replaced with an amino acid sequence comprising the corresponding portion of the SIV Gag protein. In some embodiments, the at least a portion of the 179 carboxy terminal amino acids of the synthetic HIV-I Gag polypeptide which has been replaced is at least about 5 contiguous amino acids in length, at least about 10 contiguous amino acids in length, at least about 20 contiguous amino acids in length, at least about 30 contiguous amino acids in length, at least about 40 contiguous amino acids in length, at least about 50 contiguous amino acids in length, at least about 60 contiguous amino acids in length or more than 60 contiguous amino acids in length.

[0084] In some embodiments, the carboxy terminal 179 amino acids of the synthetic HIV-I Gag polypeptide have been replaced with amino acids 333-510 from the SIV Gag protein. Alternatively, in some embodiments, at least a portion of the amino acid sequence between amino acids 358-411 of the synthetic HIV-I Gag polypeptide has been replaced with at least a portion of the corresponding region of the SIV Gag protein. For example, in some embodiments, amino acids 358-411 of the synthetic HIV-I Gag polypeptide have been replaced with amino acids 359-412 of the SIV Gag protein.

[0085] In some embodiments, amino acids 419-454 of the synthetic HIV-I Gag polypeptide have been replaced with at least a portion of the corresponding region of the SIV Gag protein. For example, in some embodiments, amino acids 419-454 of the synthetic HIV-I Gag polypeptide have been replaced with amino acids 420-457 of the SIV Gag protein. In some embodiments, at least a portion of the CypA binding domain of the synthetic HIV-I protein has been replaced with at least a portion of the SIV-I CypA binding domain. For example, in some embodiments, at least a portion of the amino acid sequence between amino acids 214-225 of the synthetic HIV-I Gag polypeptide has been replaced with at least a portion of the corresponding region of the SIV Gag protein. In some embodiments, amino acids 214-225 of the synthetic HIV-I Gag polypeptide have been replaced with amino acids 216-225 of the SIV Gag protein and amino acids 332-500 of the synthetic HIV-I Gag polypeptide have been replaced with amino acids 333-510 of the SIV Gag protein.

[0086] In some embodiments, amino acids 214-254 of the synthetic HIV-I Gag polypeptide have been replaced with amino acids 216-255 of the SIV Gag protein and amino acids 332-510 of the synthetic HIV-I Gag polypeptide have been replaced with amino acids 333-510 of the SIV Gag protein.

[0087] In some embodiments, amino acids 358-418 of the synthetic HIV-I Gag polypeptide have been replaced with at least a portion of the corresponding region of the SIV Gag protein. In some embodiments, at least a portion of the amino acid sequence between amino acids 419-462 of the synthetic HIV-I Gag polypeptide has been replaced with at least a portion of the corresponding region of the SIV Gag protein.

[0088] In some embodiments, the synthetic HIV-I /SIV Gag polypeptide comprises a plurality of any of the replacements with sequences from the SIV Gag protein described herein. [0089] Any of the synthetic HIV-I /SIV Gag polypeptides described herein may be made by means familiar to those skilled in the art. For example, the synthetic HIV-I /SIV proteins may be made by expressing them from nucleic acid vectors. Nucleic acids encoding the synthetic HIV- 1/SIV Gag polypeptides may be generated using methodology familiar to those skilled in the art. For example, nucleic acids encoding the synthetic HIV-I /SIV Gag proteins may be made by digesting a nucleic acid encoding the synthetic HIV-I protein with appropriate restriction enzymes and inserting a nucleic acid encoding the desired SIV amino acid sequence at the restriction sites. Alternatively, nucleic acids encoding the synthetic HIV-I /SIV Gag polypeptides may be made using site-directed mutagenesis or PCR-mediated mutagenesis. It will be appreciated that other techniques may also be used to prepare nucleic acids encoding the synthetic HIV-I /S IV Gag polypeptides.

[0090] Vectors comprising nucleic acids encoding the synthetic HIV-I //SIV polypeptides are also provided. In some embodiments, the vector encoding any of the modified HIV-I Gag polypeptides described herein may be a viral vector. The viral vector may be an adenovirus vector. For example, in some embodiments, the adenovirus vector may be an adenovirus 5 vector, an adenovirus 26 vector, or an adenovirus 28 vector. In some aspects of this embodiment, the vector is a gene-based vector. In further aspects of this embodiment, the vector is a plasmid DNA vector used alone or in combination with an adjuvant. Some of the vectors which may be used to make any of the synthetic HIV-I /SIV Gag polypeptides described herein are discussed below, but it will be appreciated that other vectors may also be suitable for making or administering the synthetic HIV-I /SIV Gag polypeptides.

[0091] As used herein, the term "vector" refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. One type of vector is a "plasmid", which refers to a circular double stranded DNA loop into which additional DNA segments can be ligated. Another type of vector is a viral vector, wherein additional DNA segments can be ligated into the viral genome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g., non-episomal mammalian vectors) are integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. Moreover, certain vectors are capable of directing the expression of genes to which they are operatively linked. Such vectors are referred to herein as "expression vectors". In general, expression vectors of utility in recombinant DNA techniques are often in the form of plasmids. In the present specification, "plasmid" and "vector" can be used interchangeably as the plasmid is the most commonly used form of vector. However, the embodiments described herein are intended to include such other forms of expression vectors, such as viral vectors (e.g., replication defective retroviruses, adenoviruses and adeno-associated viruses), which serve equivalent functions.

[0092] The recombinant expression vectors of the invention comprise a nucleic acid encoding any of the synthetic HIV-I /SIV Gag polypeptides described herein in a form suitable for expression of the nucleic acid in a host cell, which means that the recombinant expression vectors include one or more regulatory sequences, selected on the basis of the host cells to be used for expression, which is operatively linked to the nucleic acid sequence to be expressed. Within a recombinant expression vector, "operably linked" is intended to mean that the nucleotide sequence of interest is linked to the regulatory sequence(s) in a manner which allows for expression of the nucleotide sequence (e.g., in an in vitro transcription/translation system or in a host cell when the vector is introduced into the host cell). The term "regulatory sequence" is intended to include promoters, enhancers and other expression control elements (e.g., polyadenylation signals). Such regulatory sequences are described, for example, in Goeddel; Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990). Regulatory sequences include those which direct constitutive expression of a nucleotide sequence in many types of host cell and those which direct expression of the nucleotide sequence only in certain host cells (e.g., tissue-specific regulatory sequences). It will be appreciated by those skilled in the art that the design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of protein desired, etc. The expression vectors of the invention can be introduced into host cells to thereby produce any of the synthetic HIV-I /SIV Gag polypeptides described herein.

[0093] The recombinant expression vectors described herein can be designed for expression of any of the synthetic HIV-I /SIV Gag polypeptides described herein. For example, any of the modified HIV-I Gag polypeptides described herein can be expressed in bacterial cells such as E. coli, insect cells (using baculovirus expression vectors) yeast cells, or mammalian cells. Suitable host cells are discussed further in Goeddel, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990). Alternatively, the recombinant expression vector can be transcribed and translated in vitro, for example using T7 promoter regulatory sequences and T7 polymerase.

[0094] Expression of proteins in prokaryotes is most often carried out in E. coli with vectors containing constitutive or inducible promoters directing the expression of either fusion or non- fusion proteins. Fusion vectors add a number of amino acids to a protein encoded therein, usually to the amino terminus of the recombinant protein. Such fusion vectors typically serve three purposes: 1) to increase expression of recombinant protein; 2) to increase the solubility of the recombinant protein; and 3) to aid in the purification of the recombinant protein by acting as a ligand in affinity purification. Often, in fusion expression vectors, a proteolytic cleavage site is introduced at the junction of the fusion moiety and the recombinant protein to enable separation of the recombinant protein from the fusion moiety subsequent to purification of the fusion protein. Such enzymes, and their cognate recognition sequences, include Factor Xa, thrombin and enterokinase. Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc; Smith, D. B. and Johnson, K. S. (1988) Gene 67:31-40), pMAL (New England Biolabs, Beverly, Mass.) and pRIT5 (Pharmacia, Piscataway, NJ. ), the disclosures of which are incorporated herein by reference in their entireties, which fuse glutathione S-transferase (GST), maltose E binding protein, or protein A, respectively, to the target recombinant protein. [0095] Purified fusion or non- fusion proteins can be utilized in any of the assays described herein for assessing the immunogenicity of any of the synthetic HIV-I /SIV Gag polypeptides described herein or in the procedures for inducing an immune response against HIV-I in an individual described herein. [0096] Examples of suitable inducible non-fusion E. coli expression vectors include pTrc (Amann et al., (1988) Gene 69:301-315) and pET 1 Id (Studier et al., Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990) 60-89), the disclosures of which are incorporated herein by reference in their entireties. Target gene expression from the pTrc vector relies on host RNA polymerase transcription from a hybrid trp- lac fusion promoter. Target gene expression from the pET 11 d vector relies on transcription from a T7 gnlO-lac fusion promoter mediated by a coexpressed viral RNA polymerase (T7 gn 1). This viral polymerase is supplied by host strains BL21 (DE3) or HMS174(DE3) from a resident prophage harboring a T7 gnl gene under the transcriptional control of the lacUV 5 promoter. [0097] One strategy to maximize recombinant protein expression in E. coli is to express the protein in a host bacterium with an impaired capacity to proteolytically cleave the recombinant protein (Gottesman, S., Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990) 119-128). Another strategy is to alter the nucleic acid sequence of the nucleic acid to be inserted into an expression vector so that the individual codons for each amino acid are those preferentially utilized in E. coli (Wada et al., (1992) Nucleic Acids Res. 20:2111-2118). Such alteration of nucleic acid sequences of the invention can be carried out by standard DNA synthesis techniques.

[0098] In another embodiment, the vector encoding any of the synthetic HIV-I /SIV Gag polypeptides described herein is a yeast expression vector. Examples of vectors for expression in yeast S. cerivisae include pYepSec 1 (Baldari, et al., (1987) Embo J. 6:229-234), pMFa (Kurjan and Herskowitz, (1982) Cell 30:933-943), pJRY88 (Schultz et al., (1987) Gene 54:113- 123), pYES2 (Invitrogen Corporation, San Diego, Calif.), and picZ (Invitrogen Corp, San Diego, Calif.), the disclosures of which are incorporated herein by reference in their entireties. [0099] Alternatively, any of the synthetic HIV-I /SIV Gag polypeptides described herein can be expressed in insect cells using baculovirus expression vectors. Baculovirus vectors available for expression of proteins in cultured insect cells (e.g., Sf9 cells) include the pAc series (Smith et al. (1983) MoI. Cell Biol. 3:2156-2165) and the pVL series (Lucklow and Summers (1989) Virology 170:31-39), the disclosures of which are incorporated herein by reference in their entireties. In some embodiments, the synthetic HIV-I /SIV Gag polypeptides are expressed according to Karniski et al, Am. J. Physiol. (1998) 275: F79-87. [00100] In yet another embodiment, any of the synthetic HIV-1/SIV Gag polypeptides described herein may be expressed in mammalian cells using a mammalian expression vector. Examples of mammalian expression vectors include pCDM8 (Seed, B. (1987) Nature 329:840) and pMT2PC (Kaufman et al. (1987) EMBO J. 6:187-195), the disclosures of which are incorporated herein by reference in their entireties. When used in mammalian cells, the expression vector's control functions are often provided by viral regulatory elements. For example, commonly used promoters are derived from polyoma, Adenovirus 2, cytomegalovirus and Simian Virus 40. For other suitable expression systems for both prokaryotic and eukaryotic cells see chapters 16 and 17 of Sambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989. In another embodiment, the recombinant mammalian expression vector is capable of directing expression of the nucleic acid preferentially in a particular cell type (e.g., tissue-specific regulatory elements are used to express the nucleic acid). Tissue-specific regulatory elements are known in the art, and are further described below. [0100] In some embodiments, any of the synthetic HIV-1/SIV Gag polypeptides described herein may be expressed from vectors comprising a CMV enhancer, an HTLV-I R region and a CMV IE splicing acceptor operably linked to a nucleic acid encoding the synthetic HIV-1/SIV Gag polypeptide. For example, any of the synthetic HIV-1/SIV Gag polypeptides described herein may be expressed from the vectors described in U.S. Patent No. 7,094,598. In particular embodiments, the vectors of SEQ ID NOs: 81 , 84, 87 or 90 may be used. These vectors encode the synthetic HIV-1/SIV Gag polypeptides of SEQ ID NOs: 82, 85, 88 or 91, which are encoded by the coding regions of SEQ ID NOs: 83, 86, 89 and 92. In some embodiments, the synthetic HIV-1/SIV Gag polypeptides comprise the SIV KV9, ALl 1 and DD 13 epitopes. These epitopes were described in Liu et al., J. Virology, Vol. 80, pgs 11991-11997 (2006). It will be appreciated that, in some embodiments, synthetic HIV-1/SIV Gag polypeptides lacking one or more of these SIV epitopes or nucleic acids encoding such polypeptides may be used in any of the compositions and methods described herein.

[0101] Another aspect of the invention pertains to host cells into which a nucleic acid, such as any of the vectors described herein, encoding any of the synthetic HIV-1/SIV Gag polypeptides described herein has been introduced. The terms "host cell" and "recombinant host cell" are used interchangeably herein. It is understood that such terms refer not only to the particular subject cell but to the progeny or potential progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein.

[0102] A host cell can be any prokaryotic or eukaryotic cell. For example, any of the synthetic HIV-1/SIV Gag polypeptides described herein can be expressed in bacterial cells such as E. coli, insect cells, yeast or mammalian cells (such as Chinese hamster ovary cells (CHO) or COS cells or human cells). Other suitable host cells are known to those skilled in the art, including mouse 3T3 cells as further described in the Examples.

[0103] Vector DNA can be introduced into prokaryotic or eukaryotic cells via conventional transformation or transfection techniques. As used herein, the terms "transformation" and "transfection" are intended to refer to a variety of art-recognized techniques for introducing foreign nucleic acid (e.g., DNA) into a host cell, including calcium phosphate or calcium chloride co-precipitation, DEAE-dextran-mediated transfection, lipofection, or electroporation. Suitable methods for transforming or transfecting host cells can be found in Sambrook, et al. (Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N. Y., 1989), and other laboratory manuals. [0104] For stable transfection of mammalian cells, it is known that, depending upon the expression vector and transfection technique used, only a small fraction of cells may integrate the foreign DNA into their genome. In order to identify and select these integrants, a gene that encodes a selectable marker (e.g., resistance to antibiotics) is generally introduced into the host cells along with the gene of interest. Preferred selectable markers include those which confer resistance to drugs, such as G418, hygromycin and methotrexate. Nucleic acid encoding a selectable marker can be introduced into a host cell on the same vector as that encoding a THAP- family protein or can be introduced on a separate vector. Cells stably transfected with the introduced nucleic acid can be identified by drug selection (e.g., cells that have incorporated the selectable marker gene will survive, while the other cells die).

