AU2017200429A1 - Consensus/Ancestral Immunogens - Google Patents

Abstract

The present invention relates, in general, to an immunogen and, in particular, to an immunogen for inducing antibodies that neutralize a wide spectrum of HIV primary isolates and/or to an immunogen that induces a T cell immune response. The invention also relates to a method of inducing anti-HIV antibodies, and/or to a method of inducing a T cell immune response, using such an immunogen. The invention further relates to nucleic acid sequences encoding the present immunogens.

Description

ι 2017200429 20 Jan 2017

CONSENSUS/ANCESTRAL IMMUNOGENS

This application is a divisional of Australian Patent Application No. 2014240343 filed 7 October 2014, which is a divisional of Australian Patent Application No. 2011203095 filed 24 June 2011, which is a divisional of Australian Patent Application No. 2004274937 filed 17 5 September 2004. The subject matter of this application is related to the applicant’s International

Patent Application No. PCT/US2004/030397, filed 17 September 2004, and claims priority from United States Patent Application No. 60/503,460 filed 17 September 2003 and United States Patent Application No. 60/604,722 filed 27 August 2004, all of which are herein incorporated by cross-reference.

10 TECHNICAL FIELD

The present invention relates, in general, to an immunogen and, in particular, to an immunogen for inducing antibodies that neutralize a wide spectrum of HIV primary isolates and/or to an immunogen that induces a T cell immune response. The invention also relates to a method of inducing anti-HIV antibodies, and/or to a method of inducing a T cell immune 15 response, using such an immunogen. The invention further relates to nucleic acid sequences encoding the present immunogens.

BACKGROUND

The high level of genetic variability of HIV-1 has presented a major hurdle for AIDS vaccine development. Genetic differences among HIV-1 groups Μ, N, and O are extensive, 20 ranging from 30% to 50% in gag and env genes, respectively (Gurtler et al, J. Virol. 68:1581-1585 (1994), Vanden Haesevelde et al, J. Virol. 68:1586-1596 (1994), Simon et al, Nat. Med. 4:1032-1037 (1998), Kuiken et al, Human retroviruses and AIDS 2000: a compilation and analysis of nucleic acid and amino acid sequences (Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico)). Viruses within group M are 25 further classified into nine genetically distinct subtypes (A-D, F-H, J and K) (Kuiken et al,

Human retroviruses and AIDS 2000: a compilation and analysis of nucleic acid and amino acid sequences (Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, Robertson et al, Science 288:55-56 (2000), Robertson et al, Human retroviruses and AIDS 1999: a compilation and analysis of nucleic acid and amino acid 30 sequences, eds. Kuiken et al (Theoretical Biology and Biophysics Group, Los Alamos National 2017200429 20 Jan 2017 la

Laboratory, Los Alamos, New Mexico), pp. 492-505 (2000)). With the genetic variation as high as 30% in env genes among HIV-1 subtypes, it has been difficult to consistently elicit cross-subtype T and B cell immune responses against all HIV-1 subtypes. HIV-1 also [Text continues on page 2.] 2 2017200429 20 Jan 2017 frequently recombines among different subtypes to create circulating recombinant forms (CRFs) (Robertson et al, Science 288:55-56 (2000), Robertson et al, Human retroviruses and AIDS 1999: a compilation and analysis of nucleic acid and amino acid sequences, eds. Kuiken etal (Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los 5 Alamos, New Mexico), pp. 492-505 (2000), Carr et al, Human retroviruses and AIDS 1998: a compilation and analysis of nucleic acid and amino acid sequences, eds. Korber et al (Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico), pp. Ill-10-ΠΙ-19 (1998)). Over 20% of HIV-1 isolates are recombinant in geographic areas where multiple subtypes are common (Robertson et al, Nature 374:124-126 10 (1995), Comelissen etal, J. virol. 70:8209-8212 (1996), Dowling et al, AIDS 16:1809-1820 (2002)), and high prevalence rates of recombinant viruses may further complicate the design of experimental HIV-1 immunogens.

To overcome these challenges in AIDS vaccine development, three computer models (consensus, ancestor and center of the tree) have been used to generate centralized HIV-1 genes 15 to (Gaschen etal, Science 296:2354-2360 (2002), Gao etal, Science 299:1517-1518 (2003), Nickle etal, Science 299:1515-1517 (2003), Novitsky etal, J. Virol. 76:5435-5451 (2002), Ellenberger etal, Virology 302:155-163 (2002), Korber etal, Science 288:1789-1796 (2000)). The biology of HIV gives rise to star-like phylogenies, and as a consequence of this, the three kinds of sequences differ from each other by 2 - 5% (Gao etal, Science 299:1517-1518 (2003)). 20 Any of the three centralized gene strategies will reduce the protein distances between immunogens and field virus strains. Consensus sequences minimize the degree of sequence dissimilarity between a vaccine strain and contemporary circulating viruses by creating artificial sequences based on the most common amino acid in each position in an alignment (Gaschen et al, Science 296:2354-2360 (2002)). Ancestral sequences are similar to consensus sequences but 25 are generated using maximum-likelihood phylogenetic analysis methods (Gaschen et al,

Science 296:2354-2360 (2002), Nickle etal, Science 299:1515-1517 (2003)). In doing so, this method recreates the hypothetical ancestral genes of the analyzed current wild-type sequences (Figure 26). Nickle et al proposed another method to generate centralized HIV-1 sequences, center of the tree (COT), that is similar to ancestral sequences but less influenced by outliers 30 (Science 299:1515-1517 (2003)).

The present invention results, at least in part, from the results of studies designed to determine if centralized immunogens can induce both T and B cell immune responses in animals. These studies involved the generation of an artificial group M consensus env gene (CON6), and construction of DNA plasmids and recombinant vaccinia viruses to express CON6 3 2017200429 20 Jan 2017 envelopes as soluble gpl20 and gpl40CF proteins. The results demonstrate that CON6 Env proteins are biologically functional, possess linear, conformational and glycan-dependent epitopes of wild-type HIV-1, and induce cytokine-producing T cells that recognize T cell epitopes of both HIV subtypes B and C. Importantly, CON6 gpl20 and gpl40CF proteins 5 induce antibodies that neutralize subsets of subtype B and C HIV-1 primary isolates.

The iterative nature of study of the centralized HIV-1 gene approach is derived from the rapidly expanding evolution of HIV-1 sequences, and the fact that sequences collected in the HIV sequence database (that is, the Los Alamos National Database) are continually being updated with new sequences each year. The CON6 gpl20 envelope gene derives from Year 10 1999 Los Alamos National Database sequences, and Con-S derives from Year 2000 Los

Alamos National Database sequences. In addition, CON6 has Chinese subtype C VI, V2, V4, and V5 Env sequences, while Con-S has all group M consensus Env constant and variable regions, that have been shortened to minimal-length variable loops. Codon-optimized genes for a series of Year 2003 group M and subtype consensus sequences have been designed, as have a 15 corresponding series of wild-type HIV-1 Env genes for comparison, for use in inducing broadly reactive T and B cell responses to HIV-1 primary isolates.

SUMMARY OF THE INVENTION

The present invention relates to an immunogen for inducing antibodies that neutralize a wide spectrum of HIV primary isolates and/or to an immunogen that induces a T cell immune /0 response, and to nucleic acid sequences encoding same. The invention also relates to a method of inducing anti-HIV antibodies, and/or to a method of inducing a T cell immune response, using such an immunogen.

Objects and advantages of the present invention will be clear from the description that follows.

25 BRIEF DESCRIPTION OF THE DRAWINGS

Figures 1A-1D: Generation and expression of the group M consensus env gene (CON6). The complete amino acid sequence of CON6 gpl60 is shown. (Fig. 1 A) The five regions from the wild-type CRF08 BC (98CN006) env gene are indicated by underlined letters. Variable regions are indicated by brackets above the sequences. Potential N-liked glycosylation 30 sites are highlighted with bold-faced letters. (Fig. IB) Constructs of CON6 gp 120 and gpl40CF. CON6 gpl20 and gpl40CF plasmids were engineered by introducing a stop codon after the gpl20 cleavage site or before the transmembrane domain, respectively. The 4 2017200429 20 Jan 2017 gpl20/gp41 cleavage site and fusion domain of gp41 were deleted in the gpl40CF protein. (Fig. 1C) Expression of CON6 gpl20 and gpl40CF. CON6 gpl20 and gpl40CF were purified from the cell culture supernatants of rVV-infected 293T cells with galanthus Nivalis argarose lectin columns. Both gpl20 and gpl40CF were separated on a 10% SDS-polyarylamide gel 5 and stained with Commassie blue. (Fig. ID.) CON6 env gene optimized based on codon usage for highly expressed human genes.

Figures 2A-2E. Binding of CON6 gpl20 gpl40 CF to soluble CD4 (sCD4) and anti-Env mAbs. (Figs. 2A-2B) Each of the indicated mabs and sCD4 was covalently immobilized to a CM5 sensor chip (BIAcore) and CON6 gpl20 (Fig. 2A) or gpl40CF (Fig. 2B) (100 pg/ml 10 and 300 pg/ml, respectively) were injected over each surface. Both gpl20 and gpl40CF proteins reacted with each anti-gpl20 mabs tested except forl7b mab, which showed negligible binding to both CON6 gpl20 and gpl40CF. To determine induction of 17b mab binding to CON6 gpl20 and gpl40CF, CON6 gpl20 (Fig. 2C) or gpl40CF (Fig. 2D) proteins were captured (400-580 RU) on individual flow cells immobilized with sCD4 or mabs A32 or T8. 15 Following stabilization of each of the surface, mAb 17b was injected and flowed over each of the immobilized flow cells. Overlay of curves show that the binding of mab 17b to CON6 Env proteins was markedly enhanced on both sCD4 and mab A32 surfaces but not on the T8 surface (Figs. 2C-2D). To determine binding of CON6 gpl20 and gpl40CF to human mabs in ELISA, stock solutions of 20:g/ml of mabs 447, F39F, A32, IgGlbl2 and 2F5 on CON6 gpl20 and 20 gpl40CF were tittered (Fig. 2E). Mabs 447 (V3), F39F (V3) A32 (gpl20) and IgGlbl2 (CD4 binding site) each bound to both CON6 gpl20 and 140 well, while 2F5 (anti-gp41 ELDKWAS) only bound gpl40CF. The concentration at endpoint titer on gpl20 for mab 447 and F39F binding was <0.003 pg/ml and 0.006 pg/ml, respectively; for mab A32 was <0.125 pg/ml; for IgGlbl2 was <0.002 pg/ml; and for 2F5 was 0.016 pg/ml. 25 Figures 3A and 3B. Infectivity and coreceptor usage of CON6 envelope. (Fig. 3A) CON6 and control env plasmids were cotransfected with HTV-l/SG3)env backbone into human 293T cells to generate Env-pseudovirions. Equal amounts of each pseudovirion (5 ng p24) were used to infect JC53-BL cells. The infectivity was determined by counting the number of blue cells (infectious units, IU) per microgram of p24 of pseudovirons (IU/pg p24) after 30 staining the infected cells for 3-gal expression. (Fig. 3B) Coreceptor usage of the CON6 env gene was determined on JC53BL cells treated with AMD3100 and/or TAK-799 for 1 hr (37°C) then infected with equal amounts of p24 (5 ng) of each Env-pseudovirion. Infectivity in the control group (no blocking agent) was set as 100%. Blocking efficiency was expressed as the 5 2017200429 20 Jan 2017 percentage of IU from blocking experiments compared to those from control cultures without blocking agents. Data shown are mean ± SD.

Figure 4. Western blot analysis of multiple subtype Env proteins against multiple subtype antisera. Equal amount of Env proteins (100 ng) were separated on 10% SDS-5 polyacrylamide gels. Following electrophoresis, proteins were transferred to Hybond ECL nitrocellulose membranes and reacted with sera from HIV-1 infected patients (1:1,000) or guinea pigs immunized with CON6 gpl20 DNA prime, rVV boost (1:1,000). Protein-bound antibody was probed with fluorescent-labeled secondary antibodies and the images scanned and recorded on an infrared imager Odyssey (Li-Cor, Lincoln, NE). Subtypes are indicated by 10 single-letters after Env protein and serum IDs. Four to six sera were tested for each subtype, and reaction patterns were similar among all sera from the same subtype. One representative result for each subtype serum is shown.

Figure 5. T cell immune responses induced by CON6 Env immunogens in mice. Splenocytes were isolated from individual immunized mice (5 mice/group). After splenocytes 15 were stimulated in vitro with overlapping Env peptide pools of CON6 (black column), subtype B (hatched column), subtype C (white column), and medium (no peptide; gray column), INF-( producing cells were determined by the ELISPOT assay. T cell IFN-( responses induced by either CON6 gpl20 or gpl40CF were compared to those induced by subtype specific Env immunogens (JRFL and 96ZM651). Total responses for each envelope peptide pool are 20 expressed as SFCs per million splenocytes. The values for each column are the mean ± SEM of IFN-( SFCs (n=5 mice/group).

Figures 6A-6E. Construction of codon usage optimized subtype C ancestral and consensus envelope genes (Figs. 6A and 6B, respectively). Ancestral and consensus amino acid sequences (Figs. 6C and 6D, respectively) were transcribed to mirror the codon usage of highly 25 expressed human genes. Paired oligonucleotides (80-mers) overlapping by 20 bp were designed to contain 5’ invariant sequences including the restriction enzyme sites EcoRI, Bbsl, Bam HI and BsmBI. Bbsl and BsmBI are Type II restriction enzymes that cleave outside of their recognition sequences. Paired oligomers were linked individually using PCR and primers complimentary to the 18 bp invariant sequences in a stepwise fashion, yielding 140bp PCR 30 products. These were subcloned into pGEM-T and sequenced to confirm the absence of inadvertant mutations/deletions. Four individual pGEM-T subclones containing the proper inserts were digested and ligated together into pcDNA3.1. Multi-fragment ligations occurred 6 2017200429 20 Jan 2017 repeatly amongst groups of fragments in a stepwise manner from the 5’ to the 3’ end of the gene until the entire gene was reconstructed in pcDNA3.1. (See schematic in Fig. 6E.)

Figure 7. JC53-BL cells are a derivative of HeLa cells that express high levels of CD4 and the HIV-1 coreceptors CCR5 and CXCR4. They also contain the reporter cassettes of 5 luciferase and β-galactosidase that are each expressed from an HIV-1 LTR. Expression of the reporter genes is dependent on production of HIV-1 Tat. Briefly, cells are seeded into 24 or 96-well plates, incubated at 37°C for 24 hours and treated with DEAE-Dextran at 37°C for 30 minutes. Virus is serially diluted in 1% DMEM, added to the cells incubating in DEAE-Dextran, and allowed to incubate for 3 hours at 37°C after which an additional cell media is 10 added to each well. Following a final 48-hour incubation at 37°C, cells are either fixed, stained using X-Gal to visualize β-galactosidase expressing blue foci or frozen-thawed three times to measure luciferase activity.

Figure 8. Sequence alignment of subtype C ancestral and consensus env genes. Alignment of the subtype C ancestral (bottom line) and consensus (top line) env sequences 15 showing a 95.5% sequence homology; amino acid sequence differences are indicated. One noted difference is the addition of a glycosylation site in the C ancestral env gene at the base of the VI loop. A plus sign indicates a within-class difference of amino acid at the indicated position; a bar indicates a change in the class of amino acid. Potential N-glycosylation sites are marked in blue. The position of truncation for the gpl40 gene is also shown. 20 Figure 9. Expression of subtype C ancestral and consensus envelopes in 293T cells.

Plasmids containing codon-optimized gpl60, gpl40, or gp!20 subtype C ancestral and consensus genes were transfected into 293T cells, and protein expression was examined by Western Blot analysis of cell lysates. 48-hours post-transfection, cell lysates were collected, total protein content determined by the BCA protein assay, and 2 pg of total protein was loaded 25 per lane on a 4-20% SDS-PAGE gel. Proteins were transferred to a PVDF membrane and probed with HIV-1 plasma from a subtype C infected patient.

Figures 10A and 10B. Fig. 10A. Trans complementation of c/n’-deficient HIV-1 with codon-optimized subtype C ancestral and consensus gpl60 and gpl40. Plasmids containing codon-optimized, subtype C ancestral or consensus gp!60 or gpl40 genes were co-transfected 30 into 293T cells with an HIV-l/SG3Ae«v provirus. 48 hours post-transfection cell supernatants containing pseudotyped virus were harvested, clarified by centrifugation, filtered through at 0.2μΜ filter, and pelleted through a 20% sucrose cushion. Quantification of p24 in each virus pellet was determined using the Coulter HIV-1 p24 antigen assay; 25ng of p24 was loaded per 7 2017200429 20 Jan 2017 lane on a 4-20% SDS-PAGE gel for particles containing a codon-optimized envelope. 250ng of p24 was loaded per lane for particles generated by co-transfection of a rev-dependent wild-type subtype C 96ZAM65 lenv gene. Differences in the amount of p24 loaded per lane were necessary to ensure visualization of the rev-dependent envelopes by Western Blot. Proteins 5 were transferred to a PVDF membrane and probed with pooled plasma from HIV-1 subtype B and subtype C infected individuals. Fig. 10B. Infectivity of virus particles containing subtype C ancestral and consensus envelope glycoproteins. Infectivity of pseudotyped virus containing ancestral or consensus gpl60 or gpl40 envelope was determined using the JC53-BL assay. Sucrose cushion purified virus particles were assayed by the Coulter p24 antigen assay, and 5-10 fold serial dilutions of each pellet were incubated with DEAE-Dextran treated JC53-BL cells. Following a 48-hour incubation period, cells were fixed and stained to visualize β-galactosidase expressing cells. Infectivity is represented as infectious units per ng of p24 to normalize for differences in the concentration of the input pseudovirions.

Figure 11. Co-receptor usage of subtype C ancestral and consensus envelopes. 15 Pseudotyped particles containing ancestral or consensus envelope were incubated with DEAE-Dextran treated JC53-BL cells in the presence of AMD3100 (a specific inhibitor of CXCR4), TAK779 (a specific inhibitor of CCR5), or AMD3000+TAK779 to determine co-receptor usage. NL4.3, an isolate known to utilize CXCR4, and YXJ-2, a known CCR5-using isolate, were included as controls. 20 Figures 12A-12C. Neutralization sensitivity of subtype C ancestral and consensus envelope glycoproteins. Equivalent amounts of pseudovirions containing the ancestral, consensus or 96ZAM651 gpl60 envelopes (1,500 infectious units) were pre-incubated with a panel of plasma samples from HIV-1 subtype C infected patients and then added to the JC53-BL cell monolayer in 96-well plates. Plates were cultured for two days and luciferase activity 25 was measured as an indicator of viral infectivity. Virus infectivity is calculated by dividing the luciferase units (LU) produced at each concentration of antibody by the LU produced by the control infection. The mean 50% inhibitory concentration (IC50) and the actual % neutralization at each antibody dilution are then calculated for each virus. The results of all luciferase experiments are confirmed by direct counting of blue foci in parallel infections. 30 Figures 13A-13F. Protein expression of consensus subtype C Gag (Fig. 13A) andNef (Fig. 13B) following transfection into 293T cells. Consensus subtype C Gag and Nef amino acid sequences are set forth in Figs. 13C and 13D, respectively, and encoding sequences are set forth in Figs. 13E and 13F, respectively. 8 2017200429 20 Jan 2017

Figures 14A-14C. Figs. 14A and 14B show the Con-S Env amino acid sequence and encoding sequence, respectively. Fig. 14C shows expression of Group M consensus Con-S Env proteins using an in vitro transcription and translation system.

Figures 15A and 15B. Expression of Con-S env gene in mammalian cells. (Fig. 15A -5 cell lysate, Fig. 15B - supernatant.)

Figures 16A and 16B. Infectivity (Fig. 16A) and coreceptor usage (Fig. 16B) of CON6 and Con-S env genes.

Figures 17A-17C. Env protein incorporation in CON6 and Con-S Env-pseudovirions. (Fig. 17A - lysate, Fig. 17B - supernatant, Fig. 17C pellet.) 10 Figures 18A-18D. Figs. 18A and 18B show subtype A consensus Env amino acid sequence and nucleic acid sequence encoding same, respectively. Figs. 18C and 18D show expression of A.con env gene in mammalian cells (Fig. 18C - cell lysate, Fig. 18D -supernatant).

Figures 19A-19H. M.con.gag (Fig. 19A), M.con.pol (Fig. 19B), M.con.nef (Fig. 19C) 15 and C.con.pol (Fig. 19D) nucleic acid sequences and corresponding encoded amino acid sequences (Figs. 19E-19H, respectively).

Figures 20A-20D. Subtype B consensus gag (Fig. 20A) and env (Fig.20B) genes. Corresponding amino acid sequences are shown in Figs. 20C and 20D.

Figure 21. Expression of subtype B consensus env and gag genes in 293T cells. 20 Plasmids containing codon-optimized subtype B consensus gp!60, gpl40, and gag genes were transfected into 293T cells, and protein expression was examined by Western Blot analysis of cell lysates. 48-hours post-transfection, cell lysates were collected, total protein content determined by the BCA protein assay, and 2 pg of total protein was loaded per lane on a 4-20% SDS-PAGE gel. Proteins were transferred to a PVDF membrane and probed with serum from 25 an HIV-1 subtype B infected individual.

Figure 22. Co-receptor usage of subtype B consensus envelopes. Pseudotyped particles containing the subtype B consensus gpl60 Env were incubated with DEAE-Dextran treated JC53-BL cells in the presence of AMD3100 (a specific inhibitor of CXCR4), TAK779 (a specific inhibitor of CCR5), and AMD3000+TAK779 to determine co-receptor usage. NL4.3, 30 an isolate known to utilize CXCR4 and YU-2, a known CCR5-using isolate, were included as controls.

Figures 23A and 23B. Trans complementation of env-deficient HIV-1 with codon-optimized subtype B consensus gpl60 and gpl40 genes. Plasmids containing codon-optimized, subtype B consensus gpl60 or gpl40 genes were co-transfected into 293T cells with an HIV- 9 2017200429 20 Jan 2017 l/SG3)env provirus. 48-hours post-transfection cell supernatants containing pseudotyped virus were harvested, clarified in a tabletop centrifuge, filtered through a 0.2μΜ filter, and pellet through a 20% sucrose cushion. Quantification of p24 in each virus pellet was determined using the Coulter HIV-1 p24 antigen assay; 25 ng of p24 was loaded per lane on a 4-20% SDS-5 PAGE gel. Proteins were transferred to a PVDF membrane and probed with anti-HIV-1 antibodies from infected HIV-1 subtype B patient serum. Trans complementation with a rev-dependent NL4.3 env was included for control. Figure 23B. Infectivity of virus particles containing the subtype B concensus envelope. Infectivitiy of pseudotyped virus containing consensus B gpl60 or gpl40 was determined using the JC53-BL assay. Sucrose cushion 10 purified virus particles were assayed by the Coulter p24 antigen assay, and 5-fold serial dilutions of each pellet were incubated with DEAE-Dextran treated JC53-BL cells. Following a 48-hour incubation period, cells were fixed and stained to visualize 3-galactosidase expressing cells. Infectivity is expressed as infectious units per ng of p24.

Figures 24A-24D. Neutralization sensitivity of virions containing subtype B consensus 15 gpl60 envelope. Equivalent amounts of pseudovirions containing the subtype B consensus or NL4.3 Env (gpl60) (1,500 infectious units) were preincubated with three different monoclonal neutralizing antibodies and a panel of plasma samples from HIV-1 wubtype B infected individuals, and then added to the JC53-BL cell monolayer in 96-well plates. Plates were cultured for two days and luciferase activity was measured as an indicator of viral infectivity. >0 Virus infectivity was calculated by dividing the luciferase units (LU) produced at each concentration of antibody by the LU produced by the control infection. The mean 50% inhibitory concentration (IC50) and the actual % neutralization at each antibody dilution were then calculated for each virus. The results of all luciferase experiments were confirmed by direct counting of blue foci in parallel infections. Fig. 24 A. Neutralization of Pseudovirions 25 containing Subtype B consensus Env (gpl60). Fig. 24B. Neutralization of Pseudovirions containing NL4.3 Env (gpl60). Fig. 24C. Neutralization of Pseudovirions containing Subtype B consensus Env (gpl60). Fig. 24D. Neutralization of Pseudovirions containing NL4.3 Env (gpl60).

Figures 25A and 25B. Fig. 25A. Density and p24 analysis of sucrose gradient fractions. 30 0.5ml fractions were collected from a 20-60% sucrose gradient. Fraction number 1 represents the most dense fraction taken from the bottom of the gradient tube. Density was measured with a refractometer and the amount of p24 in each fraction was determined by the Coulter p24 antigen assay. Fractions 6-9, 10-15, 16-21, and 22-25 were pooled together and analyzed by ίο 2017200429 20 Jan 2017

Western Blot. As expected, virions sedimented at a density of 1.16-1.18 g/ml. Fig. 25B. VLP production by co-transfection of subtype B consensus gag and env genes. 293T cells were cotransfected with subtype B consensus gag and env genes. Cell supernatants were harvested 48-hours post-transfection, clarified through at 20% sucrose cushion, and further purified through a 5 20-60% sucrose gradient. Select fractions from the gradient were pooled, added to 20ml of PBS, and centrifuged overnight at 100,000 x g. Resuspended pellets were loaded onto a 4-20% SDS-PAGE gel, proteins were transferred to a PVDF membrane, and probed with plasma from an HIV-1 subtype B infected individual.

Figures 26A and 26B. Fig. 26A. 2000 Con-S 140CFI.ENV. Fig. 26B. Codon-10 optimized Year 2000 Con-S 140CFI.seq.