[0105] A host cell, such as a prokaryotic or eukaryotic host cell in culture, can be used to produce (i.e., express) any of the synthetic HIV-1/SIV Gag polypeptides described herein Accordingly, the invention further provides methods for producing a synthetic HIV-I /SIV Gag polypeptide using the host cells of the invention. In one embodiment, the method comprises culturing the host cell of invention (into which a recombinant expression vector encoding a synthetic HIV-I /S IV Gag polypeptide has been introduced) in a suitable medium such that a synthetic HIV-I /SIV Gag polypeptide is produced. In another embodiment, the method further comprises isolating a synthetic HIV-1/SIV Gag polypeptide from the medium or the host cell. [0106] Another embodiment provides methods comprising providing a cell capable of expressing any of the synthetic HIV-1/SIV Gag polypeptides described herein, culturing said cell in a suitable medium such that a synthetic HIV-1/SIV Gag polypeptide is produced, and isolating or purifying the synthetic HIV-1/SIV Gag polypeptide from the medium or cell. [0107] In some embodiments, the nucleic acid vectors for producing or administering any of the synthetic HIV-1/SIV Gag polypeptides described herein comprise regulatory elements (e.g. promoter, enhancer, etc) capable of directing the expression of the synthetic HIV-1/SIV Gag polypeptide in the targeted cell. Thus, where a human cell is targeted, it is preferable to position the nucleic acid coding region adjacent to and under the control of a promoter that is capable of being expressed in a human cell.

[0108] In various embodiments, the human cytomegalovirus (CMV) immediate early gene promoter, the SV40 early promoter, the Rous sarcoma virus long terminal repeat, P actin, rat insulin promoter and glyceraldehyde-3 -phosphate dehydrogenase can be used to obtain high- level expression of any of the synthetic HIV-1/SIV Gag polypeptides described herein. The use of other viral or mammalian cellular or bacterial phage promoters which are well-known in the art to achieve expression of a coding sequence of interest is contemplated as well, provided that the levels of expression are sufficient for a given purpose. By employing a promoter with well- known properties, the level and pattern of expression of the protein of interest following transfection or transformation can be optimized.

[0109] Selection of a promoter that is regulated in response to specific physiologic or synthetic signals can permit inducible expression of the gene product. For example in the case where expression of a transgene, or transgenes when a multicistronic vector is utilized, is toxic to the cells in which the vector is produced in, it may be desirable to prohibit or reduce expression of one or more of the transgenes. Several inducible promoter systems are available for production of viral vectors where the transgene product may be toxic.

[0110] The ecdysone system (Invitrogen, Carlsbad, CA) is one such system. This system is designed to allow regulated expression of a gene of interest in mammalian cells. It consists of a tightly regulated expression mechanism that allows virtually no basal level expression of the transgene, but over 200-fold inducibility. The system is based on the heterodimeric ecdysone receptor of Drosophila, and when ecdysone or an analog such as muristerone A binds to the receptor, the receptor activates a promoter to turn on expression of the downstream transgene high levels of mRNA transcripts are attained. In this system, both monomers of the heterodimeric receptor are constitutively expressed from one vector, whereas the ecdysone- responsive promoter which drives expression of the gene of interest is on another plasmid. Engineering of this type of system into the gene transfer vector of interest would therefore be useful. Cotransfection of plasmids containing the gene of interest and the receptor monomers in the producer cell line would then allow for the production of the gene transfer vector without expression of a potentially toxic transgene. At the appropriate time, expression of the transgene could be activated with ecdysone or muristeron A. Another inducible system that would be useful is the Tet-Off or Tet On system (Clontech, Palo Alto, CA) originally developed by Gossen and Bujard (Gossen and Bujard, 1992; Gossen et al, 1995). This system also allows high levels of gene expression to be regulated in response to tetracycline or tetracycline derivatives such as doxycycline. In the Tet-On system, gene expression is turned on in the presence of doxycycline, whereas in the Tet-Off system, gene expression is turned on in the absence of doxycycline. These systems are based on two regulatory elements derived from the tetracycline resistance operon of E. coli. The tetracycline operator sequence to which the tetracycline repressor binds, and the tetracycline repressor protein. The gene of interest is cloned into a plasmid behind a promoter that has tetracycline-responsive elements present in it. A second plasmid contains a regulatory element called the tetracycline-controlled transactivator, which is composed, in the Tet Off system, of the VP 16 domain from the herpes simplex virus and the wild-type tertracycline repressor.

[0111] Thus in the absence of doxycycline, transcription is constitutively on. In the Tet- OnTm system, the tetracycline repressor is not wild-type and in the presence of doxycycline activates transcription. For gene therapy vector production, the Tet Off system would be preferable so that the producer cells could be grown in the presence of tetracycline or doxycycline and prevent expression of a potentially toxic transgene, but when the vector is introduced to the patient, the gene expression would be constitutively on. [0112] In some circumstances, it may be desirable to regulate expression of a transgene in a gene therapy vector. For example, different viral promoters with varying strengths of activity may be utilized depending on the level of expression desired. In mammalian cells, the CMV immediate early promoter is often used to provide strong transcriptional activation. Modified versions of the CMV promoter that are less potent have also been used when reduced levels of expression of the transgene are desired. When expression of a transgene in hematopoietic cells is desired, retroviral promoters such as the LTRs from MLV or MMTV are often used. Other viral promoters that may be used depending on the desired effect include SV40, RSV LTR, HIV-I and HfV-2 LTR, adenovirus promoters such as from the ElA, E2A, or MLP region, AAV LTR, cauliflower synthetic virus, HSV-TK, and avian sarcoma virus.

[00101] Similarly tissue specific promoters may be used to effect transcription in specific tissues or cells so as to reduce potential toxicity or undesirable effects to non-targeted tissues. For example, promoters such as the PSA, probasin, prostatic acid phosphatase or prostate- specific glandular kallikrein (hK2) may be used to target gene expression in the prostate. Similarly, promoters as follows may be used to target gene expression in other tissues. [0113] Tissue specific promoters include in (a) pancreas: insulin, elastin, amylase, pdr-I, pdx-I, glucokinase; (b) liver: albumin PEPCK, HBV enhancer, alpha fetoprotein, apolipoprotein C, alpha-I antitrypsin, vitellogenin, NF-AB, Transthyretin; (c) skeletal muscle: myosin H chain, muscle creatine kinase, dystrophin, calpain p94, skeletal alpha-actin, fast troponin 1 ; (d) skin: keratin K6, keratin KI; (e) lung: CFTR, human cytokeratin IS (K 18), pulmonary surfactant proteins A, B and C, CC-10, Pi; (f) smooth muscle: sm22 alpha, SM-alpha-actin; (g) endothelium: endothelin- 1, E-selectin, von Willebrand factor, TIE (Korhonen et al., 1995), KDR/flk-I; (h) melanocytes: tyrosinase; (i) adipose tissue: lipoprotein lipase (Zechner et al., 1988), adipsin (Spiegelman et al., 1989), acetyl-CoA carboxylase (Pape and Kim, 1989), glycerophosphate dehydrogenase (Dani et al., 1989), adipocyte P2 (Hunt et al., 1986); and (J) blood: P-globin. [0114] In certain indications, it may be desirable to activate transcription at specific times after administration of the gene therapy vector. This may be done with such promoters as those that are hormone or cytokine regulatable. For example in gene therapy applications where the indication is in a gonadal tissue where specific steroids are produced or routed to, use of androgen or estrogen regulated promoters may be advantageous. Such promoters that are hormone regulatable include MMTV, MT-I, ecdysone and RuBisco. Other hormone regulated promoters such as those responsive to thyroid, pituitary and adrenal hormones are expected to be useful in the present invention. Cytokine and inflammatory protein responsive promoters that could be used include K and T Kininogen (Kageyama et al., 1987), c-fos, TNF-alpha, C-reactive protein (Arcone et al., 1988), haptoglobin (Oliviero et al., 1987), serum amyloid A2, C/EBP alpha, IL-I, IL-6 (PoIi and Cortese, 1989), Complement C3 (Wilson et al., 1990), IL-8, alpha- 1 acid glycoprotein (Prowse and Baumann, 1988), alpha- 1 antitypsin, lipoprotein lipase (Zechner et al., 1988), angiotensinogen (Ron et al., 1991), fibrinogen, c-jun (inducible by phorbol esters, TNF alpha, UV radiation, retinoic acid, and hydrogen peroxide), collagenase (induced by phorbol esters and retinoic acid), metallothionein (heavy metal and glucocorticoid inducible), Stromelysin (inducible by phorbol ester, interleukin-1 and EGF), alpha-2 macroglobulin and alpha- 1 antichymotrypsin.

[0115] It is envisioned that cell cycle regulatable promoters may be useful in the present invention. For example, in a bi-cistronic gene therapy vector, use of a strong CMV promoter to drive expression of a first gene such as pi 6 that arrests cells in the Gl phase could be followed by expression of a second gene such as p53 under the control of a promoter that is active in the Gl phase of the cell cycle, thus providing a "second hit" that would push the cell into apoptosis. Other promoters such as those of various cyclins, PCNA, galectin-3, E2FI, p53 and BRCAI could be used.

[0116] It is envisioned that any of the above promoters alone or in combination with another may be useful according to the present invention depending on the action desired. [0117] In addition, this list of promoters should not be considered to be exhaustive or limiting, those of skill in the art will know of other promoters that may be used in conjunction with the nucleic acids and methods disclosed herein. [0118] In some embodiments, the nucleic acids for producing or administering any of the synthetic HIV-I /SIV Gag polypeptides described herein may contain one or more enhancers. Enhancers are genetic elements that increase transcription from a promoter located at a distant position on the same molecule of DNA. Enhancers are organized much like promoters. That is, they are composed of many individual elements, each of which binds to one or more transcriptional proteins. The basic distinction between enhancers and promoters is operational. An enhancer region as a whole must be able to stimulate transcription at a distance; this need not be true of a promoter region or its component elements. On the other hand, a promoter must have one or more elements that direct initiation of RNA synthesis at a particular site and in a particular orientation, whereas enhancers lack these specificities. Promoters and enhancers are often overlapping and contiguous, often seeming to have a very similar modular organization. [0119] Below is a list of promoters additional to the tissue specific promoters listed above, cellular promoters/enhancers and inducible promoters/enhancers that could be used in combination with the nucleic acid encoding a gene of interest in an expression construct (see also Table 1). Additionally, any promoter/enhancer combination (as per the Eukaryotic Promoter Data Base EPDB) could also be used to drive expression of the gene. Eukaryotic cells can support cytoplasmic transcription from certain bacterial promoters if the appropriate bacterial polymerase is provided, either as part of the delivery complex or as an additional genetic expression construct.

[0120] Suitable enhancers include: Immunoglobulin Heavy Chain; Immunoglobulin Light Chain; T-CeIl Receptor; HLA DQ (x and DQ beta; beta-Interferon; Interleukin-2; Interleukin-2 Receptor; MHC Class II 5; MHC Class II HLA-DRalpha; beta-Actin; Muscle Creatine Kinase; Prealbumin (Transthyretin); Elastase I; Metallothionein; Collagenase; Albumin Gene; alpha- Fetoprotein; -Globin; beta-Globin; e-fos; c-HA-ras; Insulin; Neural Cell Adhesion Molecule (NCAM); alpha al -Antitrypsin; H2B (TH2B) Histone; Mouse or Type I Collagen; Glucose- Regulated Proteins (GRP94 and GRP78); Rat Growth Hormone; Human Serum Amyloid A (SAA); Troponin I (TN 1); Platelet-Derived Growth Factor; Duchenne Muscular Dystrophy; SV40; Polyoma; Retroviruses; THAPilloma Virus; Hepatitis B Virus; Human Immunodeficiency Virus; Cytomegalovirus; and Gibbon Ape Leukemia Virus. Table 1

[0121] In preferred embodiments of the invention, any of the synthetic HIV-1/SIV Gag polypeptides described herein may be produced or administered via a vector comprising a virus or engineered construct derived from a viral genome. The ability of certain viruses to enter cells via receptor-mediated endocytosis and to integrate into host cell genome and express viral genes stably and efficiently have made them attractive candidates for the transfer of foreign genes into mammalian cells (Ridgeway, 1988; Nicolas and Rubenstein, 1988; Baichwal and Sugden, 1986; Temin, 1986, the disclosures of which are incorporated herein by reference). The first viruses used as gene vectors were DNA viruses including the papovaviruses (simian virus 40, bovine papilloma virus, and polyoma) (Ridgeway, 1988; Baichwal and Sugden, 1986) and adenoviruses (Ridgeway, 1988; Baichwal and Sugden, 1986). These have a relatively low capacity for foreign DNA sequences and have a restricted host spectrum.

[0122] Furthermore, their oncogenic potential and cytopathic effects in permissive cells raise safety concerns. They can accommodate only up to 8 kB of foreign genetic material but can be readily introduced in a variety of cell lines and laboratory animals (Nicolas and Rubenstein, 1988; Temin, 1986).

[0123] In some methods of producing or administering any of the synthetic HIV-I /SIV Gag polypeptides described herein, the synthetic HIV-I /SIV Gag polypeptides are produced or administered using a viral vector. For example, the viral vector may be an adenovirus vector. In some embodiments, the adenovirus vector may be an adenovirus 5 vector. In other embodiments, the adenovirus vector may be an adenovirus 26 vector or an adenovirus 28 vector. [0124] Nucleic acids encoding any of the mosaic HIV-I /SIV Gag polypeptides described herein may be operably linked to a polyadenylation signal to effect proper polyadenylation of the gene transcript. The nature of the polyadenylation signal is not believed to be crucial and any such sequence may be employed such as human or bovine growth hormone and SV40 polyadenylation signals. In some embodiments, vectors for expressing any of the synthetic HIV- 1/SIV Gag polypeptides described herein may include a terminator. These elements can serve to enhance message levels and to minimize read through from the cassette into other sequences. [0125] A number of methodologies for introducing nucleic acids encoding any of the synthetic HIV-I /SIV Gag polypeptides described herein into a cell or individual. These method include viral gene transfer as well as non- viral gene transfer methods.

[0126] In some embodiments, a nucleic acid encoding any of the synthetic HIV-I /SIV Gag polypeptides described herein is incorporated into a viral infectious particle to mediate gene transfer to a cell. Alternatively, retroviral or bovine papilloma virus may be employed, both of which permit permanent transformation of a host cell with a gene(s) of interest. Thus, in one example, viral infection of cells is used in order to deliver therapeutically significant genes to a cell. Typically, the virus simply will be exposed to the appropriate host cell under physiologic conditions, permitting uptake of the virus. Though adenovirus is exemplified, the present methods may be advantageously employed with other viral or non- viral vectors, as discussed below.

[0127] Adenovirus is particularly suitable for use as a gene transfer vector because of its mid-sized DNA genome, ease of manipulation, high titer, wide target-cell range, and high infectivity. The roughly 36 kB viral genome is bounded by 100-200 base pair (bp) inverted terminal repeats (ITR), in which are contained cis acting elements necessary for viral DNA replication and packaging. The early (E) and late (L) regions of the genome that contain different transcription units are divided by the onset of viral DNA replication. [0128] The El region (ElA and ElB) encodes proteins responsible for the regulation of transcription of the viral genome and a few cellular genes. The expression of the E2 region (E2A and E2B) results in the synthesis of the proteins for viral DNA replication. [0129] These proteins are involved in DNA replication, late gene expression, and host cell shut off (Renan, 1990). The products of the late genes (L I, L2, U, L4 and L5), including the majority of the viral capsid proteins, are expressed only after significant processing of a single primary transcript issued by the major late promoter (MLP). The MLP (located at 16.8 map units) is particularly efficient during the late phase of infection, and all the mRNAs issued from this promoter possess a 5' tripartite leader (TL) sequence which makes them preferred mRNAs for translation.