Figure 27. Individual C57BL/6 mouse T cell responses to HIV-1 envelope peptides. Comparative immunogenicity of CON6 gpl40CFI and Con-S gpl40CFI in C57BL/C mice. Mice were immunized with either HTV5305 (Subtype A), 2801 (Subtype B), CON6 or Con-S Envelope genes in DNA prime, rW boost regimens, 5 mice per group. Spleen cells were 15 assayed for IFN-( spot-forming cells 10 days after rW boost, using mixtures of overlapping peptides from Envs of HIV-1 UG37(A), MN(B), Chi 9(C), 89.6(B) SF162(B) or no peptide negative control.

Figures 28A-28C. Fig. 28A. Con-B 2003 Env. pep (841 a.a.). Amino acid sequence underlined is the fusion domain that is deleted in 140CF design and the "W" underlined is the 20 last amino acid at the C-terminus, all amino acids after the "W" are deleted in the 140CF design. Fig. 28B. Con-B-140CF.pep (632 a.a ). Amino acids in bold identify the junction of the deleted fusion cleavage site. Fig. 28C. Codon-optimized Con-B 140CF.seq (1927 nt.).

Figures 29A-29C. Fig. 29A. CON_OF_CONS-2003 (829 a.a.). Amino acid sequence underlined is the fusion domain that is deleted in 140CF design and the "W" underlined is the 25 last amino acid at the C-terminus, all amino acids after the "W" are deleted in the 140CF design. Fig. 29B. ConS-2003 140CF.pep (620 a.a.). Amino acids in bold identify the junction of the deleted fusion cleavage site. Fig. 29C. CODON-OPTIMIZED ConS-2003 140CF.seq (1891 nt.).

Figures 30A-30C. Fig. 30A. CONSENSUS A1-2003 (845 a.a.). Amino acid sequence 30 underlined is the fusion domain that is deleted in 140CF design and the "W" underlined is the last amino acid at the C-terminus, all amino acids after the "W" are deleted in the 140CF design. Fig. 30B. Con-Al-2003 140CF.pep (629 a.a ). Amino acids in bold identify the 11 2017200429 20 Jan 2017 junction of the deleted fusion cleavage site. Fig. 30C. CODON-OPTIMIZED Con-Al-2003. seq.

Figures 31A-31C. Fig. 31 A. CONSENSUS C-2003 (835 a.a.). Amino acid sequence underlined is the fusion domain that is deleted in 140CF design and the "W" underlined is the 5 last amino acid at the C-terminus, all amino acids after the "W" are deleted in the 140CF design. Fig. 3 IB. Con-C 2003 140CF.pep (619 a.a ). Amino acids in bold identify the junction of the deleted fusion cleavage site. Fig. 31C. CODON-OPTIMIZED Con-C-2003 (140 CF (1,888 nt.).

Figures 32A-32C. Fig. 32A. CONSENSUSG-2003 (842 a.a.). Amino acid sequence 10 underlined is the fusion domain that is deleted in 140CF design and the "W" underlined is the last amino acid at the C-terminus, all amino acids after the "W" are deleted in the 140CF design. Fig. 32B. Con-G-2003 140CF.pep (626 a.a ). Amino acids in bold identify the junction of the deleted fusion cleavage site. Fig. 32C. CODON-OPTIMIZED Con-G-2003. seq. 15 Figures 33A-33C. Fig. 33A. CONSENSUS_01_AE-2003 (854 a.a.). Amino acid sequence underlined is the fusion domain that is deleted in 140CF design and the "W" underlined is the last amino acid at the C-terminus, all amino acids after the "W" are deleted in the 140CF design. Fig. 33B. Con-AE01-2003 140CF.pep (638 a.a ). Amino acids in bold identify the junction of the deleted fusion cleavage site. Fig. 33C. CODON-OPTIMIZED Con-20 ΑΕ01-2003.seq. (1945 nt.).

Figures 34A-34C. Fig. 34A. Wild-type subtype A Env. 00KE_MSA4076-A (Subtype A, 891 a.a.). Amino acid sequence underlined is the fusion domain that is deleted in 140CF design and the "W" underlined is the last amino acid at the C-terminus, all amino acids after the "W" are deleted in the 140CF design. Fig. 34B. 00KE MSA4076-A 140CF.pep (647 a.a.). 25 Amino acids in bold identify the junction of the deleted fusion cleavage site. Fig. 34C. CODON-OPTIMIZED 00KE_MSA4076-A 140CF.seq. (1972 nt.).

Figures 35A-35C. Fig. 35A. Wild-type subtype B. QH0515.1g gpl60 (861 a.a.). Amino acid sequence underlined is the fusion domain that is deleted in 140CF design and the "W" underlined is the last amino acid at the C-terminus, all amino acids after the "W" are 30 deleted in the 140CF design. Fig. 35B. QH0515.1g 140CF (651 a.a.). Amino acids in bold identify the junction of the deleted fusion cleavage site. Fig. 35C. CODON-OPTIMIZED QH0515.1g 140CF.seq (1984 nt.).

Figures 36A-36C. Fig. 36A. Wild-type subtype C. DU123.6 gpl60 (854 a.a.). Amino acid sequence underlined is the fusion domain that is deleted in 140CF design and the "W" 12 2017200429 20 Jan 2017 underlined is the last amino acid at the C-terminus, all amino acids after the "W" are deleted in the 140CF design. Fig. 36B. DU123.6 140CF (638 a.a.). Amino acids in bold identify the junction of the deleted fusion cleavage site. Fig. 36C. CODON-OPTIMIZED DU123 .6 140CF.seq (1945 nt). 5 Figures 37A-37C. Fig. 37A. Wild-type subtype CRF01AE. 97CNGX2F-AE (854 a.a.). Amino acid sequence underlined is the fusion domain that is deleted in 140CF design and the "W" underlined is the last amino acid at the C-terminus, all amino acids after the "W" are deleted in the 140CF design. Fig. 37B. 97CNGX2F-AE 140CF.pep (629 a.a.). Amino acids in bold identify the junction of the deleted fusion cleavage site. Fig. 37C. CODON-OPTIMIZED 10 97CNGX2F-AE 140CF.seq (1921 nt ).

Figures 38A-38C. Fig. 38A. Wild-type DRCBL-G (854 a.a ). Amino acid sequence underlined is the fusion domain that is deleted in 140CF design and the "W" underlined is the last amino acid at the C-terminus, all amino acids after the "W" are deleted in the 140CF design. Fig. 38B. DRCBL-G 140CF.pep (630 a.a.). Amino acids in bold identify the junction 15 of the deleted fusion cleavage site. Fig. 38C. CODON-OPTIMIZED DRCBL-G 140CF.seq (1921 nt.).

Figures 39A and 39B. Fig. 39A. 2003 Con-S Env. Fig. 39B. 2003 Con-S Env.seq.opt. (Seq.opt. = codon optimized encoding sequence.)

Figures 40A and 40B. Fig. 40A. 2003 M. Group.Anc Env. Fig. 40B. 2003 M. 20 Group.anc Env.seq.opt. (Seq.opt. = codon optimized encoding sequence.)

Figures 41A and 41B. Fig. 41A. 2003 C0N_A1 Env. Fig. 41B. 2003 C0N_A1 Env.seq.opt. (Seq.opt. = codon optimized encoding sequence.)

Figures 42A and 42B. Fig. 42A. 2003 Al.Anc Env. Figs. 42B. 2003 Al.anc Env.seq.opt. (Seq.opt. = codon optimized encoding sequence.) 25 Figures 43A and 43B. Fig. 43A. 2003 CON A2 Env. Fig. 43B. 2003 CON_A2

Env.seq.opt. (Seq.opt. = codon optimized encoding sequence.)

Figures 44A and 44B. Fig. 44A. 2003 CON B Env. Fig. 44B. 2003 CON B Env.seq.opt. (Seq.opt. = codon optimized encoding sequence.)

Figures 45A and 45B. Fig. 45A. 2003 B.anc Env. Figs. 45B. 2003 B anc Env.seq.opt. 30 (Seq.opt. = codon optimized encoding sequence.)

Figures 46A and 46B. Fig. 46A. 2003 CON_C Env. Fig. 46B. 2003 CON_C Env.seq.opt. (Seq.opt. = codon optimized encoding sequence.)

Figures 47A and 47B. Fig. 47A. 2003 C.anc Env. Fig. 47B. 2003 C.anc Env.seq.opt. (Seq.opt. = codon optimized encoding sequence.) 13 2017200429 20 Jan 2017

Figures 48A and 48B. Fig. 48A. 2003 CON D Env. Fig. 48B. 2003 CON D Env.seq.opt. (Seq.opt. = codon optimized encoding sequence.)

Figures 49A and 49B. Fig. 49A. 2003 CONFl Env. Fig. 49B. 2003 CONFl Env.seq.opt. (Seq.opt. = codon optimized encoding sequence.) 5 Figures 50A and 50B. Fig. 50A. 2003 CON F2 Env. Fig. 50B. 2003 CON F2

Env.seq.opt. (Seq.opt. = codon optimized encoding sequence.)

Figures 51Aand 51B. Fig. 51A. 2003 CON GEnv. Fig. 51B. 2003 CON G Env.seq.opt. (Seq.opt. = codon optimized encoding sequence.)

Figures 52A and 52B. Fig. 52A. 2003 CON H Env. Fig. 52B. 2003 CON H 10 Env.seq.opt. (Seq.opt. = codon optimized encoding sequence.)

Figures 53A and 53B. Fig. 53A. 2003 CON 01AE Env. Fig. 53B. 2003 CON 01AE Env.seq.opt. (Seq.opt. = codon optimized encoding sequence.)

Figures 54A and 54B. Fig. 54A. 2003 CON 02 AG Env. Fig. 54B. 2003 CON 02 AG Env.seq.opt. (Seq.opt. = codon optimized encoding sequence.) 15 Figures 55A and 55B. Fig. 55A. 2003 CON 03 AB Env. Fig. 55B. 2003 CON 03 AB Env.seq.opt. (Seq.opt. = codon optimized encoding sequence.)

Figures 56A and 56B. Fig. 56A. 2003 CON_04_CPX Env. Fig. 56B. 2003 CON_04_CPX Env.seq.opt. (Seq.opt. = codon optimized encoding sequence.)

Figures 57A and 57B. Fig. 57A. 2003 CON_06_CPX Env. Fig. 57B. 2003 20 CON_06_CPX Env.seq.opt. (Seq.opt. = codon optimized encoding sequence.)

Figures 58A and 58B. Fig. 58A. 2003 CON_08_BC Env. Fig. 58B. 2003 CON_08_BC Env.seq.opt. (Seq.opt. = codon optimized encoding sequence.)

Figures 59A and 59B. Fig. 59A. 2003 CON_10_CD Env. Fig. 59B. 2003 CON_10_CD Env.seq.opt. (Seq.opt. = codon optimized encoding sequence.) 25 Figures 60A and 60B. Fig. 60A. 2003 CON_l 1CPX Env. Fig. 60B. 2003 CON I 1_CPX Env.seq.opt. (Seq.opt. = codon optimized encoding sequence.)

Figures 61A and 61B. Fig. 61A. 2003 CON_12_BF Env. Fig. 61B. 2003 CON12BF Env.seq.opt. (Seq.opt. = codon optimized encoding sequence.)

Figures 62A and 62B. Fig. 62A. 2003 CON_14_BG Env. Fig. 62B. 2003 30 CON14 BG Env.seq.opt. (Seq.opt. = codon optimized encoding sequence.)

Figures 63A and 63B. Fig. 63A. 2003 CON S gag.PEP. Fig. 63B. 2003 CON S gag.OPT. (OPT = codon optimized encoding sequence.)

Figures 64A and 64B. Fig. 64A. 2003 M.GROUP.anc gag.PEP. Fig. 64B. 2003_M.GROUP.anc gag.OPT. (OPT = codon optimized encoding sequence.) 14 2017200429 20 Jan 2017

Figures 65A-65D. Fig. 65A. 2003_CON_A1 gag.PEP. Fig. 65B. 2003_CON_A1 gag.OPT. Fig. 65C. 2003_Al.anc gag.PEP. Fig. 65D. 2003_Al.anc gag.OPT. (OPT = codon optimized encoding sequence.)

Figures 66A and 66B. Fig. 66A. 2003_CON_A2 gag.PEP. Fig. 66B. 2003_CON_A2 5 gag.OPT. (OPT = codon optimized encoding sequence.)

Figures 67A-67D. Fig. 67A. 2003_CON_B gag.PEP. Fig. 67B. 2003 CON B gag.OPT. Fig. 67C. 2003_B.anc gag.PEP. Fig. 67D. 2003_B.anc gag.OPT. (OPT = codon optimized encoding sequence.)

Figures 68A-68D. Fig. 68A. 2003_CON_C gag.PEP. Fig. 68B. 2003 CON C 10 gag.OPT. Fig. 68C. 2003_C.anc.gag.PEP. Fig. 68D. 2003_C.anc.gag.OPT. (OPT = codon optimized encoding sequence.)

Figures 69A and 69B. Fig. 69A. 2003 CON D gag.PEP. Fig. 69B. 2003_CON_D gag.OPT. (OPT = codon optimized encoding sequence.)

Figures 70A and 70B. Fig. 70A. 2003_CON_F gag.PEP. Fig. 70B. 2003_CON_F 15 gag.OPT. (OPT = codon optimized encoding sequence.)

Figures 71A and 71B. Fig. 71 A. 2003 CON G gag.PEP. Fig. 71B. 2003_CON_G gag.OPT. (OPT = codon optimized encoding sequence.)

Figures 72A and 72B. Fig. 72A. 2003_CON_H gag.PEP. Fig. 72B. 2003_CON_H gag.OPT. (OPT = codon optimized encoding sequence.)

20 Figures 73A and 73B. Fig. 73 A. 2003_CON_K gag.PEP. Fig. 73B. 2003_CON_K gag.OPT. (OPT = codon optimized encoding sequence.)

Figures 74A and 74B. Fig. 74A. 2003_CON_01_AE gag.PEP. Fig. 7B. 2003_CON_01_AE gag.OPT. (OPT = codon optimized encoding sequence.)

Figures 75A and 75B. Fig. 75A. 2003_CON_02_AG gag.PEP. Fig. 75B. 25 2003_CON_02_AG gag.OPT. (OPT = codon optimized encoding sequence.)

Figures 76A and 76B. Fig. 76A. 2003_CON_03_ABG gag.PEP. Fig. 76B. 2003_CON_03_ABG gag.OPT. (OPT = codon optimized encoding sequence.)

Figures 77A and 77B. Fig. 77A. 2003_CON_04_CFX gag.PEP. Fig. 77B. 2003 CON 04 CFX gag.OPT. (OPT = codon optimized encoding sequence.) 30 Figures 78A and 78B. Fig. 78A. 2003_CON_06_CPX gag.PEP. Fig. 78B. 2003_CON_06_CPX gag.OPT. (OPT = codon optimized encoding sequence.)

Figures 79A and 79B. Fig. 79A. 2003_CON_07_BC gag.PEP. Fig. 79B. 2003_CON_07_BC gag.OPT. (OPT = codon optimized encoding sequence.) 15 2017200429 20 Jan 2017

Figures 80A and 80B. Fig. 80A. 2003_CON_08_BC gag.PEP. Fig. 80B. 2003_CON_08_BC gag.OPT. (OPT = codon optimized encoding sequence.)

Figures 81A and 81B. Fig. 81A. 2003_CON_10_CD gag.PEP. Fig. 81B. 2003_CON_10_CD gag.OPT. (OPT = codon optimized encoding sequence.) 5 Figures 82A and 82B. Fig. 82A. 2003_CON_11 CPX gag.PEP. Fig. 82B. 2003_CON_11_CPX gag.OPT. (OPT = codon optimized encoding sequence.)

Figures 83A and 83B. Fig. 83A. 2003_CON_12_BF.gag.PEP. Fig. 83B. 2003_CON_12_BF.gag.OPT. (OPT = codon optimized encoding sequence.)

Figures 84A and 84B. Fig. 84A. 2003_CON_14_BG gag.PEP. Fig. 84B. 10 2003_CON_14_BG gag.OPT. (OPT = codon optimized encoding sequence.)

Figures 85A and 85B. Fig. 85A. 2003_CONS nef.PEP. Fig. 85B. 2003_CONS nef.OPT. (OPT = codon optimized encoding sequence.)

Figures 86A and 86B. Fig. 86A. 2003_M GROUP.anc nef.PEP. Fig. 86B. 2003_M GROUP.anc.nef.OPT. (OPT = codon optimized encoding sequence.)

15 Figures 87A and 87B. Fig. 87A. 2003 CON A nef.PEP. Fig. 87B. 2003_CON_A nef.OPT. (OPT = codon optimized encoding sequence.)

Figures 88A-88D. Fig. 88A. 2003 CON A1 nef.PEP. Fig. 88B. 2003_CON_A1 nef.OPT. Fig. 88C. 2003 A1.anc nef.PEP. Fig. 88D. 2003 A1.anc nef.OPT. (OPT = codon optimized encoding sequence.) 20 Figures 89A and 89B. Fig. 89A. 2003_CON_A2 nef.PEP. Fig. 89B. 2003_CON_A2 nef.OPT. (OPT = codon optimized encoding sequence.)

Figures 90A-90D. Fig. 90A. 2003_CON_B nef.PEP. Fig. 90B. 2003_CON-B nef.OPT. Fig. 90C. 2003_B.anc nef.PEP. Fig. 90D. 2003_B.anc nef.OPT. (OPT = codon optimized encoding sequence.) 25 Figures 91A and 91B. Fig. 91A. 2003_CON_02_AG nef.PEP. Fig. 91B. 2003_CON_02_AG nef.OPT. (OPT = codon optimized encoding sequence.)

Figures 92A-92D. Fig. 92A. 2003_CON_C nef.PEP. Fig. 92B. 2003_CON_C nef.OPT. Fig. 92C. 2003_C.anc nef.PEP. Fig. 92D. 2003_C.anc nef.OPT. (OPT = codon optimized encoding sequence.)

30 Figures 93A and 93B. Fig. 93A. 2003 CON D nef.PEP. Fig. 93B. 2003_CON_D nef.OPT. (OPT = codon optimized encoding sequence.)

Figures 94A and 94B. Fig. 94A. 2003 CON F1 nef.PEP. Fig. 94B. 2003_CON_F1 nef.OPT. (OPT = codon optimized encoding sequence.) 16 2017200429 20 Jan 2017

Figures 95A and 95B. Fig. 95A. 2003 CON F2 nef.PEP. Fig. 95B. 2003_CON_F2 nef.OPT. (OPT = codon optimized encoding sequence.)

Figures 96A and 96B. Fig. 96A. 2003 CON G nef.PEP. Fig. 96B. 2003_CON_G nef.OPT. (OPT = codon optimized encoding sequence.)

5 Figures 97A and 97B. Fig. 97A. 2003 CON H nef.PEP. Fig. 97B. 2003_CON_H nef.OPT. (OPT = codon optimized encoding sequence.)

Figures 98A and 98B. Fig. 98A. 2003_CON_01_AE nef.PEP. Fig. 98B. 2003_CON_01_AE nef.OPT. (OPT = codon optimized encoding sequence.)

Figures 99A and 99B. Fig. 99A. 2003_CON_03_AE nef.PEP. Fig. 99B. 10 2003_CON_03_AE nef.OPT. (OPT = codon optimized encoding sequence.)

Figures 100A and 100B. Fig. 100A. 2003_CON_04_CFX nef.PEP. Fig. 100B. 2003_CON_04_CFX nef.OPT. (OPT = codon optimized encoding sequence.)

Figures 101A and 101B. Fig. 101 A. 2003_CON_06_CFX nef.PEP. Fig. 101B. 2003_CON_06_CFX nef.OPT. (OPT = codon optimized encoding sequence.) 15 Figures 102Aand 102B. Fig. 102A. 2003 CON 08 BC nef.PEP. Fig. 102B. 2003_CON_08_BC nef.OPT. (OPT = codon optimized encoding sequence.)

Figures 103A and 103B. Fig. 103A. 2003_CON_10_CD nef.PEP. Fig. 103B. 2003_CON_10_CD nef.OPT. (OPT = codon optimized encoding sequence.)

Figures 104Aand 104B. Fig. 104A. 2003 CON11CFX nef.PEP. Fig. 104B. 20 2003 CON11CFX nef.OPT. (OPT = codon optimized encoding sequence.)

Figures 105Aand 105B. Fig. 105A. 2003 CON12BF nef.PEP. Fig. 105B. 2003_CON_12_BF nef.OPT. (OPT = codon optimized encoding sequence.)

Figures 106Aand 106B. Fig. 106A. 2003 CON14BG nef.PEP. Fig. 106B. 2003_CON_14_BG nef.OPT. (OPT = codon optimized encoding sequence.)

25 Figures 107A and 107B. Fig. 107A. 2003 CON S pol.PEP. Fig. 107B. 2003 CON S pol.OPT. (OPT = codon optimized encoding sequence.)

Figures 108A and 108B. Fig. 108A. 2003 M GROUP anc pol.PEP. Fig. 108B. 2003 M.GROUP anc pol.OPT. (OPT = codon optimized encoding sequence.)

Figures 109A-109D. Fig. 109A. 2003 CON A1 pol.PEP. Fig. 109B. 2003 CON A1 30 pol.OPT. Fig. 109C. 2003 A1.anc pol.PEP. Fig. 109D. 2003 A1.anc pol.OPT. (OPT = codon optimized encoding sequence.)

Figures 110A and 110B. Fig. 110A. 2003 CON A2 pol.PEP. Fig. 110B. 2003 CON A2 pol.OPT. (OPT = codon optimized encoding sequence.) 17 2017200429 20 Jan 2017

Figures 111A-11 ID. Fig. 111A. 2003 CON B pol.PEP. Fig. 11 IB. 2003_CON_B pol.OPT. Fig. 111C. 2003_B.anc pol.PEP. Fig. 111D. 2003_B.anc pol.OPT. (OPT = codon optimized encoding sequence.)

Figures 112A-112D. Fig. 112A. 2003_CON_C pol.PEP. Fig. 112B. 2003_CON_C 5 pol.OPT. Fig. 112C. 2003_C.anc pol.PEP. Fig. 112D. 2003_C.anc pol.OPT. (OPT = codon optimized encoding sequence.)

Figures 113A and 113B. Fig. 113 A. 2003 CON D pol.PEP. Fig. 113B. 2003_CON_D pol.OPT. (OPT = codon optimized encoding sequence.)

Figures 114Aand 114B. Fig. 114A. 2003 CON F1 pol.PEP. Fig. 114B. 10 2003_CON_F1 pol.OPT. (OPT = codon optimized encoding sequence.)

Figures 115A and 115B. Fig. 115A. 2003 CON F2 pol.PEP. Fig. 115B. 2003_CON_F2 pol.OPT. (OPT = codon optimized encoding sequence.)

Figures 116A and 116B. Fig. 116A. 2003 CONG pol.PEP. Fig. 116B. 2003_CON_G pol.OPT. (OPT = codon optimized encoding sequence.) 15 Figures 117Aand 117B. Fig. 117A. 2003 CON H pol.PEP. Fig. 117B. 2003_CON_H pol.OPT. (OPT = codon optimized encoding sequence.)

Figures 118A and 118B. Fig. 118A. 2003_CON_01_AE pol.PEP. Fig. 118B. 2003_CON_01_AE pol.OPT. (OPT = codon optimized encoding sequence.)

Figures 119Aand 119B. Fig. 119A. 2003_CON_02_AG pol.PEP. Fig. 119B. Z0 2003_CON_02_AG pol.OPT. (OPT = codon optimized encoding sequence.)

Figures 120Aand 120B. Fig. 120A. 2003_CON_03_AB pol.PEP. Fig. 120B. 2003_CON_03_AB pol.OPT. (OPT = codon optimized encoding sequence.)

Figures 121A and 121B. Fig. 121 A. 2003_CON_04_CPX pol.PEP. Fig. 121B. 2003_CON_04_CPX pol.OPT. (OPT = codon optimized encoding sequence.) 25 Figures 122A and 122B. Fig. 122A. 2003_CON_06_CPX pol.PEP. Fig. 122B. 2003_CON_06_CPX pol.OPT. (OPT = codon optimized encoding sequence.)

Figures 123A and 123B. Fig. 123A. 2003_CON_08_BC pol.PEP. Fig. 123B. 2003_CON_08_BC pol.OPT. (OPT = codon optimized encoding sequence.)

Figures 124A and 124B. Fig. 124A. 2003_CON_10_CD pol.PEP. Fig. 124B. 30 2003_CON_10_CD pol.OPT. (OPT = codon optimized encoding sequence.)

Figures 125A and 125B. Fig. 125A. 2003_CON_11_CPX pol.PEP. Fig. 125B. 2003_CON_11CPX pol.OPT. (OPT = codon optimized encoding sequence.)

Figures 126A and 126B. Fig. 126A. 2003_CON_12_BF pol.PEP. Fig. 126B. 2003_CON_12_BF pol.OPT. (OPT = codon optimized encoding sequence.) 18 2017200429 20 Jan 2017

Figures 127A and 127B. Fig. 127A. 2003 CON14BG pol.PEP. Fig. 127B. 2003 CON14BG pol.OPT. (OPT = codon optimized encoding sequence.)

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates to an immunogen that induces antibodies that neutralize a 5 wide spectrum of human immunodeficiency virus (HIV) primary isolates and/or that induces a T cell response. The immunogen comprises at least one consensus or ancestral immunogen (e g., Env, Gag, Nef or Pol), or portion or variant thereof. The invention also relates to nucleic acid sequences encoding the consensus or ancestral immunogen, or portion or variant thereof. The invention further relates to methods of using both the immunogen and the encoding 10 sequences. While the invention is described in detail with reference to specific consensus and ancestral immunogens (for example, to a group M consensus Env), it will be appreciated that the approach described herein can be used to generate a variety of consensus or ancestral immunogens (for example, envelopes for other HIV-1 groups (e.g., N and 0)).