[0130] In order for adenovirus to be optimized for gene therapy, it is necessary to maximize the carrying capacity so that large segments of DNA can be included. It also is very desirable to reduce the toxicity and immunologic reaction associated with certain adenoviral products. The two goals are, to an extent, coterminous in that elimination of adenoviral genes serves both ends. By practice of the present invention, it is possible achieve both these goals while retaining the ability to manipulate the therapeutic constructs with relative case.

[0131] The large displacement of DNA is possible because the cis elements required for viral DNA replication all are localized in the inverted terminal repeats (ITR) (100-200 bp) at either end of the linear viral genome. Plasmids containing ITR's can replicate in the presence of a non- defective adenovirus (Hay et al., 1984). Therefore, inclusion of these elements in an adenoviral vector should permit replication.

[0132] In addition, the packaging signal for viral encapsidation is localized between 194 385 bp (0.5-1.1 map units) at the left end of the viral genome (Hearing et al., 1987). This signal mimics the protein recognition site in bacteriophage K DNA where a specific sequence close to the left end, but outside the cohesive end sequence, mediates the binding to proteins that are required for insertion of the DNA into the head structure. El substitution vectors of Ad have demonstrated that a 450 bp (0-1.25 map units) fragment at the left end of the viral genome could direct packaging in 293 cells (Levrero et al., 1991). [0133] Previously, it has been shown that certain regions of the adenoviral genome can be incorporated into the genome of mammalian cells and the genes encoded thereby expressed. These cell lines are capable of supporting the replication of an adenoviral vector that is deficient in the adenoviral function encoded by the cell line. There also have been reports of complementation of replication deficient adenoviral vectors by "helping" vectors, e.g., wild-type virus or conditionally defective mutants.

[0134] Replication-deficient adenoviral vectors can be complemented, in trans, by helper virus. This observation alone does not permit isolation of the replication-deficient vectors, however, since the presence of helper virus, needed to provide replicative functions, would contaminate any preparation. Thus, an additional element was needed that would add specificity to the replication and/or packaging of the replication-deficient vector. That element, as provided for in the present invention, derives from the packaging function of adenovirus. [0135] It has been shown that a packaging signal for adenovirus exists in the left end of the conventional adenovirus map (Tibbetts, 1977). Later studies showed that a mutant with a deletion in the EIA (194-358 bp) region of the genome grew poorly even in a cell line that complemented the early (EIA) function (Hearing and Shenk, 1983). When a compensating adenoviral DNA (0-353 bp) was recombined into the right end of the mutant, the virus was packaged normally. Further mutational analysis identified a short, repeated, position-dependent element in the left end of the Ad5 genome. One copy of the repeat was found to be sufficient for efficient packaging if present at either end of the genome, but not when moved towards the interior of the Ad5 DNA molecule (Hearing et al., 1987).

[0136] By using mutated versions of the packaging signal, it is possible to create helper viruses that are packaged with varying efficiencies. Typically, the mutations are point mutations or deletions. When helper viruses with low efficiency packaging are grown in helper cells, the virus is packaged, albeit at reduced rates compared to wild-type virus, thereby permitting propagation of the helper. When these helper viruses are grown in cells along with virus that contains wild-type packaging signals, however, the wild-type packaging signals are recognized preferentially over the mutated versions. Given a limiting amount of packaging factor, the virus containing the wild-type signals are packaged selectively when compared to the helpers. If the preference is great enough, stocks approaching homogeneity should be achieved. [0137] As discussed above, in some embodiments, the adenovirus vectors encoding any of the synthetic HIV-I /SIV Gag polypeptides described herein may be adenovirus 5, adenovirus 26 or adenovirus 28 vectors.

[0138] In some embodiments, retrovirus vectors may be used to produce or administer any of the synthetic HIV-I /SIV Gag polypeptides described herein. The retroviruses are a group of single-stranded RNA viruses characterized by an ability to convert their RNA to double-stranded DNA in infected cells by a process of reverse-transcription (Coffin, 1990). The resulting DNA then stably integrates into cellular chromosomes as a pro virus and directs synthesis of viral proteins.

[0139] The integration results in the retention of the viral gene sequences in the recipient cell and its descendants. The retroviral genome contains three genes - gag, pol and env - that code for capsid proteins, polymerase enzyme, and envelope components, respectively. A sequence found upstream from the gag gene, termed T, functions as a signal for packaging of the genome into virions. Two long terminal repeat (LTR) sequences are present at the 5' and 3' ends of the viral genome. These contain strong promoter and enhancer sequences and also are required for integration in the host cell genome (Coffin, 1990).

[0140] In order to construct a retroviral vector, a nucleic acid encoding a promoter is inserted into the viral genome in the place of certain viral sequences to produce a virus that is replication- defective. In order to produce virions, a packaging cell line containing the gag, pol and env genes but without the LTR and T components is constructed (Mann et al., 1983). When a recombinant plasmid containing a human cDNA, together with the retroviral LTR and T sequences is introduced into this cell line (by calcium phosphate precipitation for example), the T sequence allows the RNA transcript of the recombinant plasmid to be packaged into viral particles, which are then secreted into the culture media (Nicolas and Rubenstein, 1988; Temin, 1986; Mann et al., 1983, the disclosures of which are incorporated herein by reference). The media containing the recombinant retroviruses is collected, optionally concentrated, and used for gene transfer. Retroviral vectors are able to infect a broad variety of cell types. However, integration and stable expression of many types of retroviruses require the division of host cells (Paskind et al., 1975). [0141] An approach designed to allow specific targeting of retrovirus vectors recently was developed based on the chemical modification of a retrovirus by the chemical addition of galactose residues to the viral envelope. This modification could permit the specific infection of cells such as hepatocytes via asialoglycoprotein receptors, should this be desired.

[0142] A different approach to targeting of recombinant retroviruses was designed in which biotinylated antibodies against a retroviral envelope protein and against a specific cell receptor were used. The antibodies were coupled via the biotin components by using streptavidin (Roux et al., 1989). Using antibodies against major histocompatibility complex class I and class II antigens, the infection of a variety of human cells that bore those surface antigens was demonstrated with an ecotropic virus in vitro (Roux et al., 1989).

[0143] In some embodiments, adenoassociated virus (AAV) vectors may be used to produce or administer any of the synthetic HIV-I /SIV Gag polypeptides described herein. AAV utilizes a linear, single-stranded DNA of about 4700 base pairs. Inverted terminal repeats flank the genome. Two genes are present within the genome, giving rise to a number of distinct gene products. The first, the cap gene, produces three different virion proteins (VP), designated VP-I,

VP 2 and VP-3.

[0144] The second, the rep gene, encodes four non-structural proteins (NS). One or more of these rep gene products is responsible for transactivating AAV transcription.

[0145] The three promoters in AAV are designated by their location, in map units, in the genome. These are, from left to right, p5, pi 9 and p40. Transcription gives rise to six transcripts, two initiated at each of three promoters, with one of each pair being spliced.

[0146] The splice site, derived from map units 42-46, is the same for each transcript. The four non- structural proteins apparently are derived from the longer of the transcripts, and three virion proteins all arise from the smallest transcript.

[0147] AAV is not associated with any pathologic state in humans. Interestingly, for efficient replication, AAV requires "helping" functions from viruses such as herpes simplex virus I and II, cytomegalovirus, pseudorabies virus and, of course, adenovirus.

[0148] The best characterized of the helpers is adenovirus, and many "early" functions for this virus have been shown to assist with AAV replication. Low level expression of AAV rep proteins is believed to hold AAV structural expression in check, and helper virus infection is thought to remove this block.

[0149] The terminal repeats of the AAV vector can be obtained by restriction endonuclease digestion of AAV or a plasmid such as p201, which contains a modified AAV genome (Samulski et al, 1987), or by other methods known to the skilled artisan, including but not limited to chemical or enzymatic synthesis of the terminal repeats based upon the published sequence of AAV. The ordinarily skilled artisan can determine, by well-known methods such as deletion analysis, the minimum sequence or part of the AAV ITRs which is required to allow function, i.e., stable and site specific integration.

[0150] The ordinarily skilled artisan also can determine which minor modifications of the sequence can be tolerated while maintaining the ability of the terminal repeats to direct stable, site-specific integration.

[0151] AAV-based vectors have proven to be safe and effective vehicles for gene delivery in vitro, and these vectors are being developed and tested in pre-clinical and clinical stages for a wide range of applications in potential gene therapy, both ex vivo and in vivo (Carter and Flotte, 1996; Chattedee et al., 1995; Ferrari et al., 1996; Fisher et al., 1996; Flotte et al., 1993; Goodman et al., 1994; Kaplitt et al., 1994; 1996, Kessler et al., 1996; Koeberl et al., 1997; Mizukami et al., 1996; Xiao et al., 1996, the disclosures of which are incorporated herein by reference in their entireties).

[0152] AAV-mediated efficient gene transfer and expression in the lung has led to clinical trials for the treatment of cystic fibrosis (Carter and Flotte, 1996; Flotte et al., 1993, the disclosures of which are incorporated herein by reference). Similarly, the prospects for treatment of muscular dystrophy by AAV-mediated gene delivery of the dystrophin gene to skeletal muscle, of Parkinson's disease by tyrosine hydroxylase gene delivery to the brain, of hemophilia B by Factor IX gene delivery to the liver, and potentially of myocardial infarction by vascular endothelial growth factor gene to the heart, appear promising since AAV-mediated transgene expression in these organs has recently been shown to be highly efficient (Fisher et al., 1996; Flotte et al., 1993; Kaplitt et al., 1994; 1996; Koeberl et al., 1997; McCown et al., 1996; Ping et al., 1996; and Xiao et al., 1996, the disclosures of which are incorporated herein by reference in their entireties.). [0153] Other viral vectors may be employed to produce or administer any of the modified HIV-I proteins described herein. Vectors derived from viruses such as vaccinia virus (Ridgeway, 1988; Baichwal and Sugden, 1986; Coupar et al., 1988) and hepatitis B viruses have also been developed and are useful in the present invention. They offer several attractive features for various mammalian cells (Friedmann, 1989; Ridgeway, 1988; Baichwal and Sugden, 1986; Coupar et al., 1988; and Horwich et al., 1990, the disclosures of which are incorporated herein by reference in their entireties.).

[0154] With the recent recognition of defective hepatitis B viruses, new insight was gained into the structure-function relationship of different viral sequences. In vitro studies showed that the virus could retain the ability for helper dependent packaging and reverse transcription despite the deletion of up to 80% of its genome (Horwich et al., 1990). This suggested that large portions of the genome could be replaced with foreign genetic material. Chang et al., recently introduced the chloramphenicol acetyltransferase (CAT) gene into duck hepatitis B virus genome in the place of the polymerase, surface, and pre-surface coding sequences. It was cotransfected with wild-type virus into an avian hepatoma cell line. Culture media containing high titers of the recombinant virus were used to infect primary duckling hepatocytes. Stable CAT gene expression was detected for at least 24 days after transfection (Chang et al., 1991). [0155] In still further embodiments, the nucleic acids encoding any of the synthetic HIV- 1/SIV Gag polypeptides described herein are housed within an infective virus that has been engineered to express a specific binding ligand. The virus particle will thus bind specifically to the cognate receptors of the target cell and deliver the contents to the cell. A novel approach designed to allow specific targeting of retrovirus vectors was recently developed based on the chemical modification of a retrovirus by the chemical addition of lactose residues to the viral envelope. This modification can permit the specific infection of hepatocytes via sialoglycoprotein receptors.

[0156] Another approach to targeting of recombinant retroviruses was designed in which biotinylated antibodies against a retroviral envelope protein and against a specific cell receptor were used. The antibodies were coupled via the biotin components by using streptavidin (Roux et al., 1989). Using antibodies against major histocompatibility complex class I and class II antigens, they demonstrated the infection of a variety of human cells that bore those surface antigens with an ecotropic virus in vitro (Roux et al., 1989).

[0157] In some embodiments, non-viral methods are used to produce or administer nucleic acids encoding any of the synthetic HIV-I /SIV Gag polypeptides described herein. DNA constructs of the present invention are generally delivered to a cell. In certain situations, the nucleic acid to be transferred is non-infectious, and can be transferred using non-viral methods. [0158] Several non-viral methods for the transfer of expression constructs into cultured mammalian cells are contemplated by the present invention. These include calcium phosphate precipitation (Graham and Van Der Eb, 1973; Chen and Okayama, 1987; Rippe et al., 1990) DEAE-dextran (Gopal, 1985), electroporation (Tur Kaspa et al., 1986; Potter et al., 1984), direct microinjection (Harland and Weintraub, 1985), DNA loaded liposomes (Nicolau and Sene, 1982; Fraley et al., 1979), cell sonication (Fechheimer et al., 1987), gene bombardment using high velocity microprojectiles (Yang et al., 1990), and receptor-mediated transfection (Wu and Wu, 1987; Wu and Wu, 1988), the disclosures of which are incorporated herein by reference in their entireties.

[0159] Once the construct has been delivered into the cell the nucleic acid encoding the synthetic HIV-I /SIV Gag polypeptide may be positioned and expressed at different sites. In certain embodiments, the nucleic acid encoding the therapeutic gene may be stably integrated into the genome of the cell. This integration may be in the cognate location and orientation via homologous recombination (gene replacement) or it may be integrated in a random, non-specific location (gene augmentation). In yet further embodiments, the nucleic acid may be stably maintained in the cell as a separate, episomal segment of DNA. Such nucleic acid segments or "episomes" encode sequences sufficient to permit maintenance and replication independent of or in synchronization with the host cell cycle.

[0160] How the expression construct is delivered to a cell and where in the cell the nucleic acid remains is dependent on the type of expression construct employed.

[0161] In a particular embodiment, the expression construct may be entrapped in a liposome. Liposomes are vesicular structures characterized by a phospholipid bilayer membrane and an inner aqueous medium. Multilamellar liposomes have multiple lipid layers separated by aqueous medium. They form spontaneously when phospholipids are suspended in an excess of aqueous solution. The lipid components undergo self-rearrangement before the formation of closed structures and entrap water and dissolved solutes between the lipid bilayers (Ghosh and Bachhawat, 1991). The addition of DNA to cationic liposomes causes a topological transition from liposomes to optically birefringent liquid-crystalline condensed globules (Radler et al., 1997). These DNA-lipid complexes are potential non- viral vectors for use in gene therapy. [0162] Liposome-mediated nucleic acid delivery and expression of foreign DNA in vitro has been very successful. Using the P-lactamase gene, Wong et al. (1980) demonstrated the feasibility of liposome-mediated delivery and expression of foreign DNA in cultured chick embryo, HeLa, and hepatoma cells. Nicolau et al. (1987) accomplished successful liposome- mediated gene transfer in rats after intravenous injection. Also included are various commercial approaches involving "lipofection" technology.