In accordance with one embodiment of the invention, a consensus env gene can be 15 constructed by generating consensus sequences of env genes for each subtype of a particular HIV-1 group (group M being classified into subtypes A-D, F-H, J an K), for example, from sequences in the Los Alamos HIV Sequence Database (using, for example, MASE (Multiple Aligned Sequence Editor)). A consensus sequence of all subtype consensuses can then be generated to avoid heavily sequenced subtypes (Gaschen et al, Science 296:2354-2360 (2002), /0 Korber et al, Science 288:1789-1796 (2000)). In the case of the group M consensus env gene described in Example 1 (designated CON6), five highly variable regions from a CRF08 BC recombinant strain (98CN006) (VI, V2, V4, V5 and a region in cytoplasmic domain of gp41) are used to fill in the missing regions in the sequence (see, however, corresponding regions for Con-S). For high levels of expression, the codons of consensus or ancestral genes can be 25 optimized based on codon usage for highly expressed human genes (Haas et al, Curr. Biol. 6:315-324 (2000), Andre et al, J. Virol. 72:1497-1503 (1998)).

With the Year 1999 consensus group M env gene, CON6, it has been possible to demonstrate induction of superior T cell responses by CON6 versus wild-type B and C env by the number of ELISPOT (-interferon spleen spot forming cells and the number of epitopes 30 recognized in two strains of mice (Tables 1 and 2 show the data in BALB/c mice). The ability of CON6 Env protein to induce neutralizing antibodies to HIV-1 primary isolates has been compared to that of several subtype B Env. The target of neutralizing antibodies induced by CON6 includes several non-B HIV-1 strains. 19 2017200429 20 Jan 2017

Immunogen

Table 1. T cell epitope mapping of CON6, JRFL and 96ZM651 Env immunogen in BALB/c mice ^eptiae CON6 JRFL (B) 96ZM651 (C) response CON 6 (group M consensus) 16 DTEVHNVWATHACVP + + CD4 48 49 KNSSEYYRLINCNTS EYYRLINCNTSAITQ + + CD4 53 54 CPKVSFEPIPIHYCA SFEPIPIHYCAPAGF + CD4 62 NVSTVQCTHGIKPW + CD4 104 105 ETITLPCRIKQIINM LPCRIKQIINMWQGV + CD8 130 131 GIVQQQSNLLRAIEA VQQSNLLRAIEAQQHL + CD4 134 135 AQQ H LLQ LTVWGIKQLQ LQLTVWGIKQLQARVL + CD4 Subtype B (MN) 6223 6224 AKAYDTEVHNVWATQ DTEVHNVWATQACVP + CD4 6261 6262 ACPKISFEPIPIHYC ISFEPIPIHYCAPAG + CD4 6286 6287 RKRIHIGPGRAFYTT HIGPGRAFYTTKNII + CD8 6346 6347 IVQQQNNLLRAIEAQ QNNLLRAIEAQQHML + CD4 Subtype C (Chn19) 4834 VPVWKEAKTTLFCASDAKSY + CD4 4836 GKEVHNVWATHACVPTDPNP + + CD4 4848 SSENSSEYYRLINCNTSAIT + + CD4 4854 STVQCTHGIKPWSTQLLLN + CD4 4884 QQSNLLRAIEAQQHLLQLTV + CD4 4885 AQQHLLQLTVWGIKQLQTRV + CD4 20 2017200429 20 Jan 2017

Table 2. T cell epitope mapping of CON6.gpl20 immunogen in C57BL/6 mice Peptide Peptide sequence T cell response CON 6 (consensus) 2 GIQRNCQHLWRW GTM CD8 3 NCQH LWRWGTMILGM 16 DTEVHNVWATHACVP CD4 53 CPKVSFEPIPIHY C A CD4 97 FY CNTSGLFN STWMF CD8 99 FNSTWMFNGTYMFNG CD8 Subtype B (MN) 6210 GIRRNYQHWWGWGTM CD8 6211 NYQHWWGWGTMLLGL 6232 NMWKNNMVEQMHEDI CD4 6262 ISFEPIPIHY CAP AG CD4 6290 NIIGTIRQ AHCNI SR CD4 6291 TIRQAHCNISRAKWN Subtype C (Chn 19) 4830 MRVTGIRKNYQHLWRWGTML CD8 5446 RWGTMLLGMLMICSAAEN CD8 4836 GKE VHN V W ATH AC VPTDPNP CD4 4862 GDIRQAHCNISKDKWNETLQ CD4 4888 LLGIWGCSGKLICTTTVPWN CD8

For the Year 2000 consensus group M env gene, Con-S, the Con-S envelope has been 5 shown to be as immunogenic as the CON6 envelope gene in T cell (interferon ELISPOT assays in two strains of mice (the data for C57BL/6 are shown in Fig. 27). Furthermore, in comparing CON6 and Con-S gpl40 Envs as protein immunogens for antibody in guinea pigs (Table 3), both gpl40 Envs were found to induce antibodies that neutralized subtype B primary isolates. However, Con-S gpl40 also induced robust neutralization of the subtype C isolates TV-1 and 10 DU 123 as well as one subtype A HIV-1 primary isolate, while CON6 did not. 2017200429 20 Jan 2017

_I_COH6 [jpUOCF_|_j_COH6 gp140 CFI_|_J_CONS gp140 CFI TABLE 3 Ability of Group M Consensus CON6 and Con-S Ejiysto Induce Neutralization o^ HIV-1 Isolate j Guinea Pig Number (Subtype) | 770 771 772 ί 775 ! 781 783 784 i 786 M 776 777 778 780 j BXOS(B) I 520 257 428 | 189 | 218 164 >540 i 199 | | >540 >540 >540 >540 ί QH0692 (B) j 46 55 58 | 77 | <20 91 100 76 H 109 <20 <20 <20 j SS1196(B) | 3Θ8 306 284 | 222 | 431 242 >540 351 >540 296 >540 >540 ,F,LF.L(B) ........]......<20..... ......<20..... <20 I <20 I <20 169 <20 <20 <20 <20 <20 <20 j BG1168(B) j <20 <20 <20 | <20 | <20 <20 <20 <20 <20 <20 : <20 <20 i 3988(B) | <20 <20 <20 | <20 | <20 <20 <20 <20 : <20 <20 <20 <20 j 6101(B) .........I.....<20...... .....<20...... .....<20..... <20.....|..... .....<20..... .....<20 .......<20 ] <20.....|.....I <20 <20 '1........<20........ .........<20........i j TV-1(C) ........|......<20..... ......<20..... ......<20..... <20.....|..... <20 <20 <20 i <20 i 1 356 439 >540 >540 i DU1 23(C) I <20 <20 71 ! 74 | <20 72 <20 i <711 i 176 329 387 378 j DU1 72(C) I <20 <20 96 | 64 | <20 <20 <20 j <20 j <20 235 <20 213 j ZM1 81 08.6(C) | ND ND ND | ND | <20 <20 <20 i <20 M 84 61 86 43 j ZM1 4654.7(C) \ ND ND ND | ND | <20 <20 <20 i <20 M <20 <20 30 <20 j DU1 51(C) I <20 <20 <20 | <20 | <20 <20 <20 j <2° i j <20 <20 <20 <20 ! DU422(C) I <20 <20 <20 | <20 | <20 <20 <20 i <20 M <20 <20 <20 <20 I DU1 56(C) j <20 <20 <20 | <20 | <20 <20 <20 i <20 M <20 <20 <20 <20 | 92RWO20(A) j ..:20 <20 <20 Γ -;- <20 I <20 <20 <20 ! ...20 i I 116......... 204 1 95 .........177 i i 92UG037(A) | <20 <20 30 | <20 I <20 44 <20 j <20 j <20 <20 j <20 <20 j : =|= 5G % N eutralizafi on tIters aft e r 4th or 5th i rn rnuri Izatlo ri s j i Year 2000 Con-S 140.CELENY sequence is shown in Fig. 26A. Gp140 CFI refers to an HIV-1 envelope design in which the cleavage-site is deleted (c), the fusion-site is deleted j I (F) and the gp41 iιχιnnyripdpfrtingnt region is deleted (I), in addition to the deletion of trqnsrhqrnJQrane and .cytqplqgrr)iq domains. The codon-optimized Year 2000 Con-S 140 CFI i [sequencejs shown in.Fig. 26B................................................................................................................................................................................................................................................................................... 2017200429 20 Jan 2017 22

As the next iteration of consensus immunogens, and in recognition of the fact that a practical HIV-1 immunogen can be a polyvalent mixture of either several subtype consensus genes, a mixture of subtype and consensus genes, or a mixture of centralized genes and wild type genes, a series of 11 subtype consensus, and wild type genes have been designed from 5 subtypes A, B, C, CRF AE01, and G as well as a group M consensus gene from Year 2003 Los Alamos National Database sequences. The wild type sequences were chosen either because they were known to come from early transmitted HIV-1 strains (those strains most likely to be necessary to be protected against by a vaccine) or because they were the most recently submitted strains in the database of that subtype. These nucleotide and amino acid sequences 10 are shown in Figures 28-38 (for all 140CF designs shown, 140CF gene can be flanked with the 5' sequence "TTCAGTCGACGGCCACC" that contains a Kozak sequence (GCCACCATGG/A) and Sail site and 3' sequence of TAAAGATCTTACAA containing stop codon and BglII site). Shown in Figures 39-62 are 2003 centralized (consensus and ancestral) HIV-1 envelope proteins and the codon optimized gene sequences.

15 Major differences between CON6 gpl40 (which does not neutralize non-clade B HIV

strains) and Con-S gpl40 (which does induce antibodies that neutralize non-clade B HIV strains) are in Con-S VI, V2, V4 and V5 regions. For clade B strains, peptides of the V3 region can induce neutralizing antibodies (Haynes et al, J. Immunol. 151:1646-1653 (1993)). Thus, construction of Th-Vl, Th-V2, Th-V4, Th-V5 peptides can be expected to give rise to the 20 desired broadly reactive anti-non-clade B neutralizing antibodies. Therefore, the Th-V peptides set forth in Table 4 are contemplated for use as a peptide immunogen(s) derived from Con-S gpl40. The gag Th determinant (GTH, Table 4) or any homologous GTH sequence in other HIV strains, can be used to promote immunogenicity and the C4 region of HIV gpl20 can be used as well (KQIINMWQVVGKAMYA) or any homologous C4 sequence from other HIV 25 strains (Haynes et al, J. Immunol. 151:1646-1653 (1993)). Con-S VI, V2, V4, V5 peptides with an N-terminal helper determinant can be used singly or together, when formulated in a suitable adjuvant such as Corixa's RC529 (Baldridge etal, J. Endotoxin Res. 8:453-458 (2002)), to induce broadly cross reactive neutralizing antibodies to non-clade B isolates. 2017200429 20 Jan 2017

23 Table 4 1) GTH Con-S VI 132-150 YKRWIILGLNKIVRMYTNVNVTNTTNNTEEKGEIKN 2) GTH Con-S V2 157-189 YKRWIILGLN KIVRMYTEIRDKKQKVYALFYRLDWPIDDN N N NSSNYR 3) GTH Con-S V3 294-315 YKRWIILGLN KIVRMYTRPN N NTRKSIRIGPGQAFYAT 4) GTH Con-S V4 381-408 YKRWIILGLN KIVRMYNTSGLFNSTWIGNGTKN N N NTN DTITLP 5) GTH Con-S V5 447-466 YKRWIILGLN KIVRMYRDGGNN NTN ETEIFRPGGGD 6) GTH Con-6 VI 132-150 YKRWIILGLN KIVRMYNVRNVSSNGTETDN EEIKN 7) GTH Con-6 V2 157-196 YKRWIILGLN KIVRMYTELRDKKQKVYALFYRLDVVPIDDKNSSEISGKNSSEYYR 8) GTH-Con 6 V3 301-322 YKRWIILGLN KIVRMYTRPN N NTRKSIHIGPGQAFYAT 9) GTH Con-6 V4 388-418 YKRWIILGLN KIVRMYNTSGLFNSTWMFNGTYMFNGTKDNSETTTLP 10 GTH Con 6 V5 457-477 YKRWIILGLN KIVRMYRDGGNNSNKNKTETFRPGGGD

It will be appreciated that the invention includes portions and variants of the sequences specifically disclosed herein. For example, forms of codon optimized consensus encoding sequences can be constructed as gpl40CF, gpl40 CFI, gpl20 or gpl60 forms with either 5 gpl20/41 cleaved or uncleaved. For example, and as regards the consensus and ancestral envelope sequences, the invention encompasses envelope sequences devoid of V3. Alternatively, V3 sequences can be selected from preferred sequences, for example, those described in U.S. Application No. 10/431,596 and U.S. Provisional Application No. 60/471,327. In addition, an optimal immunogen for breadth of response can include 10 mixtures of group M consensus gag, pol, nef and env encoding sequences, and as well as consist of mixtures of subtype consensus or ancestral encoding sequences for gag, pol, nef and env HIV genes. For dealing with regional differences in virus strains, an efficacious mixture can include mixtures of consensus/ancestral and wild type encoding sequences. A consensus or ancestral envelope of the invention can be been "activated" to expose 15 intermediate conformations of neutralization epitopes that normally are only transiently or less well exposed on the surface of the HIV virion. The immunogen can be a "frozen" triggered form of a consensus or ancestral envelope that makes available specific epitopes for presentation to B lymphocytes. The result of this epitope presentation is the production of antibodies that broadly neutralize HIV. (Attention is directed to WO 02/024149 and to the 20 activated/triggered envelopes described therein.) 24 2017200429 20 Jan 2017

The concept of a fusion intermediate immunogen is consistent with observations that the gp41 HR-2 region peptide, DP178, can capture an uncoiled conformation of gp41 (Furata et al, Nature Struct. Biol. 5:276 (1998)), and that formalin-fixed HIV-infected cells can generate broadly neutralizing antibodies (LaCasse et al, Science 283:357 (1997)). Recently a 5 monoclonal antibody against the coiled-coil region bound to a conformational determinant of gp41 in HR1 and HR2 regions of the coiled-coil gp41 structure, but did not neutralize HIV (Jiang et al, J. Virol. 10213 (1998)). However, this latter study proved that the coiled-coil region is available for antibody to bind if the correct antibody is generated.

The immunogen of one aspect of the invention comprises a consensus or ancestral 10 envelope either in soluble form or anchored, for example, in cell vesicles or in liposomes containing translipid bilayer envelope. To make a more native envelope, gpl40 or gpl60 consensus or ancestral sequences can be configured in lipid bilayers for native trimeric envelope formation. Alternatively, triggered gpl60 in aldrithio 1-2 inactivated HIV-1 virions can be used as an immunogen. The gpl60 can also exist as a recombinant protein either as 15 gpl60 or gpl40 (gpl40 is gpl60 with the transmembrane region and possibly other gp41 regions deleted). Bound to gpl60 or gpl40 can be recombinant CCR5 or CXCR4 co-receptor proteins (or their extracellular domain peptide or protein fragments) or antibodies or other ligands that bind to the CXCR4 or CCR5 binding site on gpl20, and/or soluble CD4, or antibodies or other ligands that mimic the binding actions of CD4. Alternatively, vesicles or 20 liposomes containing CD4, CCR5 (or CXCR4), or soluble CD4 and peptides reflective of CCR5 or CXCR4 gpl20 binding sites. Alternatively, an optimal CCR5 peptide ligand can be a peptide from the N-terminus of CCR5 wherein specific tyrosines are sulfated (Bormier et al, Proc. Natl. Acad. Sci. USA 97:5762 (2001)). The triggered immunogen may not need to be bound to a membrane but may exist and be triggered in solution. Alternatively, soluble CD4 25 (sCD4) can be replaced by an envelope (gpl40 or gpl60) triggered by CD4 peptide mimetopes (Vitra et al, Proc. Natl. Acad. Sci. USA 96:1301 (1999)). Other HIV co-receptor molecules that "trigger" the gpl60 or gpl40 to undergo changes associated with a structure of gpl60 that induces cell fusion can also be used. Ligation of soluble HIV gpl40 primary isolate HIV 89.6 envelope with soluble CD4 (sCD4) induced conformational changes in gp41. 30 In one embodiment, the invention relates to an immunogen that has the characteristics of a receptor (CD4)-ligated consensus or ancestral envelope with CCR5 binding region exposed but unlike CD4-ligated proteins that have the CD4 binding site blocked, this immunogen has the CD4 binding site exposed (open). Moreover, this immunogen can be devoid of host CD4, 25 2017200429 20 Jan 2017 which avoids the production of potentially harmful anti-CD4 antibodies upon administration to a host.

The immunogen can comprise consensus or ancestral envelope ligated with a ligand that binds to a site on gpl20 recognized by an A32 monoclonal antibodies (mab) (Wyatt et al, J. 5 Virol. 69:5723 (1995), Boots et al, AIDS Res. Hum. Retro. 13:1549 (1997), Moore et al, J. Virol. 68:8350 (1994), Sullivan et al, J. Virol. 72:4694 (1998), Fouts et al, J. Virol. 71:2779 (1997), Ye et al, J. Virol. 74:11955 (2000)). One A32 mab has been shown to mimic CD4 and when bound to gpl20, upregulates (exposes) the CCR5 binding site (Wyatt et al, J. Virol. 69:5723 (1995)). Ligation of gpl20 with such a ligand also upregulates the CD4 binding site 10 and does not block CD4 binding to gpl20. Advantageously, such ligands also upregulate the HR-2 binding site of gp41 bound to cleaved gpl20, uncleaved gpl40 and cleaved gp41, thereby further exposing HR-2 binding sites on these proteins - each of which are potential targets for anti-HIV neutralizing antibodies.

In a specific aspect of this embodiment, the immunogen comprises soluble HIV 15 consensus or ancestral gpl20 envelope ligated with either an intact A32 mab, a Fab2 fragment of an A32 mab, or a Fab fragment of an A32 mab, with the result that the CD4 binding site, the CCR5 binding site and the HR-2 binding site on the consensus or ancestral envelope are exposed/upregulated. The immunogen can comprise consensus or ancestral envelope with an A32 mab (or fragment thereof) bound or can comprise consensus or ancestral envelope with an 20 A32 mab (or fragment thereof) bound and cross-linked with a cross-linker such as .3% formaldehyde or a heterobifunctional cross-linker such as DTSSP (Pierce Chemical Company). The immunogen can also comprise uncleaved consensus or ancestral gpl40 or a mixture of uncleaved gpl40, cleaved gp41 and cleaved gpl20. An A32 mab (or fragment thereof) bound to consensus or ancestral gpl40 and/or gpl20 or to gpl20 non-covalently bound to gp41, 25 results in upregulation (exposure) of HR-2 binding sites in gp41, gpl20 and uncleaved gpl40. Binding of an A32 mab (or fragment thereof) to gpl20 or gpl40 also results in upregulation of the CD4 binding site and the CCR5 binding site. As with gpl20 containing complexes, complexes comprising uncleaved gpl40 and an A32 mab (or fragment thereof) can be used as an immunogen uncross-linked or cross-linked with cross-linker such as .3% formaldehyde or 30 DTSSP. In one embodiment, the invention relates to an immunogen comprising soluble uncleaved consensus or ancestral gpl40 bound and cross linked to a Fab fragment or whole A32 mab, optionally bound and cross-linked to an HR-2 binding protein.

The consensus or ancestral envelope protein triggered with a ligand that binds to the A32 mab binding site on gpl20 can be administered in combination with at least a second 26 2017200429 20 Jan 2017 immunogen comprising a second envelope, triggered by a ligand that binds to a site distinct from the A32 mab binding site, such as the CCR5 binding site recognized by mab 17b. The 17b mab (Kwong etal, Nature 393:648 (1998) available from the AIDS Reference Repository, NIAID, NIH) augments sCD4 binding to gpl20. This second immunogen (which can also be 5 used alone or in combination with triggered immunogens other than that described above) can, for example, comprise soluble HIV consensus or ancestral envelope ligated with either the whole 17b mab, a Fab2 fragment of the 17b mab, or a Fab fragment of the 17b mab. It will be appreciated that other CCR5 ligands, including other antibodies (or fragments thereof), that result in the CD4 binding site being exposed can be used in lieu of the 17b mab. This further 10 immunogen can comprise gpl20 with the 17b mab, or fragment thereof, (or other CCR5 ligand as indicated above) bound or can comprise gpl20 with the 17b mab, or fragment thereof, (or other CCR5 ligand as indicated above) bound and cross-linked with an agent such as .3% formaldehyde or a heterobifunctional cross-linker, such as DTSSP (Pierce Chemical Company). Alternatively, this further immunogen can comprise uncleaved gpl40 present alone or in a 15 mixture of cleaved gp41 and cleaved gpl20. Mab 17b, or fragment thereof (or other CCR5 ligand as indicated above) bound to gpl40 and/or gpl20 in such a mixture results in exposure of the CD4 binding region. The 17b mab, or fragment thereof, (or other CCR5 ligand as indicated above) gpl40 complexes can be present uncross-linked or cross-linked with an agent such as .3% formaldehyde or DTSSP. 20 Soluble HR-2 peptides, such as T649Q26L and DP 178, can be added to the above- described complexes to stabilize epitopes on consensus gpl20 and gp41 as well as uncleaved consensus gpl40 molecules, and can be administered either cross-linked or uncross-linked with the complex. A series of monoclonal antibodies (mabs) have been made that neutralize many HIV 25 primary isolates, including, in addition to the 17b mab described above, mab IgGlbl2 that binds to the CD4 binding site on gpl20(Roben et al, J. Virol. 68:482 (1994), Mo et al, J. Virol. 71:6869 (1997)), mab 2G12 that binds to a conformational determinant on gpl20 (Trkola et al, J. Virol. 70:1100 (1996)), and mab 2F5 that binds to a membrane proximal region of gp41 (Musteredal, J. Virol. 68:4031 (1994)). 30 As indicated above, various approaches can be used to "freeze" fusogenic epitopes in accordance with the invention. For example, "freezing" can be effected by addition of the DP-178 or T-649Q26L peptides that represent portions of the coiled coil region, and that when added to CD4-triggered consensus or ancestral envelope, result in prevention of fusion (Rimsky etal, J. Virol. 72:986-993 (1998)). HR-2 peptide bound consensus or ancestral gpl20, gpl40, 27 2017200429 20 Jan 2017 gp41 or gpl60 can be used as an immunogen or crosslinked by a reagent such as DTSSP or DSP (Pierce Co.), formaldehyde or other crosslinking agent that has a similar effect. "Freezing" can also be effected by the addition of 0.1% to 3% formaldehyde or paraformaldehyde, both protein cross-linking agents, to the complex, to stabilize the CD4, 5 CCR5 or CXCR4, HR-2 peptide gpl60 complex, or to stabilize the "triggered" gp41 molecule, or both (LaCasse etal, Science 283:357-362 (1999)).

Further, "freezing" of consensus or ancestral gp41 or gpl20 fusion intermediates can be effected by addition of heterobifunctional agents such as DSP (dithiobis[succimidylproprionate]) (Pierce Co. Rockford, ILL., No. 22585ZZ) or the water 10 soluble DTSSP (Pierce Co.) that use two NHS esters that are reactive with amino groups to cross link and stabilize the CD4, CCR5 or CXCR4, HR-2 peptide gpl60 complex, or to stabilize the "triggered" gp41 molecule, or both.

Analysis of T cell immune responses in immunized or vaccinated animals and humans shows that the envelope protein is normally not a main target for T cell immune response 15 although it is the only gene that induces neutralizing antibodies. HIV-1 Gag, Pol and Nef proteins induce a potent T cell immune response. Accordingly, the invention includes a repertoire of consensus or ancestral immunogens that can induce both humoral and cellular immune responses. Subunits of consensus or ancestral sequences can be used as T or B cell immunogens. (See Examples 6 and 7, and Figures referenced therein, and Figures 63-127. 20 The immunogen of the invention can be formulated with a pharmaceutically acceptable carrier and/or adjuvant (such as alum) using techniques well known in the art. Suitable routes of administration of the present immunogen include systemic (e.g. intramuscular or subcutaneous). Alternative routes can be used when an immune response is sought in a mucosal immune system (e.g., intranasal). 25 The immunogens of the invention can be chemically synthesized and purified using methods which are well known to the ordinarily skilled artisan. The immunogens can also be synthesized by well-known recombinant DNA techniques. Nucleic acids encoding the immunogens of the invention can be used as components of, for example, a DNA vaccine wherein the encoding sequence is administered as naked DNA or, for example, a minigene 30 encoding the immunogen can be present in a viral vector. The encoding sequence can be present, for example, in a replicating or non-replicating adenoviral vector, an adeno-associated virus vector, an attenuated mycobacterium tuberculosis vector, a Bacillus Calmette Guerin (BCG) vector, a vaccinia or Modified Vaccinia Ankara (MVA) vector, another pox virus vector, recombinant polio and other enteric virus vector, Salmonella species bacterial vector, 28 2017200429 20 Jan 2017

Shigella species bacterial vector, Venezuelean Equine Encephalitis Virus (VEE) vector, a Semliki Forest Virus vector, or a Tobacco Mosaic Virus vector. The encoding sequence, can also be expressed as a DNA plasmid with, for example, an active promoter such as a CMV promoter. Other live vectors can also be used to express the sequences of the invention. 5 Expression of the immunogen of the invention can be induced in a patient's own cells, by introduction into those cells of nucleic acids that encode the immunogen, preferably using codons and promoters that optimize expression in human cells. Examples of methods of making and using DNA vaccines are disclosed in ET.S. Pat. Nos. 5,580,859, 5,589,466, and 5,703,055. 10 The composition of the invention comprises an immunologically effective amount of the immunogen of this invention, or nucleic acid sequence encoding same, in a pharmaceutically acceptable delivery system. The compositions can be used for prevention and/or treatment of immunodeficiency virus infection. The compositions of the invention can be formulated using adjuvants, emulsifiers, pharmaceutically-acceptable carriers or other ingredients routinely 15 provided in vaccine compositions. Optimum formulations can be readily designed by one of ordinary skill in the art and can include formulations for immediate release and/or for sustained release, and for induction of systemic immunity and/or induction of localized mucosal immunity (e.g., the formulation can be designed for intranasal administration). The present compositions can be administered by any convenient route including subcutaneous, intranasal, 20 oral, intramuscular, or other parenteral or enteral route. The immunogens can be administered as a single dose or multiple doses. Optimum immunization schedules can be readily determined by the ordinarily skilled artisan and can vary with the patient, the composition and the effect sought.