[0163] In certain embodiments of the invention, the liposome may be complexed with a hemagglutinating virus (HVJ). This has been shown to facilitate fusion with the cell membrane and promote cell entry of liposome-encapsulated DNA (Kaneda et al., 1989). [0164] In other embodiments, the liposome may be complexed or employed in conjunction with nuclear nonhistone chromosomal proteins (HMG-I) (Kato et al., 1991). In yet further embodiments, the liposome may be complexed or employed in conjunction with both HVJ and HMG-I. In that such expression constructs have been successfully employed in transfer and expression of nucleic acid in vitro and in vivo, then they are applicable for the present invention. [0165] Other vector delivery systems which can be employed to deliver a nucleic acid encoding any of the synthetic HIV-I /SIV Gag polypeptides described herein into cells are receptor-mediated delivery vehicles. These take advantage of the selective uptake of macromolecules by receptor mediated endocytosis in almost all eukaryotic cells. Because of the cell type specific distribution of various receptors, the delivery can be highly specific (Wu and Wu, 1993).

[0166] Receptor-mediated gene targeting vehicles generally consist of two components: a cell receptor-specific ligand and a DNA-binding agent. Several ligands have been used for receptor-mediated gene transfer. The most extensively characterized ligands are asialoorosomucoid (ASOR) (Wu and Wu, 1987) and transferring (Wagner et al., 1990). [0167] Recently, a synthetic neoglycoprotein, which recognizes the same receptor as ASOR, has been used as a gene delivery vehicle (Ferkol et al., 1993; Perales et al., 1994) and epidermal growth factor (EGF) has also been used to deliver genes to squamous carcinoma cells (Myers, EPO 0273085).

[0168] In other embodiments, the delivery vehicle may comprise a ligand and a liposome. For example, Nicolau et al, (1987) employed lactosyl-ceramide, a galactose terminal asialganglioside, incorporated into liposomes and observed an increase in the uptake of the insulin gene by hepatocytes. Thus, it is feasible that a nucleic acid encoding a therapeutic gene also may be specifically delivered into a cell type such as prostate, epithelial or tumor cells, by any number of receptor-ligand systems with or without liposomes. For example, the human prostate-specific antigen (Watt et al, 1986) may be used as the receptor for mediated delivery of a nucleic acid in prostate tissue.

[0169] In another embodiment of the invention, the expression construct may simply consist of naked recombinant DNA or plasmids. Transfer of the construct may be performed by any of the methods mentioned above which physically or chemically permeabilize the cell membrane. This is applicable particularly for transfer in vitro, however, it may be applied for in vivo use as well. Dubensky et al, (1984) successfully injected polyomavirus DNA in the form of CaP04 precipitates into liver and spleen of adult and newborn mice demonstrating active viral replication and acute infection.

[0170] Benvenisty and Neshif (1986) also demonstrated that direct intraperitoneal injection of CaP04 precipitated plasmids results in expression of the transfected genes. It is envisioned that DNA encoding a CAM may also be transferred in a similar manner in vivo and express CAM.

[0171] Another embodiment for transferring a naked DNA expression construct into cells may involve particle bombardment. This method depends on the ability to accelerate DNA coated microprojectiles to a high velocity allowing them to pierce cell membranes and enter cells without killing them (Klein et al, 1987). Several devices for accelerating small particles have been developed. One such device relies on a high voltage discharge to generate an electrical current, which in turn provides the motive force (Yang et al, 1990). The microprojectiles used have consisted of biologically inert substances such as tungsten or gold beads. [0172] Some embodiments relate to methods for inducing an immune response to HIV-I comprising administering any of the synthetic HIV-I /SIV Gag polypeptides described herein to an individual. In some embodiments, the synthetic HIV-I /SIV Gag polypeptides are administered via a nucleic acid encoding the synthetic HIV-I /SIV Gag polypeptide. The nucleic acids may be any of those described herein or other suitable nucleic acids. In this regard, the invention provides a method of inducing an immune response against HIV-I in a mammal, which method comprises administering at least one nucleic acid sequence to a mammal, wherein the at least one nucleic acid sequence encodes a polypeptide comprising a HIV-I Gag amino acid sequence and an immunogenic SIV Gag amino acid sequence. Preferably, the inventive method comprises administering two or more different nucleic acid sequences to a mammal, wherein each nucleic acid sequence encodes a polypeptide comprising a HIV-I Gag amino acid sequence, except that amino acids 358-411 or amino acids 355-408 of the HIV-I Gag amino acid sequence have been replaced with amino acids 359-412 of a SIV Gag polypeptide. Most preferably, the inventive method comprises administering two different nucleic acid sequences to a mammal, wherein each nucleic acid sequence encodes a polypeptide comprising a HIV-I Gag amino acid sequence, except that amino acids 358-411 or amino acids 355-408 of the HIV-I Gag amino acid sequence have been replaced with amino acids 359-412 of a SIV Gag polypeptide. [0173] In some embodiments, the synthetic HIV-1/SIV Gag polypeptides are administered in addition to other proteins which induce an immune response against HIV-I . In some embodiments, the other proteins may be other HIV-I proteins. For example, in some embodiments, the other proteins may be Pol, Nef and Env. In some embodiments, the synthetic HIV-1/SIV Gag polypeptides and one or more of the other proteins which induce an immune response against HIV-I may be administered as fusion proteins. Alternatively, in other embodiments, the synthetic HIV-1/SIV Gag polypeptides and one or more of the other proteins which induce an immune response against HIV-I may be administered as separate proteins. [0174] One aspect of the present disclosure relates to compositions capable of eliciting an immune response against HIV. For example, the compositions can be capable of eliciting a protective immune response against HIV when administered alone or in combination with at least one additional immunogenic compositions. It will be understood by those of skill in the art, the ability to produce an immune response after exposure to an antigen is a function of complex cellular and humoral processes, and that different subjects have varying capacity to respond to an immunological stimulus. Accordingly, the compositions disclosed herein are capable of eliciting an immune response in an immunocompetent subject, that is a subject that is physiologically capable of responding to an immunological stimulus by the production of a substantially normal immune response, e.g., including the production of antibodies that specifically interact with the immunological stimulus, and/or the production of functional T cells (CD4⁺ and/or CD8⁺ T cells) that bear receptors that specifically interact with the immunological stimulus. It will further be understood, that a particular effect of infection with HIV is to render a previously immunocompetent subject immunodeficient. Thus, with respect to therapeutic methods discussed below, it is generally desirable to administer the compositions to a subject prior to exposure to HIV (that is, prophylactically, e.g., as a vaccine) or therapeutically at a time following exposure to HIV during which the subject is nonetheless capable of developing an immune response to a stimulus, such as an antigenic polypeptide.

[0175] The compositions may comprise one or more nucleic acid molecules encoding any of the synthetic HIV-I /SIV Gag polypeptides described herein or the compositions may comprise the synthetic HIV-I /SIV Gag polypeptide itself. In one embodiment, the composition comprises two or more nucleic acid molecules, wherein each nucleic acid molecule encodes a synthetic HIV-I /SIV Gag polypeptide described herein (which can be the same or different). For example, the composition preferably comprises a nucleic acid sequence encoding a polypeptide, wherein the polypeptide comprises a HIV-I Gag amino acid sequence, except that amino acids 358-411 or amino acids 355-408 of the HIV-I Gag amino acid sequence have been replaced with amino acids 359-412 of a SIV Gag polypeptide, and a pharmaceutically acceptable carrier. More preferably, the composition comprises two or more different nucleic acid sequences, wherein each nucleic acid sequence encodes a polypeptide comprising a HIV-I Gag amino acid sequence, except that amino acids 358-411 or amino acids 355-408 of the HIV-I Gag amino acid sequence have been replaced with amino acids 359-412 of a SIV Gag polypeptide. When administered in conjunction with nucleic acids encoding one or more other polypeptides capable of inducing an immune response against HIV-I, the synthetic HIV-I /SIV Gag polypeptides may be encoded by the same nucleic acid as the one or more other polypeptides. Alternatively, the synthetic HIV- 1/SIV Gag polypeptide may be encoded on a separate nucleic acid from the one or more other polypeptides. Likewise, where the synthetic HIV-I /SIV Gag polypeptide itself is administered with one or more other polypeptides which induce an immune response against HIV-I, the synthetic HIV-I /SIV Gag polypeptide may be fused to one or more of the other polypeptides. Alternatively, the synthetic HIV-I /SIV Gag polypeptide may be administered as a separate polypeptide from the one or more other polypeptides.

[0176] Typically, when formulated for administration to a subject, the compositions also include a pharmaceutically acceptable carrier or excipient, for example, an aqueous carrier, such as phosphate buffered saline (PBS) or another neutral physiological salt solution. The composition can also include an adjuvant or other immunostimulatory molecule. The composition can be administered one or more times to a subject to elicit an immune response. For example, the composition can be administered multiple times at intervals of at least about 28 days, or at different intervals as dictated by logistical or therapeutic concerns. [0177] Thus, a feature of the disclosure includes pharmaceutical compositions or medicaments for the therapeutic or prophylactic treatment of an HIV infection. The use of the compositions disclosed herein in the production of medicament for the therapeutic or prophylactic treatment of HIV is also expressly contemplated. Any of the limitations or formulations disclosed above with respect to compositions are applicable to their use in or as medicaments for the treatment of an HIV infection.

[0178] Another aspect of the disclosure relates to methods for eliciting an immune response against HIV by administering the compositions described above to an individual. In some embodiment, the individual is a human subject. The composition may comprise any of the nucleic acids described herein encoding any of the synthetic HIV-I /SIV Gag polypeptides described herein. Alternatively, the composition may comprise any of the synthetic HIV-I /SIV Gag polypeptides described herein.

[0179] One dose or multiple doses of the composition can be administered to a subject to elicit an immune response with desired characteristics, including the production of HIV specific antibodies, or the production of functional T cells that react with HIV. In certain embodiments, the T cells may be CD8 T cells. The compositions may be administered using any suitable route. For example, in some embodiments, the composition is administered intramuscularly, for example, using a syringe or needleless delivery device. Alternatively, the composition is administered by other routes, such as intravenous, transdermal, intranasal, oral (or via another mucosa).

[0180] In some embodiments, the compositions comprise any of the viral vectors described herein. In some cases, the viral vectors are adenoviral vectors (for example a replication deficient adenoviral vectors). In some embodiments, the adenovirus vector is an adenovirus 5 vector. In other embodiments, the viral vector is an adenovirus 26 vector or and adenovirus 28 vector. A single vector can contain one or more nucleic acid sequence encoding a HIV/SIV Gag polypeptide as described herein. For example, multiple different vectors can be administered to an animal, each of which comprises one nucleic acid sequence which encodes a HIV/SIV Gag polyepeptide as described herein. Alternatively, a single vector can be administered to an animal, which comprises two or more (e.g., 2, 3, 5, 7, or 10 or more) nucleic acid sequences which each encode a HIV/SIV Gag polyepeptide as described herein. In a preferred embodiment, the vector comprises the nucleic acid sequence of SEQ ID NO: 81 and/or SEQ ID NO: 84.

[0181] In some embodiments, one or more doses of a "primer" composition can be administered to a subject, followed by administration of one or more doses of a "booster" composition including viral particles comprising any of the viral vectors described above. In some embodiments, the "primer" composition can comprise any of the vectors described above as naked DNA. In certain embodiments, the "booster" composition can comprise adenoviral particles comprising any of the adenovirus vectors described above.

[0182] In some embodiments, the compositions for inducing an immune response comprise a pharmaceutically acceptable carrier or excipient. The pharmaceutically acceptable carriers or excipients of use are conventional. Remington 's Pharmaceutical Sciences, by E. W. Martin, Mack Publishing Co., Easton, PA, 15th Edition (1975), describes compositions and formulations suitable for pharmaceutical delivery of the polypeptides and polynucleotides disclosed herein. [0183] In general, the nature of the carrier will depend on the particular mode of administration being employed. For instance, parenteral formulations usually comprise injectable fluids that include pharmaceutically and physiologically acceptable fluids such as water, physiological saline, balanced salt solutions, aqueous dextrose, glycerol or the like as a vehicle. For solid compositions (for example, powder, pill, tablet, or capsule forms), conventional non-toxic solid carriers can include, for example, pharmaceutical grades of mannitol, lactose, starch or magnesium stearate. In addition to biologically neutral carriers, pharmaceutical compositions to be administered can contain minor amounts of non-toxic auxiliary substances, such as wetting or emulsifying agents, preservatives, and pH buffering agents and the like, for example sodium acetate or sorbitan monolaurate. [0184] The synthetic HIV-I /SIV Gag polypeptides may be used, for example, as pharmaceutical compositions (medicaments) for use in therapeutic, for example, prophylactic regimens (e.g., vaccines) and administered to subjects (e.g., human subjects) to elicit an immune response against HIV-I. For example, the compositions described herein can be administered to a human (or non-human) subject prior to infection with HIV to inhibit infection by or replication of the virus. In some embodiments, the pharmaceutical compositions described above can be administered to a subject to elicit a protective immune response against HIV. To elicit an immune response, a therapeutically effective (e.g., immunologically effective) amount of the nucleic acid constructs are administered to a subject, such as a human (or non-human) subject. [0185] A "therapeutically effective amount" is a quantity of a chemical composition (such as a nucleic acid construct, vector, or polypeptide) used to achieve a desired effect in a subject being treated. For instance, this can be the amount necessary to express an adequate amount of antigen to elicit an antibody or T cell response, or to inhibit or prevent infection by or replication of the virus, or to prevent, lessen or ameliorate symptoms caused by infection with the virus. When administered to a subject, a dosage will generally be used that will achieve target tissue or systemic concentrations that are empirically determined to achieve an in vitro effect. Such dosages can be determined without undue experimentation by those of ordinary skill in the art. Exemplary dosages are described in detail in the Examples.

[0186] A pharmaceutical composition including a nucleic acid encoding any of the synthetic HIV-I /SIV Gag polypeptides described herein or the synthetic HIV-I /SIV Gag polypeptide itself can be administered by any means known to one of skill in the art (see Banga, A., "Parenteral Controlled Delivery of Therapeutic Peptides and Proteins," in Therapeutic Peptides and Proteins, Technomic Publishing Co., Inc., Lancaster, PA, 1995; DNA Vaccines: Methods and Protocols (Methods in Molecular Medicine) by Douglas B. Lowrie and Robert G. Whalen (Eds.), Humana Press, 2000) such as by intramuscular, subcutaneous, or intravenous injection, but even oral, nasal, or anal administration is contemplated. In one embodiment, administration is by subcutaneous or intramuscular injection. Actual methods for preparing administrable compositions will be known or apparent to those skilled in the art and are described in more detail in such publications as Remingtons Pharmaceutical Sciences, 19^l Ed., Mack Publishing Company, Easton, Pennsylvania, 1995.