The invention contemplates the direct use of both the immunogen of the invention 25 and/or nucleic acids encoding same and/or the immunogen expressed as minigenes in the vectors indicated above. For example, a minigene encoding the immunogen can be used as a prime and/or boost.

The invention includes any and all amino acid sequences disclosed herein and, where applicable, CF and CFI forms thereof, as well as nucleic acid sequences encoding same (and 30 nucleic acids complementary to such encoding sequences).

Certain aspects of the invention can be described in greater detail in the non-limiting Examples that follows. 29 2017200429 20 Jan 2017 EXAMPLE 1

Artificial HIV-1 Group M Consensus Envelope EXPERIMENTAL DETAILS

Expression of CON6 gpl20 andgpl40 proteins in recombinant vaccinia viruses (W). 5 To express and purify the secreted form of HIV-1 CON6 envelope proteins, CON6 gpl20 and gpl40CF plasmids were constructed by introducing stop codons after the gpl20 cleavage site (REKR) and before the transmembrane domain (YIKIFIMIVGGLIGLRIVFAVLSIVN), respectively. The gpl20/gp41 cleavage site and fusion domain of gp41 were deleted in the gpl40CF protein. Both CON6 gpl20 and gpl40CF DNA constructs were cloned into the 10 pSC65 vector (from Bernard Moss, NIH, Bethesda, MD) at Sail and Kpnl restriction enzyme sites. This vector contains the lacZ gene that is controlled by the p7.5 promoter. A back-to-back P E/L promoter was used to express CON6 env genes. BSC-1 cells were seeded at 2 x 105 in each well in a 6-well plate, infected with wild-type vaccinia virus (WR) at a MOI of 0.1 pfu/cell, and 2 hr after infection, pSC65-derived plasmids containing CON6 env genes were 15 transfected into the W-infected cells and recombinant (r) VV selected as described (Moss and Earl, Current Protocols in Molecular Biology, eds, Ausubel et al (John Wiley &amp; Sons, Inc. Indianapolis, IN) pp. 16.15.1-16.19.9 (1998)). Recombinant VV that contained the CON6 env genes were confirmed by PCR and sequencing analysis. Expression of the CON6 envelope proteins was confirmed by SDS-PAGE and Western blot assay. Recombinant CON6 gpl20 20 and gpl40CF were purified with agarose galanthus Nivalis lectin beads (Vector Labs,

Burlingame, CA), and stored at -70°C until use. Recombinant VV expressing JRFL (vCB-28) or 96ZM651 (vT241R) gpl60 were obtained from the NIH AIDS Research and Reference Reagent Program (Bethesda, MD).

Monoclonal Antibodies andgpl20 Wild-type Envelopes. Human mabs against a 25 conformational determinant on gpl20 (A32), the gpl20 V3 loop (F39F) and the CCR5 binding site (17b) were the gifts of James Robinson (Tulane Medical School, New Orleans, LA) (Wyatt et al, Nature 393;705-711 (1998), Wyatt et al, J. Virol. 69:5723-5733 (1995)). Mabs 2F5, 447, b 12, 2G12 and soluable CD4 were obtained from the NIH AIDS Research and Reference Reagent Program (Bethesda, MD) (Gorny etal, J. Immunol. 159:5114-5122 (1997), Nyambi et 30 al, J. Virol. 70:6235-6243 (1996), Purtscher et al, AIDS Res. Hum. Retroviruses 10:1651-1658 (1994), Trkola etal, J. Virol 70:1100-1108 (1996)). T8 is a murine mab that maps to the gpl20 Cl region (a gift from P. Earl, NIH, Bethesda, MD). BaL (subtype B), 96ZM651 (subtype C), and 93TH975 (subtype E) gpl20s were provided by QBI, Inc. and the Division of AIDS, NIH. 30 2017200429 20 Jan 2017 CHO cell lines that express 92U037 (subtype A) and 93BR029 (subtype F) gpl40 (secreted and uncleaved) were obtained from NICBS, England.

Surface Plasmon Resonance Biosensor (SPR) Measurements and ELISA. SPR biosensor measurements were determined on a BIAcore 3000 instrument (BIAcore Inc., 5 Uppsala, Sweden) instrument and data analysis was performed using BIAevaluation 3.0 software (BIAcore Inc, Upsaala, Sweden). Anti-gpl20 mabs (T8, A32, 17b, 2G12) or sCD4 in lOmM Na-acetate buffer, pH 4.5 were directly immobilized to a CM5 sensor chip using a standard amine coupling protocol for protein immobilization. FPLC purified CON6 gpl20 monomer or gpl40CF oligomer recombinant proteins were flowed over CM5 sensor chips at 10 concentrations of 100 and 300 pg/ml, respectively. A blank in-line reference surface (activated and de-activated for amine coupling) or non-bonding mab controls were used to subtract nonspecific or bulk responses. Soluble 89.6 gpl20 and irrelevant IgG was used as a positive and negative control respectively and to ensure activity of each mab surface prior to injecting the CON6 Env proteins. Binding of CON6 envelope proteins was monitored in real-time at 25°C 15 with a continuous flow of PBS (150 mM NaCl, 0.005% surfactant P20), pH 7.4 at 10-30 μΐ/min. Bound proteins were removed and the sensor surfaces were regenerated following each cycle of binding by single or duplicate 5-10 :1 pulses of regeneration solution (10 mM glycine-HC1, pH 2.9). ELISA was performed to determine the reactivity of various mabs to CON6 gpl20 and gpl40CF proteins as described (Haynes etal, AIDS Res. Hum. Retroviruses 11:211-20 221 (1995)). For assay of human mab binding to rgpl20 or gpl40 proteins, end-point titers were defined as the highest titer of mab (beginning at 20 pg/ml) at which the mab bound CON6 gpl20 and gpl40CF Env proteins > 3 fold over background control (non-binding human mab).

Infectivity and coreceptor usage assays. HIV-l/SG3)env and CON6 or control env plasmids were cotransfected into human 293T cells. Pseudotyped viruses were harvested, 25 filtered and p24 concentration was quantitated (DuPont/NEN Life Sciences, Boston, MA).

Equal amounts of p24 (5 ng) for each pseudovirion were used to infect JC53-BL cells to determine the infectivity (Derdeyn e al, J. Virol. 74:8358-8367 (2000), Wei et al, Antimicrob Agents Chemother. 46:1896-1905 (2002)). JC53-BL cells express CD4, CCR5 and CXCR4 receptors and contain a 3-galactosidase (3-gal) gene stably integrated under the transcriptional 30 control of an HIV-1 long terminal repeat (LTR). These cells can be used to quantify the infectious titers of pseudovirion stocks by staining for 3-gal expression and counting the number of blue cells (infectious units) per microgram of p24 of pseudovirons (IU/pg p24) (Derdeyn et al, J. Virol. 74:8358-8367 (2000), Wei et al, Antimicrob Agents Chemother. 31 2017200429 20 Jan 2017 46:1896-1905 (2002)). To determine the coreceptor usage of the CON6 env gene, JC53BL cells were treated with 1.2 μΜ AMD3100 and 4 μΜ TAK-799 for 1 hr at 37°C then infected with equal amounts of p24 (5 ng) of each Env pseudotyped virus. The blockage efficiency was expressed as the percentage of the infectious units from blockage experiments compared to that 5 from control culture without blocking agents. The infectivity from control group (no blocking agent) was arbitrarily set as 100%.

Immunizations. All animals were housed in the Duke University Animal Facility under AALAC guidelines with animal use protocols approved by the Duke University Animal Use and Care Committee. Recombinant CON6 gpl20 and gpl40CF glycoproteins were formulated 10 in a stable emulsion with RIBI-CWS adjuvant based on the protocol provided by the manufacturer (Sigma Chemical Co., St. Louis, MO). For induction of anti-envelope antibodies, each of four out-bred guinea pigs (Harlan Sprague, Inc., Chicago, IL) was given 100 :g either purified CON6 gpl20 or gpl40CF subcutaneously every 3 weeks (total of 5 immunizations). Serum samples were heat-inactivated (56°C, 1 hr), and stored at -20°C until use. 15 For induction of anti-envelope T cell responses, 6-8 wk old female BALB/c mice (Frederick Cancer Research and Developmental Center, NCI, Frederick, MD) were immunized i.m. in the quadriceps with 50 pg plasmid DNA three times at a 3-week interval. Three weeks after the last DNA immunization, mice were boosted with 107 PFU of rW expressing Env proteins. Two weeks after the boost, all mice were euthanized and spleens were removed for 20 isolation of splenocytes.

Neutralization assays. Neutralization assays were performed using either a MT-2 assay as described in Bures et al, AIDS Res. Hum. Retroviruses 16:2019-2035 (2000), a luciferase-based multiple replication cycle HIV-1 infectivity assay in 5.25.GFP.Luc.M7 cells using a panel of HIV-1 primary isolates (Bures etal, AIDS Res. Hum. Retroviruses 16:2019-2035 25 (2000), Bures et al, J. Virol. 76:2233-2244 (2002)), or a syncytium (fusion from without) inhibition assay using inactivated HIV-1 virions (Rossio etal, J. Virol. 72:7992-8001 (1998)). In the luciferase-based assay, neutralizing antibodies were measured as a function of a reduction in luciferase acitivity in 5.25.EGFP.Luc.M7 cells provided by Nathaniel R. Landau, Salk Institute, La Jolla, CA (Brandt et al, J. Biol. Chem. 277:17291-17299 (2002)). Five 30 hundred tissue culture infectious dose 50 (TCID50) of cell-free virus was incubated with indicated serum dilutions in 150 μΐ (1 hr, at 37°C) in triplicate in 96-well flat-bottom culture plates. The 5.25.EGFP.Luc.M7 cells were suspended at a density of 5 x 105/ml in media containing DEAE dextran (10 pg/ml). Cells (100 μΐ) were added and until 10% of cells in 32 2017200429 20 Jan 2017 control wells (no test serum sample) were positive for GFP expression by fluorescence microscopy. At this time the cells were concentrated 2-fold by removing one-half volume of media. A 50 μΐ suspension of cells was transferred to 96-well white solid plates (Costar, Cambridge, MA) for measurement of luciferase activity using Bright-Glo™ substrate 5 (Promega, Madison, WI) on a Wallac 1420 Multilabel Counter (PerkinElmer Life Sciences, Boston, MA). Neutralization titers in the MT-2 and luciferase assays were those where > 50% virus infection was inhibited. Only values that titered beyond 1:20 (i.e. >1:30) were considered significantly positive. The syncytium inhibition “fusion from without” assay utilized HIV-1 aldrithiol-2 (AT-2) inactivated virions from HIV-1 subtype B strains ADA and AD8 (the gift of 10 Larry Arthur and Jeffrey Lifson, Frederick Research Cancer Facility, Frederick, MD) added to SupTl cells, with syncytium inhibition titers determined as those titers where >90% of syncytia were inhibited compared to prebleed sera.