[0187] Suitable formulations for the compositions comprising any of the synthetic HIV- 1/SIV Gag polypeptides described herein or a nucleic acid encoding any of the synthetic HIV- 1/SIV Gag polypeptides described herein, for example, the primer or booster compositions disclosed herein, include aqueous and non-aqueous solutions, isotonic sterile solutions, which can contain anti-oxidants, buffers, and bacteriostats, and aqueous and non-aqueous sterile suspensions that can include suspending agents, solubilizers, thickening agents, stabilizers, and preservatives. The formulations can be presented in unit-dose or multi-dose sealed containers, such as ampules and vials, and can be stored in a freeze-dried (lyophilized) condition requiring only the addition of the sterile liquid carrier, for example, water, immediately prior to use. Extemporaneous solutions and suspensions can be prepared from sterile powders, granules, and tablets. Preferably, the carrier is a buffered saline solution. More preferably, the composition for use in the inventive method is formulated to protect the nucleic acid constructs from damage prior to administration. For example, the composition can be formulated to reduce loss of the adenoviral vectors on devices used to prepare, store, or administer the expression vector, such as glassware, syringes, or needles. The compositions can be formulated to decrease the light sensitivity and/or temperature sensitivity of the components. To this end, the composition preferably comprises a pharmaceutically acceptable liquid carrier, such as, for example, those described above, and a stabilizing agent selected from the group consisting of polysorbate 80, L- arginine, polyvinylpyrrolidone, trehalose, and combinations thereof. Use of such an adenoviral vector composition will extend the shelf life of the vector, facilitate administration, and increase the efficiency of the inventive method. Formulations for adenoviral vector-containing compositions are further described in, for example, U.S. Patent 6,225,289, 6,514,943, U.S. Patent Application Publication No. 2003/0153065 Al, and International Patent Application Publication WO 00/34444, the disclosures of which are incorporated herein by reference in their entireties. An adenoviral vector composition also can be formulated to enhance transduction efficiency. In addition, one of ordinary skill in the art will appreciate that the composition can comprise other therapeutic or biologically-active agents. For example, factors that control inflammation, such as ibuprofen or steroids, can be part of the adenoviral vector composition to reduce swelling and inflammation associated with in vivo administration of the adenoviral vectors. As discussed herein, immune system stimulators can be administered to enhance any immune response to the antigens. Antibiotics, i.e., microbicides and fungicides, can be present to treat existing infection and/or reduce the risk of future infection, such as infection associated with gene transfer procedures.

[0188] The compositions can be administered for therapeutic treatments. In therapeutic applications, a therapeutically effective amount of the composition is administered to a subject prior to or following exposure to or infection by HIV. When administered prior to exposure, the therapeutic application can be referred to as a prophylactic administration (e.g., a vaccine). Single or multiple administrations of the compositions are administered depending on the dosage and frequency as required and tolerated by the subject. In one embodiment, the dosage is administered once as a bolus, but in another embodiment can be applied periodically until a therapeutic result, such as a protective immune response, is achieved. Generally, the dose is sufficient to treat or ameliorate symptoms or signs of disease without producing unacceptable toxicity to the subject. Systemic or local administration can be utilized.

[0189] Controlled release parenteral formulations can be made as implants, oily injections, or as particulate systems. Particulate systems include microspheres, microparticles, microcapsules, nanocapsules, nanospheres, and nanoparticles. Particles, microspheres, and microcapsules smaller than about 1 μm are generally referred to as nanoparticles, nanospheres, and nanocapsules, respectively. Capillaries have a diameter of approximately 5 μm so that only nanoparticles are administered intravenously. Microparticles are typically around 100 μm in diameter and are administered subcutaneously or intramuscularly (see, Kreuter, Colloidal Drug Delivery Systems, J. Kreuter, ed., Marcel Dekker, Inc., New York, NY, pp. 219-342, 1994; Tice & Tabibi, Treatise on Controlled Drug Delivery, A. Kydonieus, ed., Marcel Dekker, Inc. New York, NY, pp. 315-339, 1992).

[0190] In certain embodiments, the pharmaceutical composition includes an adjuvant. An adjuvant can be a suspension of minerals, such as alum, aluminum hydroxide, aluminum phosphate, on which antigen is adsorbed; or water-in-oil emulsion in which antigen solution is emulsified in oil (MF-59, Freund's incomplete adjuvant), sometimes with the inclusion of killed mycobacteria (Freund's complete adjuvant) to further enhance antigenicity (inhibits degradation of antigen and/or causes influx of macrophages). In the context of nucleic acid vaccines, naturally-occurring or synthetic immunostimulatory compositions that bind to and stimulate receptors involved in innate immunity can be administered along with nucleic acid constructs encoding any of the synthetic HIV-I /SIV Gag polypeptides described herein. For example, agents that stimulate certain Toll-like receptors (such as TLR7, TLR8 and TLR9) can be administered in combination with the nucleic acid constructs encoding HIV antigenic polypeptides. In some embodiments, the nucleic acid construct is administered in combination with immunostimulatory CpG oligonucleotides.

[0191] In some embodiments, nucleic acid constructs encoding any of the synthetic HIV- 1/SIV Gag polypeptides described herein can be introduced in vivo as naked DNA plasmids. DNA vectors can be introduced into the desired host cells by methods known in the art, including but not limited to transfection, electroporation (e.g., transcutaneous electroporation), microinjection, transduction, cell fusion, DEAE dextran, calcium phosphate precipitation, use of a gene gun, or use of a DNA vector transporter (See e.g., Wu et al. J. Biol. Chem., 267:963-967, 1992; Wu and Wu J. Biol. Chem., 263:14621-14624, 1988; and Williams et al. Proc. Natl. Acad. Sci. USA 88:2726-2730, 1991). As described in detail in the Examples, a needleless delivery device, such as a BIOJECTOR® needleless injection device can be utilized to introduce the therapeutic nucleic acid constructs in vivo. Receptor-mediated DNA delivery approaches can also be used (Curiel et al. Hum. Gene Ther., 3:147-154, 1992; and Wu and Wu, J. Biol. Chem., 262:4429-4432, 1987). Methods for formulating and administering naked DNA to mammalian muscle tissue are disclosed in U.S. Pat. Nos. 5,580,859 and 5,589,466, both of which are herein incorporated by reference in their entireties. Other molecules are also useful for facilitating transfection of a nucleic acid in vivo, such as a cationic oligopeptide (e.g., International Patent Application Publication WO 95/21931), peptides derived from DNA binding proteins (e.g., International Patent Application Publication WO 96/25508), or a cationic polymer (e.g., WO95/21931), the disclosures of which are incorporated herein by reference in their entireties. [0192] Alternatively, electroporation can be utilized conveniently to introduce nucleic acid constructs encoding any of the synthetic HIV-I /SIV Gag polypeptides described herein into cells. Electroporation is well known by those of ordinary skill in the art (see, for example: Lohr et al. Cancer Res. 61:3281-3284, 2001 ; Nakano et al. Hum Gene Ther. 12:1289-1297, 2001; Kim et al. Gene Ther. 10:1216-1224, 2003; Dean et al. Gene Ther. 10:1608-1615, 2003; and Young et al. Gene Ther 10:1465-1470, 2003). For example, in electroporation, a high concentration of vector DNA is added to a suspension of host cell (such as isolated autologous peripheral blood or bone marrow cells) and the mixture shocked with an electrical field. Transcutaneous electroporation can be utilized in animals and humans to introduce heterologous nucleic acids into cells of solid tissues (such as muscle) in vivo. Typically, the nucleic acid constructs are introduced into tissues in vivo by introducing a solution containing the DNA into a target tissue, for example, using a needle or trochar in conjunction with electrodes for delivering one or more electrical pulses. For example, a series of electrical pulses can be utilized to optimize transfection, for example, between 3 and ten pulses of 100V and 50 msec. In some cases, multiple sessions or administrations are performed.

[0193] Another well known method that can be used to introduce nucleic acid constructs encoding any of the synthetic HIV-I /SIV Gag polypeptides described herein into host cells is particle bombardment (also know as biolistic transformation). Biolistic transformation is commonly accomplished in one of several ways. One common method involves propelling inert or biologically active particles at cells. This technique is disclosed in, e.g., U.S. Pat. Nos. 4,945,050, 5,036,006; and 5,100,792, all to Sanford et al., the disclosures of which are hereby incorporated by reference in their entireties. Generally, this procedure involves propelling inert or biologically active particles at the cells under conditions effective to penetrate the outer surface of the cell and to be incorporated within the interior thereof. When inert particles are utilized, the plasmid can be introduced into the cell by coating the particles with the plasmid containing the exogenous DNA. Alternatively, the target cell can be surrounded by the plasmid so that the plasmid is carried into the cell by the wake of the particle. [0194] Alternatively, the vector can be introduced in vivo by lipofection. For the past decade, there has been increasing use of liposomes for encapsulation and transfection of nucleic acids in vitro. Synthetic cationic lipids designed to limit the difficulties and dangers encountered with liposome mediated transfection can be used to prepare liposomes for in vivo transfection of a gene encoding a marker (Feigner et. al. Proc. Natl. Acad. ScL USA 84:7413-7417, 1987; Mackey, et al. Proc. Natl. Acad. ScL USA 85:8027-8031, 1988; Ulmer et al. Science 259:1745- 1748, 1993, the disclosures of which are incorporated herein by reference in their entireties). The use of cationic lipids can promote encapsulation of negatively charged nucleic acids, and also promote fusion with negatively charged cell membranes (Feigner and Ringold Science 337:387-388, 1989). Particularly useful lipid compounds and compositions for transfer of nucleic acids are described in International Patent Application Publications WO 95/18863 and WO 96/17823, and in U.S. Pat. No. 5,459,127, the disclosures of which are incorporated herein by reference in their entireties.

[0195] As discussed above, in some embodiments, the nucleic acid constructs encoding any of the synthetic HIV-I /SIV Gag polypeptides described herein are viral vectors. Methods for constructing and using viral vectors are known in the art (See e.g., Miller and Rosman, BioTech, 7:980-990, 1992). Preferably, the viral vectors are replication defective, that is, they are unable to replicate autonomously in the target cell. In general, the genome of the replication defective viral vectors that are used within the scope of the present disclosure lack at least one region that is necessary for the replication of the virus in the infected cell. These regions can either be eliminated (in whole or in part), or be rendered non-functional by any technique known to a person skilled in the art. These techniques include the total removal, substitution (by other sequences, in particular by the inserted nucleic acid), partial deletion or addition of one or more bases to an essential (for replication) region. Such techniques can be performed in vitro (for example, on the isolated DNA).

[0196] In some cases, the replication defective virus retains the sequences of its genome that are necessary for encapsidating the viral particles. DNA viral vectors commonly include attenuated or defective DNA viruses, including, but not limited to, herpes simplex virus (HSV), papillomavirus, Epstein Barr virus (EBV), adenovirus, adeno-associated virus (AAV), Moloney leukemia virus (MLV) and human immunodeficiency virus (HIV) and the like. Defective viruses, that entirely or almost entirely lack viral genes, are preferred, as defective virus is not infective after introduction into a cell. Use of defective viral vectors allows for administration to cells in a specific, localized area, without concern that the vector can infect other cells. Thus, a specific tissue can be specifically targeted. Examples of particular vectors include, but are not limited to, a defective herpes virus 1 (HSVl) vector (Kaplitt et al. MoI. Cell. Neurosci., 2:320- 330, 1991), defective herpes virus vector lacking a glycoprotein L gene (See for example, Patent Publication RD 371005 A), or other defective herpes virus vectors (See e.g., WO 94/21807; and WO 92/05263, the disclosures of which are incorporated herein by reference in their entireties); an attenuated adenovirus vector, such as the vector described by Stratford-Perricaudet et al. (J Clin. Invest., 90:626-630 1992; La Salle et al., Science 259:988-990, 1993); and a defective adeno-associated virus vector (Samulski et al., J. Virol., 61 :3096-3101, 1987; Samulski et al., J Virol., 63:3822-3828, 1989; and Lebkowski et al., MoI. Cell. Biol., 8:3988-3996, 1988, , the disclosures of which are incorporated herein by reference in their entireties). [0197] As discussed above, in some embodiments, the vectors encoding any of the synthetic HIV-I /SIV Gag polypeptides described herein may be adenovirus vectors. Adenoviruses are eukaryotic DNA viruses that can be modified to efficiently deliver a nucleic acid of the disclosure to a variety of cell types. Various serotypes of adenovirus exist. Of these serotypes, preference is given, within the scope of the present disclosure, to type 2, type 5, type 26, and type 28 human adenoviruses (i.e., Ad2, Ad5, Ad26, or Ad28), or adenoviruses of animal origin (See e.g., International Patent Application Publications WO 94/26914 and WO 2006/020071, the disclosures of which are incorporated herein by reference in their entireties). Those adenoviruses of animal origin that can be used within the scope of the present disclosure include adenoviruses of canine, bovine, murine (e.g., Mavl, Beard et al. Virol., 75-81, 1990), ovine, porcine, avian, and simian (e.g., SAV) origin. In some embodiments, the adenovirus of animal origin is a canine adenovirus, such as a CAV2 adenovirus (e.g. Manhattan or A26/61 strain (ATCC VR-800)). [0198] The replication defective adenoviral vectors may include the ITRs, an encapsidation sequence and the polynucleotide sequence of interest. In some embodiments, at least the El region of the adenoviral vector is non- functional. The deletion in the El region preferably extends from nucleotides 455 to 3329 in the sequence of the Ad5 adenovirus (PvwII-i?g7II fragment) or 382 to 3446 (Hinfll-Sau3A fragment). Other regions can also be modified, in particular the E3 region (e.g., International Patent Application Publication WO 95/02697), the E2 region (e.g., International Patent Application Publication WO 94/28938), the E4 region (e.g., International Patent Application Publications WO 94/28152, WO 94/12649 and WO 95/02697), or in any of the late genes L1-L5.

[0199] In other embodiments, the adenoviral vector has a deletion in the El region (Ad 1.0). Examples of El-deleted adenoviruses are disclosed in EP 185,573, the contents of which are incorporated herein by reference. In another embodiment, the adenoviral vector has a deletion in the El and E4 regions (Ad 3.0). Examples of El/E4-deleted adenoviruses are disclosed in International Patent Application Publications WO 95/02697 and WO 96/22378. [0200] The replication defective recombinant adenoviruses can be prepared by any technique known to the person skilled in the art (See e.g., Levrero et al. Gene 101:195, 1991; EP 185 573; and Graham EMBO J., 3:2917, 1984, the disclosures of which are incorporated herein by reference in their entireties). In particular, they can be prepared by homologous recombination between an adenovirus and a plasmid, which includes, inter alia, the DNA sequence of interest. The homologous recombination is accomplished following co-transfection of the adenovirus and plasmid into an appropriate cell line. The cell line that is employed should preferably (i) be transformable by the elements to be used, and (ii) contain the sequences that are able to complement the part of the genome of the replication defective adenovirus, preferably in integrated form in order to avoid the risks of recombination. Examples of cell lines that can be used are the human embryonic kidney cell line 293 (Graham et al. J. Gen. Virol. 36:59, 1977), which contains the left-hand portion of the genome of an Ad5 adenovirus (12%) integrated into its genome, and cell lines that are able to complement the El and E4 functions, as described in International Patent Application Publications WO 94/26914 and WO 95/02697. Recombinant adenoviruses are recovered and purified using standard molecular biological techniques that are well known to one of ordinary skill in the art. Nucleic acids encoding HIV antigens can also be introduced using other viral vectors, such as retroviral vectors, for example, lentivirus vectors or adenovirus-associated viral (AAV) vectors.

[0201] In one embodiment, a pharmaceutical composition including a nucleic acid construct encoding any of the synthetic HIV-I /SIV Gag polypeptides described herein is introduced into a subject prior to exposure to HIV to elicit a protective immune response. In some embodiments, the nucleic acid construct is a plasmid. [0202] The dose range can be varied according to the physical, metabolic and immunological characteristics of the subject. In some embodiments, a dose of at least about 1 mg of DNA is administered. In some embodiments 12 mg or less of DNA is administered. For example, in some embodiments a single dose can be at least about 2 mg, or at least about 3 mg, or at least about 4 mg of DNA. In some embodiments, a single dose does not exceed about 6 mg, or about 8 mg or about 10 mg of DNA.

[0203] A single dose, or multiple doses separated by a time interval can be administered to elicit an immune response against HIV-I . For example, two doses, or three doses, or four doses, or five doses, or six doses or more can be administered to a subject over a period of several weeks, several months or even several years, to optimize the immune response. [0204] As discussed above, in some embodiments a "prime-boost" regimen may be utilized to administer any of the synthetic HIV-I /SIV Gag polypetides described herein. In such an approach a nucleic acid encoding the synthetic HIV-I /SIV Gag polypeptide is administered as a DNA vaccine prime followed by an adenoviral vector boost. Prime-boost regimens have shown promise in non-human primate models of HIV infection. Such regimens have the potential for raising high levels of immune responses. For example, a "primer" composition including a synthetic HIV-I /SIV Gag polypeptide that is the same as a synthetic HIV-I /SIV Gag polypeptide encoded by an adenoviral vector of an adenoviral vector composition can be administered to a subject. For example, in some embodiments, the primer composition can be administered at least about one week before the administration of the "booster" composition including one or more adenoviral vectors. The nucleic acid "primer" encoding the synthetic HIV-I /SIV Gag polypeptide can be administered as part of a gene transfer vector or as naked DNA. Any gene transfer vector can be employed in the primer composition, including, but not limited to, a plasmid, a retrovirus, an adeno-associated virus, a vaccine virus, a herpesvirus, or an adenovirus. In an exemplary embodiment, the transfer vector is a plasmid.

[0205] Thus, in some embodiments, the nucleic acids encoding any of the synthetic HIV- 1/SIV Gag polypeptides described above can be used to prime an immune response against HIV- 1 , in combination with administration of a composition including an adenovirus vector encoding a synthetic HIV-I /SIV Gag polypeptide. [0206] While the synthetic HIV-I /SIV Gag polypeptide encoded by the nucleic acid sequence of the boost composition often is the same as the synthetic HIV-I /SIV Gag polypeptide encoded by the nucleic acid constructs of the primer composition, in some embodiments it may be appropriate to use a primer composition comprising a nucleic acid sequence encoding a synthetic HIV-I /SIV Gag polypeptide that is different from synthetic HIV-I /SIV Gag polypeptide encoded by the adenoviral vector composition.

[0207] The primer composition is administered to the mammal to prime the immune response to HIV-I . In some embodiments, more than one dose of primer composition can be provided in any suitable timeframe (e.g., at least about 1 week, 2 weeks, 4 weeks, 8 weeks, 12 weeks, 16 weeks, or more prior to boosting). Preferably, the primer composition is administered to the mammal at least three months (e.g., three, six, nine, twelve, or more months) before administration of the booster composition. Most preferably, the primer composition is administered to the mammal at least about six months to about nine months before administration of the booster composition. More than one dose of booster composition can be provided in any suitable timeframe to maintain immunity.

[0208] Any route of administration can be used to deliver the adenoviral vector composition and/or the primer composition to the mammal. Indeed, although more than one route can be used to administer the adenoviral vector composition and/or the primer composition, a particular route can provide a more immediate and more effective reaction than another route. Most commonly, the adenoviral vector composition and/or the primer composition is administered via intramuscular injection. The adenoviral vector composition and/or the primer composition also can be applied or instilled into body cavities, absorbed through the skin (for example, via a transdermal patch), inhaled, ingested, topically applied to tissue, or administered parenterally via, for instance, intravenous, peritoneal, or intraarterial administration. [0209] In some embodiments, the adenoviral primer composition and/or the booster composition can be administered in or on a device that allows controlled or sustained release, such as a sponge, biocompatible meshwork, mechanical reservoir, or mechanical implant. Implants (see, e.g., U.S. Patent 5,443,505), devices (see, e.g., U.S. Patent 4,863,457), such as an implantable device, e.g., a mechanical reservoir or an implant or a device comprised of a polymeric composition, are particularly useful for administration of the composition. The adenoviral vector composition and/or the primer composition also can be administered in the form of sustained-release formulations (see, e.g., U.S. Patent 5,378,475) comprising, for example, gel foam, hyaluronic acid, gelatin, chondroitin sulfate, a polyphosphoester, such as bis- 2-hydroxyethyl-terephthalate (BHET), and/or a polylactic-glycolic acid. [0210] In some embodiments, a booster composition can include a single dose of adenoviral vector comprising at least about 1x10⁵ particles (which also is referred to as particle units) of adenoviral vector. The dose preferably is at least about 1x10⁶ particles (for example, about lxl0⁶-lxl0¹² particles), more preferably at least about IxIO⁷ particles, more preferably at least about IxIO⁸ particles (e.g., about lxl0⁸-lxl0ⁿ particles or about lxl0⁸-lxl0¹² particles), and most preferably at least about IxIO⁹ particles (e.g., about lxl0⁹-lxl0¹⁰ particles or about IxIO⁹- IxIO¹² particles), or even at least about IxIO¹ particles (e.g., about lxl0¹⁰-lxl0¹² particles) of the adenoviral vector. Alternatively, the dose comprises no more than about IxIO¹⁴ particles, preferably no more than about 1x10¹³ particles, even more preferably no more than about 1x10¹² particles, even more preferably no more than about 1x10¹¹ particles, and most preferably no more than about IxIO¹⁰ particles (e.g., no more than about IxIO⁹ particles). In other words, the adenoviral vector composition can comprise a single dose of adenoviral vector comprising, for example, about 1x10⁶ particle units (pu), 2x10⁶ pu, 4x10⁶ pu, 1x10⁷ pu, 2x10⁷ pu, 4x10⁷ pu, IxIO⁸ pu, 2xlO⁸ pu, 4xlO⁸ pu, IxIO⁹ pu, 2xlO⁹ pu, 4xlO⁹ pu, IxIO¹⁰ pu, 2xlO¹⁰ pu, 4xlO¹⁰ pu, IxIO¹¹ pu, 2xlOⁿ pu, 4xlOⁿ pu, IxIO¹² pu, 2xlO¹² pu, or 4xlO¹² pu of adenoviral vector. [0211] The following examples further illustrate the invention but, of course, should not be construed as in any way limiting its scope.

EXAMPLE 1

[0212] This example describes the identification of SIV regions which provide enhanced immunogenicity against HIV-I.

[0213] Regions in SIV which provide enhanced immunogenicity when substituted for natural

HIV-I sequences in chimeric HIV-I /SIV Gag polypeptides (which do not contain a synthetic

HIV-I Gag gene but instead contain a modified chimeric HIV-I Gag gene in which certain sequences from the SIV Gag gene have replaced certain natural HIV-I sequences) were identified. [0214] Specifically, the immunogenicity of modified HIV-Gag polypeptides was assessed by performing ALl 1 tetramer assays. Mice were immunized with DNA vectors encoding chimeric HIV-I Gag proteins. Lymphocytes or PBMCs were obtained from the mice and stained with PE- conjugated D^d/6433 tetramer and then FITC-conjugated anti -mouse CD3 mAb (clone 145-2C11, BD Pharmingen), PerCP-CyS.S-conjugated anti-mouse CD8α mAb (clone 53-6.7, BD Pharmingen), and APC-conjugated anti-mouse CD 19 mAb (clone 6D5, Biolegend). The stained cells were examined by BD LSR-II (BD Pharmingen), and the data were analyzed by FlowJo software (Tree Star Inc.).

[0215] The plasmids encoding chimeric HIV-I Gag/SIV polypeptides utilized in these experiments are depicted in Figures 25-49 and their sequences are provided in the accompanying Sequence Listing as specified in Table 2. The SEQ ID NOs. of the modified Gag polypeptides encoded by these plasmids are also provided in Table 2 (see also Figure 53).

Table 2

[0216] The results are shown in Figures 38-40. As shown in Figure 38, replacing the HIV-I Gag COOH-terminal (179.a.a.) with the corresponding SIV region significantly increased CD8 T lymphocytes (2.42%, day 14 after immunization) vs. HIV-I Gag (0.75%). This increase was larger than that observed in the wild type SIV Gag (1.87%). It will be appreciated that the 179 COOH terminal amino acids of a synthetic HIV-I Gag polypeptide may be replaced with the corresponding region from the SIV Gag polypeptide.

[0217] In addition, as shown in Figure 39, replacing the CypA binding site (N7) or Helix 5, 6 (NlO) also markedly enhanced the modified HIV-I Gag polypeptide's immunogenicity. Furthermore, as shown in Figure 40, the region in HIV-I Gag between amino acids 358 to 418 (construct N5) and the region between amino acids 419 to 462 (construct N6) also affected immunogenicity. It will be appreciated that the CypA binding site and/ or Helix 5, 6 of a synthetic HIV-I Gag polypeptide may also be replaced with the corresponding region from the SIV Gag polypeptide. EXAMPLE 2

[0218] This example describes experiments which demonstrate the immunogenicity of the chimeric N5 and N6 HIWSIV Gag polypeptides generated in Example 1. [0219] Two chimeric HIV/SIV Gag immunogens generated in Example 1, i.e., Gag N5 and Gag N6, were analyzed in comparison to HIV-I Gag by ELISPOT using potential T-cell epitope (PTE) peptides designed to react with the most abundant T-cell targets of CTL recognition. Mice were immunized with DNA/rAd5 encoding these chimeras, and gamma interferon (IFN-γ) enzyme-linked immunospot (ELISPOT) assays were performed. 320 HIV-I Gag PTE 15-mers were grouped into 32 pools (10 peptides in each pool based on their frequency order), and spot- forming cells (SFC) per 10⁶ cells were determined. Both N5 and N6 chimeras elicited similar ELISPOT responses against pools 1, 3, and 6 to HIV-I Gag, but demonstrated higher reactivity to pool 3 than wild type HIV-I Gag. In addition, Gag N5 elicited detectable T cell responses to pools 4, 18, 22 and 28 while Gag N6 only responded to pool 21. Thus, the N5 chimeric Gag protein showed responsiveness to a larger number of subdominant epitopes compared to N6 or wild type Gag in this inbred mouse strain.

[0220] The N5 chimeric HIV/SIV Gag construct was compared to wild-type HIV Gag by intracellular cytokine staining (ICS) after immunization with DNA/rAd5 vectors encoding these genes. Briefly, B6D2F1 (H2 Haplotype b/d) mice were injected three times with DNA followed by rAd5 at two week intervals. To map the epitope-specific response, 127 individual 15-mer HIV Gag peptides were analyzed. Using DNA/rAd5 immunization, the N5 chimeric Gag elicited similar magnitude and breadth of T cell responses to CD4 and CD8 epitopes compared to wild-type Gag.

[0221] This example demonstrates that the N5 HIV/SIV Gag chimeric polypeptide is immunogenic in mice.

EXAMPLE 3

[0222] This example describes the generation of mosaic HIV-I Gag polypeptides. [0223] Gag polypeptides from all known M Group HIV-I Gag sequences were input into the genetic algorithm described in Fischer et al., Nature Medicine, Vol. 13, Number 1, January 2007, pages 100-106 and International Patent Application Publication WO 2007/024941. [0224] Because the N5 chimera described above appeared to have no effect on the magnitude and breadth of the response on wide type Gag, it was unclear whether it might have effects on mosaic Gag proteins, which are generated informatically to include the most common T-cell epitopes in diverse naturally-occurring isolates (see, e.g., Fischer et al., Nat. Med., 13: 100-106 (2007), Gao et al., Science, 299: 1517-1518 (2003), and Gaschen et al., Science, 296: 2354-2360 (2002)). Thus, the N5 modification was introduced into a previously described mosaic Gag immunogen, and the magnitude and effect of this sequence on epitope-specific T-cell responses was determined. A set of two mosaic HIV Gag genes (mosaic Gagl and mosaic Gag2) were generated using a similar informatic approach as for mosaic HIV Env (Kong et al., J. Virol., 83: 2201-2215 (2009)). The N5 chimeras of these two mosaic HIV Gag genes (mosaic Gagl N5 and mosaic Gag2 N5) were then synthesized.

[0225] Vectors encoding the resulting mosaic HIV-I Gag polypeptides described above were constructed by ligating synthetic oligonucleotides encoding fragments of the mosaic HIV-I polypeptides together to generate a nucleic acid encoding the full length mosaic HIV-I Gag polypeptide.

EXAMPLE 4

[0226] This example describes the construction of vectors encoding synthetic HIV-I /SIV Gag polypeptides

[0227] Vectors encoding the mosaic HIV-I Gag polypeptides described above were constructed by replacing portions of the nucleic acid encoding the HIV-I Gag mosaic with sequences from the SIV Gag protein. These vectors are depicted in Figures 2-5 and the sequences of these vectors are provided as SEQ ID NOs: 81, 84, 87 and 90. These vectors include SEQ ID NOs: 83, 86, 89 and 92 which encode the synthetic HIV-1/SIV Gag polypeptides of SEQ ID NOs:: 82, 85, 88 and 91. A summary of the structures of these vectors is provided in Table 3. Table 3

EXAMPLE 5

[0228] This example describes immunogenicity assays for mosaic HIV-I /SIV Gag polypeptides.

[0229] Groups of Balb/c mice (N=4/group) were injected with the vectors listed below:

1. VRC B Gag (WT)-VRC4401, which is described in International Patent Application Publication WO 2006/020071.

2. VRC B Gag (chimeric N5H) -CMVR HIV gag new 5h (SEQ ID NO: 77)

3. VRC B Gag (chimeric N6H)- CMVR HIV gag new 6h (SEQ ID NO: 79)

4. 2-valent synthetic Gag (WT)-VRC4700 and VRC4704

5. 2-valent synthetic Gag (chimeric N5H)- (VRC4701 and VRC4705)

6. 2-valent synthetic Gag (chimeric N6H) - (CMVR Mosaic HIV-gagl-SIV-gag (420-457) and CMVR Mosaic HIV-gag 2-SIV-gag, SEQ ID NOs; 87 and 90)

[0230] Mice were injected with 50 μg of DNA one time followed by 10⁹ viral particles of a matching adenoviral vector four weeks after the DNA injection. ELISPOT analysis was conducted at eight weeks after the initial DNA injection. Mice were sacrificed and analyses were carried out to evaluate and compare immune responses.

[0231] The ELISPOT method was initially used to assess the magnitude and breadth of the immune responses using subpools of 10 HIV-I Gag PTE (potential T cell epitopes) peptides (32 subpools in total). The results are shown in Figure 6A-F. Enhanced reactivity and increased number of responsive epitopes were observed in the chimeric constructs when compared to the parental constructs (VRC B Gag WT vs. VRC B Gag N5H; synthetic Gag WT vs. synthetic Gag N5H). In addition, as illustrated in Figure 7, synthetic HIV-I /SIV Gag constructs generated an immune response against a larger number of epitopes than non-synthetic HIV-I /SIV Gag constructs.

EXAMPLE 6

[0232] This example describes the T cell responses elicited by HIV-I clade B Gag and mosaic HIV-I Gag immunogens, as determined by ELISPOT analysis using HIV Gag PTE peptides in B6C57 mice. [0233] B6C57 mice were injected once with 50μg DNA followed by a boost four weeks later with 1x10⁹ particles of adenoviral vectors expressing the same protein. The DNA and adenoviral vectors encoded wild type HIV Gag, Clade B (Figure 8A, B Gag (WT)); and wild type informatic mosaic HIV Gag (Figure 8B, mosaic Gag (WT)).

[0234] Groups of four mice were injected intramuscularly with DNA followed by adenoviral vector boosting. Splenocytes from the mice were isolated and gamma interferon (IFN-I) enzyme-linked immunospot (ELISPOT) assays were performed on the individual samples four weeks after the adenoviral vector immunization. 320 HIV Gag PTE 15-mers were grouped into 32 pools (10 peptides in each pool) for this assay, as indicated on the x-axis (Gag PTE pools). The numbers of spot- forming cells (SFC) per 10⁶ cells are shown in Figure 8A and 8B. The minimal threshold response was determined to be four times the medium background values (25 SFC per 10⁶ cells) as indicated by the dashed line. Solid bars show the mean values of the ELISPOT responses in the four mice (error bars indicate the standard deviation).

EXAMPLE 7

[0235] This example describes ELISPOT analysis of T cell responses elicited by mosaic Gag as compared to T cell responses elicited by chimeric HIV/SIV mosaic Gag measured with PTE peptide subpools.

[0236] B6D2F1/J mice were injected once with 50μg DNA followed by a boost six weeks later with 1x10⁹ particles of an adenoviral vector expressing the same protein at four week intervals. The DNA and adenoviral vectors each encoded the following proteins: wild type informatic mosaic HIV Gag (Mosaic Gag (WT)); N5H modified informatic mosaic HIV Gag (Mosaic Gag (N5H)) containing amino acids 359-412 of the SIV Gag polypeptide (VRC4701 and VRC4705) and N6H modified informatic mosaic HIV Gag (Mosaic Gag(N6H)) containing amino acids 420-457 of the SIV Gag polypeptide(CMVR Mosaic HIV-gagl-SIV-gag (420-457) and CMVR Mosaic HIV-gag 2-SIV-gag). Briefly, groups of four mice were injected intramuscularly with DNA followed by adenoviral vector boosting. Splenocytes from the mice were isolated and gamma interferon (IFN-I) enzyme-linked immunospot (ELISPOT) assays were performed on the individual samples four weeks after adenoviral immunization. 320 HIV Gag PTE 15-mers were grouped into 32 pools (10 peptides in each pool) for this assay, as indicated on the x-axis (Gag PTE pools). The numbers of spot-forming cells (SFC) per 10⁶ cells are shown in Figures 9A-C. The minimal threshold response was determined to be four times the medium background values (25 SFC per 10⁶ cells) as indicated in the Figure. Solid bars show the mean values of the ELISPOT responses in the four mice (error bars indicate the standard deviation). The Mosaic Gag (N5H) group showed statistically significant ELISPOT responses to Gag PTE pool 5 and pool 8 (P value 0.015 and 0.029, respectively) compared to the control group. The significance of the responses was calculated using the Student's t test (tails = 1, type = 2) as indicated by the P value.

EXAMPLE 8

[0237] This example describes the characterization of CD4 and CD8 responses elicited by mosaic HIV-I Gag as compared to chimeric HIV/SIV mosaic Gag immunogens determined using HIV Gag PTE peptides in B6D2F1/J mice.

[0238] The T cell response to PTE peptides provided by synthetic HIV-I /SIV Gag relative to that provided by synthetic HIV-I Gag was evaluated. For immunization, B6D2F1/J mice were injected with 20μg DNA/injection three times at two week interval followed by one boost with IxIO⁹ particles of an adenoviral vector expressing the same protein at the final two weeks interval. The DNA and adenoviral vectors encoded the following antigens: wild type mosaic HIV Gag (Mosaic Gag(WT)); N5H modified informatic mosaic HIV Gag containing amino acids 359-412 of the SIV Gag polypeptide (Mosaic Gag (N5H)-VRC4701 and VRC4705); N6H modified informatic mosaic HIV Gag containing amino acids 420-457 of the SIV Gag polypeptide (CMVR Mosaic HIV-gagl-SIV-gag (420-457) and CMVR Mosaic HIV-gag 2-SIV- gag). (Mosaic Gag (N6H)); and empty vectors as controls. The positions of N5H and N6H, represent regions that were substituted with SIV sequences. Briefly, groups of 10 mice were injected intramuscularly with DNA followed by adenoviral vector boosting. Splenocytes from three mice per group were isolated and combined for intracellular cytokine staining (ICS) two weeks after the adenoviral vector immunization to measure T cell responses. Another three mice per group were sacrificed to repeat the analysis. For ICS stimulation, sixty 15-mer HIV Gag PTE (potential T cell epitopes) single peptides, which were previously shown to be ELISPOT positive after stimulation with pools of 10 15-mer HIV Gag PTE peptides, were positioned as shown in the HIV gag protein diagrams at the bottom of each panel.

[0239] T cell responses to PTE peptides after DNA/rAd immunization with the two mosaic Gag vs. HIV/SIV chimeric mosaic Gag inserts were determined and the results are depicted in Figure 1OA and B. Figure 1OA shows the response in CD4 cells and Figure 1OB shows the response in CD8 cells. The minimal threshold response is indicated by the dashed line. The positive IFN-γ responses and the positive TNF-α responses are indicated as described in Figure 10, while black bars show the level of the negative response that is below the threshold. The positions and the PTE sequences of the CD4 and CD 8 positive epitopes in the Gag protein (HXB2 sequence is used as a reference) are indicated in Figure 10. The positive dominant and subdominant 15-mer HIV Gag PTE sequences and their frequency (value in parentheses) are indicated at their relative position in the Gag protein. The frequencies of the 15-mer peptides are calculated as the average frequency of the 7 PTEs in the HIV sequence database (which includes "subtypes" A, B, C and others). All data are the mean values of the responses from the two experiments.

[0240] In a separate experiment, 320 individual peptides were used for ICS analysis. Immunization with DNA/rAd5 expression vectors elicited similar CD4 and CD8 responses. The CD4 responses elicited by the mosaic Gag and N5H-modified mosaic Gag vectors were similar. The peptide 57-298 was the common dominant CD4 epitope and six other weak subdominant epitopes were found. N5H-modified mosaic Gag elicited one additional CD4 epitope with a significant response which was not found in the wild type Gag, at amino acid position 277 in Gag PTE #81. In contrast, the CD8 responses elicited by the mosaic Gag and N5H-modified mosaic Gag vectors were similar, with only one common CD8 epitope at amino acid position 194 of Gag PTE #24. In addition, the N5H-modifϊed mosaic Gag elicited two additional epitopes not found in the wild type Gag: at amino acid position 154 of Gag PTE#75 and at amino acid position 398 of Gag PTE #69. TNF-α response analysis confirmed the results of the IFN-γ response analysis.

[0241] This results of this example suggest that the N5H modification of HIV mosaic Gag proteins elicits both CD4 and CD8 T cell responses to additional epitopes as compared to the wild type mosaic Gag in B6D2F1 mice after gene-based vaccination. EXAMPLE 9

[0242] This example demonstrates increased subdominant CD8 responses to PTE peptides elicited by mosaic Gag (N5H) containing amino acids 359-412 of the SIV Gag polypeptide as compared to HIV Gag in immunized B6D2F1/J mice.

[0243] Intracellular cytokine staining (ICS) of CD8 T cell responses to three subdominant HIV Gag 15mer PTE peptides are shown in Figure 1 IA-C. The three 15-mer PTE peptides sequences and their positions (relative to HXB2 positions) are indicated in Figures 1 IA-C. Solid bars show the average IFN-γ responses and open bars show TNF-α responses from two experiments (error bars indicate standard deviation). Only the mosaic Gag N5H (VRC4701 and VRC4705) group elicited statistically significant CD8 responses compared to the control groups. The significance of the cellular responses was calculated using the Student's / test (tails = 1, type = 2) as indicated by the P value.

[0244] For immunizations, B6D2F1/J mice were injected with DN A/adeno viral vectors encoding: wild type informatic mosaic HIV Gag (Mosaic Gag (WT)); N5H modified informatic mosaic HIV Gag (Mosaic Gag (N5H) containing amino acids 359-412 of the SIV Gag polypeptide (VRC4701 and VRC4705); N6H modified informatic mosaic HIV Gag (Mosaic Gag (N6H)) containing amino acids 420-457 of the SIV Gag polypeptide (CMVR Mosaic HIV-gagl- SIV-gag (420-457) and CMVR Mosaic HIV-gag 2-SIV-gag); and empty vectors as Control. Immunizations and analyses were performed as described herein.

EXAMPLE 10

[0245] This example demonstrates the immunogenicity of the N5H-modified mosaic Gag in mice.

[0246] The wild type mosaic Gag and the N5H-modified mosaic Gag (mosaic Gag(N5)) constructs were further compared by ICS after only one rAd immunization. The CD4 responses elicited by the mosaic Gag and N5-modified mosaic Gag vectors were limited. The peptide 57- 298 was the common CD4 epitope. Only N5H-modified mosaic Gag elicited one additional CD4 epitope with a significant high response, which was found with very weak response in the wild type mosaic Gag, at amino acid position 259 in Gag PTE #7. However, this 7-259 peptide was also a common subdominant epitope in the DNA/rAd immunization of wild type Gag and the mosaic Gag N5H. These results suggest that a single rAd immunization may not be strong enough to elicit a positive response to this common CD4 epitope. In contrast, the CD8 responses elicited one common dominant epitope by the mosaic Gag and N5H-modifϊed mosaic Gag vectors at amino acid position 194 of Gag PTE #51 at the same position as found in the DNA/rAd immunization. However, the N5H-modified mosaic Gag elicited two additional epitopes not found in the wild type: at amino acid position 348 of Gag PTE#45 and at amino acid position 354 of Gag PTE #76. TNF-α response analysis confirmed the results of the IFN- γ response analysis.

[0247] This example demonstrates that the N5H modification of HIV mosaic Gag proteins elicits T cell responses to various additional epitopes as compared to the wild type mosaic Gag in B6D2F1 mice after different vaccination regimens.

EXAMPLE 11

[0248] This example describes the expression of nucleic acid sequences encoding synthetic HIV-I /SIV Gag polypeptides.

[0249] The expression of any of the synthetic HIV-I /SIV Gag polypeptides described herein may be assessed using the methodology that was employed to assess the expression of chimeric HIV-I /SIV constructs (which do not contain a synthetic HIV-I Gag gene but instead contain a modified chimeric HIV-I Gag gene in which certain sequences from the SIV Gag gene have replaced certain natural HIV-I sequences). The structures of the chimeric vectors are described in Table 2 above. The following plasmids were transfected into HEK293 cells: #1, #2, #4, #14, #8, N2, N5, N6, N7, and NlO. Expression of the modified chimeric HIV-I Gag polypeptides was confirmed by performing a Western Blot using HIV-I positive human serum. The results are shown in Figure 12.

EXAMPLE 12

[0250] This example describes determining the immunogenicity of synthetic HIV-I /SIV Gag polypeptides using ELISPOT assays. [0251] The following methodology may be used to assess the immunogenicity of any of the synthetic HIV-I /SIV Gag polypeptides described herein. Methodology to detect T cell responsiveness to HIV peptides via ELISPOT is based upon modification of the method described in Helms et al., J. Immunol, 164(1): 3723-32 (2000). Analysis is performed using a commercially available ELISPOT Kit (BD Biosciences). PBMC are stimulated with the modified HIV-I Gag polypeptides overnight at 37⁰C in replicate wells at an optimized density of 2 x 10⁵ cell/well for all stimulations other than SEB, which is conducted at 5 x 10⁴ cell/well. Following incubation, cells are lysed, wells are washed and incubated for 2 hours at room temperature with the optimized dilution of biotinylated cytokine detection antibodies. Subsequently the plate is incubated with the optimized dilution of Avidin-HRP solution for 1 hour at room temperature, followed by 20 minute incubation with the AEC (3-amino-9- ethylcarbazole) substrate solution. Extensive washing occurs between the aforementioned steps and the plate is air-dried for a minimum of two hours prior to spot quantitation on the ELISPOT image analyzer.

EXAMPLE 13

[0252] This example describes the construction of chimeric HIV-I Gag polypeptides having multiple replacements with SIV sequences.

[0253] In some instances it may be desirable to replace more than one segment of the HIV-I

Gag polypeptide with segments of the SIV Gag polypeptide or to make additional modified HIV-

1 Gag polypeptides. In this regard, constructs with the structures shown in Table 4 were generated.

Table 4

[0254] It will be appreciated that the any of the foregoing replacements of HIV sequences with SIV sequences may be made in synthetic HIV-I Gag polypeptides.

EXAMPLE 14

[0255] This example describes a method of assessing the immunogenicity of synthetic HIV- 1/SIV Gag polypeptides in a mouse model.

[0256] Six to 8-week-old mice are immunized with a total of 15 μg of DNA encoding a synthetic HIV-I /SIV Gag polypeptide at each immunization. The groups include mice injected with 15 μg of vector with no insert (Control) or those injected with 15μg of the vector. All mice receive lOOμl DNA immunizations bilaterally in the muscle using needle and syringe at 4 timepoints with 2-week intervals. Blood is collected prior to immunizations and at specified timepoints for immune analysis. All animal experiments are reviewed and approved by the Animal Care and Use Committee, Vaccine Research Center (VRC), National Institute of Allergy and Infectious Diseases (http://www.niaid.nih.gov/vrc) and performed in accordance with all relevant federal and National Institutes of Health guidelines and regulations. [0257] The level of immunogenicity is assessed using the methods described herein. It will be appreciated that the methods above may be used to assess the immunogenicity of any of the synthetic HIV-I /SIV Gag polypeptides described herein.

EXAMPLE 15

[0258] This example describes a method of assessing the immunogenicity of synthetic HIV- 1/SIV Gag polypeptides in a primate model.

[0259] Immunogenicity of modified HIV-I Gag polypeptides may be assessed in a primate model using a prime-boost assay. Specifically, DNA vectors encoding the synthetic HIV-I /SIV Gag polypeptide of interest in a suitable carrier are administered to adult cynomolgus monkeys. If desired, the vectors may be administered multiple times at desired time intervals. Control animals are administered carrier alone. For example, the monkeys may receive three immunizations of 8 mg total DNA vaccine intramuscularly at weeks 0, 4, and 8. Thereafter, recombinant adenovirus encoding the modified HIV-I Gag protein may be administered at a desired time. For control animals, carrier without adenovirus is administered. For example, the recombinant adenovirus may be administered at week 38 or week 24. The recombinant adenovirus may be administered at any desired dosage. For example, the recombinant adenovirus may be administered at 10¹¹ PU.

[0260] Monkeys are bled at various intervals through week 42 post-immunization. [0261] ELISPOT assays are utilized to monitor the emergence of vaccine-elicited T cell immune responses. To perform the ELISPOT assays, 96-well multiscreen plates are coated overnight with 100 μl/well of 5μg/ml anti-human IFN-γ (B27; BD Pharmingen) in endotoxin- free Dulbecco's PBS (D-PBS). The plates are then washed three times with D-PBS containing 0.25% Tween-20 (D-PB S/Tween), blocked for 2 h with D-PBS containing 5% FBS at 37 °C, washed three times with D-PBS/Tween, rinsed with RPMI 1640 containing 10% FBS to remove the Tween-20, and incubated with modified HIV-I Gag polypeptide and 2 x 10⁵ PBMC in triplicate in 100 μl reaction volumes. Following an 18h incubation at 37 ⁰C, the plates are washed nine times with D-PBS/Tween and once with distilled water. The plates are then incubated with 2 μg/ml biotinylated rabbit anti-human IFN-γ (Biosource) for 2 h at room temperature, washed six times with Coulter Wash (Beckman-Coulter), and incubated for 2.5 h with a 1 :500 dilution of streptavidin-AP (Southern Biotechnology). Following five washes with Coulter Wash and one with PBS, the plates are developed with NBT/BCIP chromogen (Pierce), stopped by washing with tap water, air dried, and read using an ELISPOT reader (Hitech Instruments). Spot-forming cells (SFC) per 10⁶ PBMC are calculated. [0262] The cellular immune responses in monkeys receiving synthetic HIV-I /SIV Gag polypeptide are compared to those in control animals.

[0263] The evolution of mean IFN-γ ELISPOT responses in these groups of monkeys is evaluated at weeks 0, 2, 6, 10, and 12.

[0264] Monkeys receiving a synthetic HIV-I /SIV Gag protein exhibit an immune response against HIV-I Gag which is significantly higher than that observed in control animals.

EXAMPLE 16

[0265] This example describes the use of synthetic HIV-I /SIV Gag polypeptides administered in the form of naked DNA to induce an immune response against HIV-I in humans.

[0266] Plasmid DNA encoding a synthetic HIV-I /SIV Gag polypeptide of interest is prepared from bacterial cell cultures containing an appropriate selection medium. Following growth of bacterial cells harboring the plasmid, the plasmid DNA is purified from cellular components.

[0267] Vaccines are prepared under cGMP conditions. The vaccines meet lot release specifications prior to administration. The DNA vaccine is manufactured at an appropriate dose in phosphate buffered saline (PBS). Vials are aseptically filled to the desired volume.

[0268] The resulting DNA is administered via a desired route. For example, the DNA may be administered to the deltoid muscle using the Biojector 2000^® Needle-Free Injection Management System™. In brief, the injection site is disinfected and the area allowed to dry completely. The skin around the injection site is held firmly while the syringe is placed against the injection site at a 90° angle. The actuator is pressed and the material is released into the muscle. Continue to hold firmly for 3 seconds. After the injection, the site is covered with a sterile covering and pressure applied with 3 fingers for 1 minute. BIOJECTOR 2000® utilizes sterile, single-use syringes for variable dose, up to 1.0 mL, medication administration. The DNA composition agent is delivered under pressure by a compressed CO₂ gas cartridge that is stored inside the BIOJECTOR®. When the BIOJECTOR®'s actuator is depressed, CO₂ is released, causing the plunger to push the study agent out of the sterile syringe through the skin and into the underlying tissue. The study agent is expelled through a micro-orifice at high velocity in a fraction of a second to pierce the skin. The CO₂ does not come in contact with the injectate and the syringe design prevents any back splatter or contamination of the device by tissue from the subject.

[0269] Vaccination is repeated at a desired interval to achieve the desired level of immune response.

EXAMPLE 17

[0270] This example describes a method of inducing of an immune response against HIV-I in a human using a prime-boost regimen.

[0271] An immune response against HIV-I is primed by administering DNA encoding a synthetic HIV-I /SIV Gag polypeptide described herein to a human. Alternatively, the synthetic HIV-I /SIV Gag polypeptide itself may be administered. Preferably, multiple doses of DNA encoding the synthetic HIV-I /SIV Gag polypeptide or the synthetic HIV-I /SIV Gag polypeptide are administered at desired time intervals to prime an immune response against the HIV-I . [0272] After the immune response has been primed, it is boosted by administering a viral vector, such as an adenovirus vector. The viral vector may be administered in multiple doses at desired time intervals.

[0273] An immune response sufficient to inhibit HIV-I infection or to reduce at least one symptom of HIV-I infection is generated. EXAMPLE 18

[0274] This example describes experiments which assess the immunogenicity of a combination of a mosaic Env polypeptide and a mosaic Gag N5H polypeptides. [0275] In order to determine whether a Gag N5H chimeric polypeptide can be used as an immunogen in combination with other immunogens in a multi-valent vaccine, mosaic Gag N5H polypeptides were mixed with mosaic Env polypeptides and intracellular cytokine staining (ICS) was performed after immunization with rAd vectors encoding these genes. Briefly, B6D2F1 mice were injected one time with rAd and the T cell responses of immunized animals were determined three weeks after immunization. To compare the T cell response, 320 Gag PTE peptides grouped into 32 pools of 10 PTE peptides and 492 Env PTE peptides grouped into 82 pools of 6 peptides each were analyzed. Using rAd immunization, the mixing of N5H chimeric Gag with mosaic Env elicited CD4 and CD8 responses similar to responses elicited by mosaic Env alone or mosaic Gag N5H alone. These results suggest that mixing mosaic Env with mosaic Gag N5H does not affect the magnitude and breadth of T cell responses after rAd5 immunization in mice. In addition, there was no immunogenicity interference from the mixture of N5H- modified mosaic Gag and mosaic Env.

[0276] It was then determined whether N5H-modified B Gag would be expressed differently as compared to unmodified Gag in mouse muscle cell line C2C12, mice dendritic cells, and human CD4 T cells. Mouse muscle cell line C2C12, mice dendritic cells, and human CD4 T cells transfected with plasmids expressing N5H-modified B Gag showed higher expression of Gag proteins than unmodified Gag transfected cells after 48 hours. In mouse muscle cell line C2C12 , N5H-modifϊed Gag expressed 30% more Gag protein in cell lysates and expressed 70% more Gag protein in supernatants than that of unmodified Gag-transfected cells. In mouse dendritic cells, N5H-modified Gag expressed 70% more Gag protein in cell lysates and expressed 130% more Gag protein in supernatants than that of unmodified Gag transfected-cells. In human CD4 T cells, N5H-modified Gag expressed 230% more Gag protein in cell lysates and expressed 270% more Gag protein in supernatants. These data suggest that N5H-modified Gag proteins are expressed more efficiently than wild type Gag, and that their expression levels likely contribute to the observed differences in immunogenicity. [0277] This example demonstrates that mixing mosaic Env with mosaic Gag N5H affects the magnitude and breadth of T cell responses after rAd5 immunization in mice.

[0278] All references, including publications, patent applications, and patents, cited herein are hereby incorporated by reference to the same extent as if each reference were individually and specifically indicated to be incorporated by reference and were set forth in its entirety herein. [0279] The use of the terms "a" and "an" and "the" and similar referents in the context of describing the invention (especially in the context of the following claims) are to be construed to cover both the singular and the plural, unless otherwise indicated herein or clearly contradicted by context. The terms "comprising," "having," "including," and "containing" are to be construed as open-ended terms (i.e., meaning "including, but not limited to,") unless otherwise noted. Recitation of ranges of values herein are merely intended to serve as a shorthand method of referring individually to each separate value falling within the range, unless otherwise indicated herein, and each separate value is incorporated into the specification as if it were individually recited herein. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g., "such as") provided herein, is intended merely to better illuminate the invention and does not pose a limitation on the scope of the invention unless otherwise claimed. No language in the specification should be construed as indicating any non- claimed element as essential to the practice of the invention.

[0280] Preferred embodiments of this invention are described herein, including the best mode known to the inventors for carrying out the invention. Variations of those preferred embodiments may become apparent to those of ordinary skill in the art upon reading the foregoing description. The inventors expect skilled artisans to employ such variations as appropriate, and the inventors intend for the invention to be practiced otherwise than as specifically described herein. Accordingly, this invention includes all modifications and equivalents of the subject matter recited in the claims appended hereto as permitted by applicable law. Moreover, any combination of the above-described elements in all possible variations thereof is encompassed by the invention unless otherwise indicated herein or otherwise clearly contradicted by context.

Claims

CLAIMS:

1. A composition capable of eliciting an immune response against HIV-I in a mammal, which comprises a nucleic acid sequence encoding a polypeptide, wherein the polypeptide comprises a HIV-I Gag amino acid sequence, except that amino acids 358-411 or amino acids 355-408 of the HIV-I Gag amino acid sequence have been replaced with amino acids 359-412 of a SIV Gag polypeptide, and a pharmaceutically acceptable carrier.

2. The composition of claim 1, wherein the composition comprises two or more different nucleic acid sequences, wherein each nucleic acid sequence encodes a polypeptide comprising a HIV-I Gag amino acid sequence, except that amino acids 358-411 or amino acids 355-408 of the HIV-I Gag amino acid sequence have been replaced with amino acids 359-412 of a SIV Gag polypeptide.

3. The nucleic acid sequence of claim 1 or claim 2, wherein the HIV-I Gag amino acid sequence is a mosaic HIV-I Gag amino acid sequence.

4. The nucleic acid sequence of any one of claims 1-3, wherein the polypeptide is shorter than a full length naturally-occurring HIV-I Gag polypeptide.

5. The composition of claim 2, wherein the composition comprises a nucleic acid sequence of SEQ ID NO: 83 and a nucleic acid sequence of SEQ ID NO: 86.

6. A nucleic acid sequence encoding a polypeptide, wherein the polypeptide comprises a HIV-I Gag amino acid sequence, except that amino acids 358-411 or amino acids 355-408 of the HIV-I Gag amino acid sequence have been replaced with amino acids 359-412 of a SIV Gag polypeptide.

7. The nucleic acid sequence of claim 6, wherein the HIV-I Gag amino acid sequence is a mosaic HIV-I Gag amino acid sequence.

8. The nucleic acid sequence of claim 6 or claim 7, wherein the polypeptide is shorter than a full length naturally-occurring HIV-I Gag polypeptide.

9. The nucleic acid sequence of claim 6, which comprises a nucleic acid sequence of SEQ ID NO: 83 or SEQ ID NO: 86.

10. A polypeptide encoded by a nucleic acid sequence of any one of claims 6-9.

11. A vector comprising the nucleic acid sequence of any one of claims 6-9.

12. The vector of claim 11 , wherein the vector is a viral vector.

13. The vector of claim 12, wherein the viral vector is an adenovirus vector.

14. The vector of claim 13, wherein the adenovirus vector is an adenovirus 5 vector, an adenovirus 26 vector, or an adenovirus 28 vector.

15. The vector of claim 11 , wherein the vector is a plasmid.

16. An isolated host cell comprising the vector of any one of claims 11-15.

17. A composition comprising the vector of any one of claims 11-15 and a pharmaceutically acceptable carrier.

18. A syringe comprising the composition of any one of claims 1-5 and 17.

19. A needleless delivery device comprising the composition of any one of claims 1-5 and 17.

20. Use of a composition of any one of claims 1-5 and 17, a nucleic acid sequence of any one of claims 6-9, or a vector of any one of claims 11-15 to induce an immune response against HIV-I in a mammal.

21. Use of a polypeptide of claim 10 to induce an immune response against HIV-I in a mammal.

22. A method of inducing an immune response against HIV-I in a mammal, which method comprises administering two or more different nucleic acid sequences to a mammal, wherein each nucleic acid sequence encodes a polypeptide comprising a HIV-I Gag amino acid sequence, except that amino acids 358-411 or amino acids 355-408 of the HIV-I Gag amino acid sequence have been replaced with amino acids 359-412 of a SIV Gag polypeptide.

23. The method of claim 22, wherein the HIV-I Gag amino acid sequence is a mosaic HIV-I Gag amino acid sequence.

24. The method of claim 22 or claim 23, wherein the polypeptide comprises two or more T cell epitopes which are not present in a naturally-occurring HIV-I Gag polypeptide.

25. The method of any one of claims 22-24, wherein the HIV-I Gag amino acid sequence comprises at least five T cell epitopes which are not present in a single naturally- occurring HIV-I Gag polypeptide.

26. The method of any one of claims 22-25, wherein the polypeptide is shorter than a full length naturally-occurring HIV-I Gag polypeptide.

27. The method of any one of claims 22-26, which method comprises administering two different nucleic acid sequences to a mammal, wherein each nucleic acid sequence encodes a polypeptide comprising a HIV-I Gag amino acid sequence, except that amino acids 358-411 or amino acids 355-408 of the HIV-I Gag amino acid sequence have been replaced with amino acids 359-412 of a SIV Gag polypeptide.

28. The method of claim 27, wherein one nucleic acid sequence comprises SEQ ID NO: 83, and the other nucleic acid sequence comprises SEQ ID NO: 86.

29. The method of any one of claims 22-28, wherein the nucleic acid sequences are present in a single vector.

30. The method of any one of claims 22-28, wherein each of the nucleic acid sequences is present in a different vector.

31. The method of claim 29 or claim 30, wherein the vector is a plasmid vector.

32. The method of claim 31 , wherein the plasmid vector comprises the nucleic acid sequence of SEQ ID NO: 81 and/or SEQ ID NO: 84.

33. The method of claim 29 or claim 30, wherein the vector is an adenoviral vector.

34. The method of any one of claims 22-33, which further comprises the administration of a primer composition or a booster composition to the mammal.

35. The method of claim 34, which comprises the administration of a primer composition to the mammal.

36. The method of claim 35, wherein the primer composition comprises two or more plasmids, wherein each plasmid comprises a different nucleic acid sequence encoding a polypeptide comprising a HIV-I Gag amino acid sequence, except that amino acids 358-411 or amino acids 355-408 of the HIV-I Gag amino acid sequence have been replaced with amino acids 359-412 of a SIV Gag polypeptide.

37. The method of claim 34, which comprises the administration of a booster composition to the mammal.

38. The method of claim 37, wherein the booster composition comprises two or more adenoviral vectors, and wherein each adenoviral vector comprises a different nucleic acid sequence encoding a polypeptide comprising a HIV-I Gag amino acid sequence, except that amino acids 358-411 or amino acids 355-408 of the HIV-I Gag amino acid sequence have been replaced with amino acids 359-412 of a SIV Gag polypeptide.