Enzyme linked immune spot (ELISPOT) assay. Single-cell suspensions of splenocytes from individual immunized mice were prepared by mincing and forcing through a 70 :m Nylon 15 cell strainer (BD Labware, Franklin Lakes, NJ). Overlapping Env peptides of CON6 gpl40 (159 peptides, 15mers overlapping by 11) were purchased from Boston Bioscence, Inc (Royal Oak, MI). Overlapping Env peptides of AIN gpl40 (subtype B; 170 peptides, 15mers overlapping by 11) and Chnl9 gpl40 (subtype C; 69 peptides, 20mers overlapping by 10) were obtained from the NIH AIDS Research and Reference Reagent Program (Bethesda, MD). 20 Splenocytes (5 mice/group) from each mouse were stimulated in vitro with overlapping Env peptides pools from CON6, subtype B and subtype C Env proteins. 96-well PVDF plates (MultiScreen-IP, Millipore, Billerica, MA) were coated with anti-IFN-( mab (5 :g/ml, AN18; Mabtech, Stockholm, Sweden). After the plates were blocked at 37°C for 2 hr using complete Hepes buffered RPMI medium,50:1 of the pooled overlapping envelope peptides (13 CON6 and 25 MN pools, 13-14 peptides in each pool; 9 Chnl9 pool, 7-8 peptide in each pool) at a final concentration of 5 pg/ml of each were added to the plate. Then 50 μΐ of splenocytes at a concentration of 1.0 X 107/ml were added to the wells in duplicate and incubated for 16 hr at 37°C with 5% C02. The plates were incubated with 100 μΐ of a 1:1000 dilution of streptavidin alkaline phosphatase (Mabtech, Stockholm, Sweden), and purple spots developed using 100 μΐ 30 of BCIP/NBT (Plus) Alkaline Phosphatase Substrate (Moss, Pasadena, MD). Spot forming cells (SFC) were measured using an Immunospot counting system (CTL Analyzers, Cleveland, OH). Total responses for each envelope peptide pool are expressed as SFCs per 106 splenocytes. 33 2017200429 20 Jan 2017

RESULTS CON6 Envelope Gene Design, Construction and Expression. An artificial group M consensus env gene (CON6) was constructed by generating consensus sequences of env genes for each HIV-1 subtype from sequences in the Los Alamos HIV Sequence Database, and then 5 generating a consensus sequence of all subtype consensuses to avoid heavily sequenced subtypes (Gaschen etal, Science 296:2354-2360 (2002), Korber etal, Science 288:1789-1796 (2000)). Five highly variable regions from a CRF08_BC recombinant strain (98CN006) (VI, V2, V4, V5 and a region in cytoplasmic domain of gp41) were then used to fill in the missing regions in CON6 sequence. The CON6 V3 region is group M consensus (Figure 1 A). For high 10 levels of expression, the codons of CON6 env gene were optimized based on codon usage for highly expressed human genes (Haas etal, Curr. Biol. 6:315-324 (2000), Andre etal, J. Virol. 72:1497-1503 (1998)). (See Fig. ID.) The codon optimized CON6 env gene was constructed and subcloned into pcDNA3.1 DNA at EcoR I and BamH I sites (Gao et al, AIDS Res. Hum. Retroviruses, 19:817-823 (2003)). High levels of protein expression were confirmed with 15 Western-blot assays after transfection into 293T cells. To obtain recombinant CON6 Env proteins for characterization and use as immunogens, rVV was generated to express secreted gpl20 and uncleaved gpl40CF (Figure IB). Purity for each protein was >90% as determined by Coomassie blue gels under reducing conditions (Figure 1C). CD4 Binding Domain and Other Wild-type HIV-1 Epitopes are Preserved on CON6 20 Proteins. To determine if CON6 proteins can bind to CD4 and express other wild-type HIV-1 epitopes, the ability of CON6 gpl20 and gpl40CF to bind soluble(s) CD4, to bind several well-characterized anti-gpl20 mabs, and to undergo CD4-induced conformational changes was assayed. First, BIAcore CM5 sensor chips were coated with either sCD4 or mabs to monitor their binding activity to CON6 Env proteins. It was found that both monomeric CON6 gpl20 25 and oligomeric gpl40CF efficiently bound sCD4 and anti-gpl20 mabs T8, 2G12 and A32, but did not constitutively bind mab 17b, that recognizes a CD4 inducible epitope in the CCR5 binding site of gpl20 (Figures 2A and 2B). Both sCD4 and A32 can expose the 17b binding epitope after binding to wild-type gpl20 (Wyatt et al, Nature 393;705-711 (1998), Wyatt et al, J. Virol. 69:5723-5733 (1995)). To determine if the 17b epitope could be induced on CON6 30 Envs by either sCD4 or A32, sCD4, A32 and T8 were coated on sensor chips, then CON6 gpl20 or gpl40CF captured, and mab 17b binding activity monitored. After binding sCD4 or mab A32, both CON6 gpl20 and gpl40CF were triggered to undergo conformational changes and bound mab 17b (Figures 2C and 2D). In contrast, after binding mab T8, the 17b epitope was not exposed (Figures 2C and 2D). ELISA was next used to determine the reactivity of a 34 2017200429 20 Jan 2017 panel of human mabs against the gpl20 V3 loop (447, F39F), the CD4 binding site (b 12), and the gp41 neutralizing determinant (2F5) to CON6 gpl20 and gpl40CF (Figure 2E). Both CON6 rgpl20 and rgpl40CF proteins bound well to neutralizing V3 mabs 447 and F39F and to the potent neutralizing CD4 binding site mab bl2. Mab 2F5, that neutralizes HTV-1 primary 5 isolates by binding to a C-terminal gp41 epitope, also bound well to CON6 gpl40CF (Figure 2E). CON6 env Gene is Biologically Functional and Uses CCR5 as its Coreceptor. To determine whether CON6 envelope gene is biologically functional, it was co-transfected with the e^v-defective SG3 proviral clone into 293T cells. The pseudotyped viruses were harvested 10 and JC53BL cells infected. Blue cells were detected in JC53-BL cells infected with the CON6 Env pseudovirions, suggesting that CON6 Env protein is biologically functional (Figure 3A). However, the infectious titers were 1-2 logs lower than that of pseudovirions with either YU2 orNL4-3 wild-type HIV-1 envelopes.

The co-receptor usage for the CON6 env gene was next determined. When treated with 15 CXCR4 blocking agent AMD3100, the infectivity of NL4-3 Env-pseudovirons was blocked while the infectivity of YU2 or CON6 Env-pseudovirons was not inhibited (Figure 3B). In contrast, when treated with CCR5 blocking agent TAK-779, the infectivity of NL4-3 Env-pseudovirons was not affected, while the infectivity of YTJ2 or CON6 Env-pseudovirons was inhibited. When treated with both blocking agents, the infectivity of all pseudovirions was 20 inhibited. Taken together, these data show that the CON6 envelope uses the CCR5 co-receptor for its entry into target cells.

Reaction of CON6 gpl20 With Different Subtype Sera. To determine if multiple subtype linear epitopes are preserved on CON6 gpl20, a recombinant Env protein panel (gpl20 and gpl40) was generated. Equal amounts of each Env protein (100 ng) were loaded on SDS-25 polyacrylamide gels, transferred to nitrocellulose, and reacted with subtype A through G patient sera as well as anti-CON6 gpl20 guinea pig sera (1:1,000 dilution) in Western blot assays. For each HIV-1 subtype, four to six patient sera were tested. One serum representative for each subtype is shown in Figure 4.

It was found that whereas all subtype sera tested showed variable reactivities among 30 Envs in the panel, all group M subtype patient sera reacted equally well with CON6 gpl20 Env protein, demonstrating that wild-type HIV-1 Env epitopes recognized by patient sera were well preserved on the CON6 Env protein. A test was next made as to whether CON6 gpl20 antiserum raised in guinea pigs could react to different subtype Env proteins. It was found that 35 2017200429 20 Jan 2017 the CON6 serum reacted to its own and other subtype Env proteins equally well, with the exception of subtype A Env protein (Figure 4).

Induction of T Cell Responses to CON6, Subtype B and Subtype C Envelope Overlapping Peptides. To compare T cell immune responses induced by CON6 Env 5 immunogens with those induced by subtype specific immunogens, two additional groups of mice were immunized with subtype B or subtype C DNAs and with corresponding rVV expressing subtype B or C envelope proteins. Mice immunized with subtype B (JRFL) or subtype C (96ZM651) Env immunogen had primarily subtype-specific T cell immune responses (Figure 5). IFN-( SFCs from mice immunized with JRFL (subtype B) immunogen 10 were detected after stimulation with subtype B (MN) peptide pools, but not with either subtype C (Chnl9) or CON6 peptide pools. IFN-( SFCs from mice immunized with 96ZM651 (subtype C) immunogen were detected after the stimulation with both subtype C (Chnl9) and CON6 peptide pools, but not with subtype B (MN) peptide pools. In contrast, IFN-( SFCs were identified from mice immunized with CON6 Env immunogens when stimulated with either 15 CON6 peptide pools as well as by subtype B or C peptide pools (Figure 5). The T cell immune responses induced by CON6 gpl40 appeared more robust than those induced by CON6 gpl20. Taken together, these data demonstrated that CON6 gpl20 and gpl40CF immunogens were capable of inducing T cell responses that recognized T cell epitopes of wild-type subtype B and C envelopes. 20 Induction of Antibodies by Recombinant CON6 gp!20 and gp!40CF Envelopes that

Neutralize HIV-1 Subtype B and C Primary Isolates. To determine if the CON6 envelope immunogens can induce antibodies that neutralize HIV-1 primary isolates, guinea pigs were immunized with either CON6 gpl20 or gpl40CF protein. Sera collected after 4 or 5 immunizations were used for neutralization assays and compared to the corresponding prebleed sera. 25 Two AT-2 inactivated HIV-1 isolates (ADA and AD8) were tested in syncytium inhibition assays (Table 5A). Two subtype B SHIV isolates, eight subtype B primary isolates, four subtype C, and one each subtype A, D, and E primary isolates were tested in either the MT-2 or the luciferase-based assay (Table 5B). In the syncytium inhibition assay, it was found that antibodies induced by both CON 6 gpl20 and gpl40CF proteins strongly inhibited AT-2 30 inactivated ADA and AD8-induced syncytia (Table 5A). In the MT-2 assay, weak neutralization of 1 of 2 SHIV isolates (SHIV SF162P3) by two gpl20 and one gpl40CF sera was found (Table 5B). In the luciferase-based assay, strong neutralization of 4 of 8 subtype B primary isolates (BX08, SF162, SSI 196, and BAL) by all gpl20 and gpl40CF sera was found, and 2017200429 20 Jan 2017 36 weak neutralization of 2 of 8 subtype B isolates (6101, 0692) by most gpl20 and gpl40CF sera was found. No neutralization was detected against HIV-1 PAVO (Table 5B). Next, the CON6 anti-gpl20 and gpl40CF sera were tested against four subtype C HIV-1 isolates, and weak neutralization of 3 of 4 isolates (DU179, DU368, and S080) was found, primarily by anti-5 CON6 gpl20 sera. One gpl40CF serum, no. 653, strongly neutralized DU179 and weakly neutralized S080 (Table 5B). Finally, anti-CON6 Env sera strongly neutralized a subtype D isolate (93ZR001), weakly neutralized a subtype E (CM244) isolate, and did not neutralize a subtype A (92RW020) isolate.

Table 5A

Ability of HIV-1 Group M Consensus Envelope CON6 Proteins to Induce _Fusion Inhibiting Antibodies_

Syncytium Inhibition antibody titer1 Guinea Pig No. Immunogen AD8 ADA 646 gpi20 270 270 647 gpi20 90 90 648 gpi20 90 270 649 gpi20 90 90 Geometric Mean Titer 119 156 650 gp140 270 270 651 gpi40 90 90 652 gpi40 >810 810 653 gpi40 270 90 Geometric Mean Titer 270 207

Reciprocal serum dilution at which HIV-induced syncytia of Sup T1 cells was inhibited by >90% compared to pre-immune serum. All prebleed sera were negative (titer <10). 2017200429 20 Jan 2017

Tattle 5B...................................................................................................................................................................

Ability of Croup M Consensus HIV-1 Envelope CONG gpl20 and gpldOCF Proteins to Induce Antibodies that Neutralize HIV Primary Isolates HIV Isolate (Subtype) CONG gpl20 Protein Guinea Pig No. CONG gpl40CF Protein Guinea Pig No. Controls i 646 647 648 649 ! GMT. 650 651 652 653 | GMT TriMsibi=|= \ CD4-IgG2 ! HIV+ Serum $Ijiy,89.6P*(B) i <20 <20 <20 <20 | <20 <20 <20 <20 <20 i <20 NT j NT ! NT OT'SF1'62P3'*(B') j <20 30 40 ......<20.....Γ <20 .......27....... .....<20...... .......<20 .......<20.....X" <20 ..........NT..........]" 0.2μ^πι1 .............NT........ BX08(B)................. P 270 103 254 55 \ 102 199 ........64 229 150 Γ 107 0.7jig(m[ Γ .....nt ; 23g4 610i(B)...............................Γ <20 30 ......35....... .....<20......X <20 ........<20 90 .......72...... ......73........f" 39 l.ljigfml i .......NT..........T...... ............NT....... BG 1168(B) j '<20"' "<20"' .....<20..... .....<20......X '<20...... 40 <20 .....<20..... ......'25........i " <20...... 2.7μ^ιη1 j .......NT..........;....... ............NT....... 0692(B)...............................p .....31..... ""32"'" ......34...... .....<20......!" 24 .........20 33 30 ......'45........p .....33..... D.Sjigiml \ .......NT..........:....... ............769....... mom...........................p SF 162(B).............................Γ <20 <20 .....<20..... .....<20......1' <20 ........<20 <20 <20 <20 i <20 2.9μg/ml \ .......NT..........;....... ............NT....... 2,146 300 110 202 ( "379...... 206 5,502 15,090 .........174 1,313 ..........NT..........(' ........nt..........; >540......... SSI 196(B) P 206 26 140 ......59......X 03 301 401 333 81 253 ...........NT 1" NT 1 301# BAL(B) p 123 90 107 130......X 113 107 146 136 85 116 ..... NT |" NT.........1...... ........3307 "92RW020(xA).....................f" <20 <20 ""<20..... ......<20.....X <20...... ......<20..... <20..... <20 ......<20.....[ <20 ...........NT..........f .......NT..........T...... ............693....... DUI79(C)..........................p <20 ""43"" ""<20..... ......24.......f '<20....... ........<20 ......<20"" .........24"" .....515.......| 33 ...........NT...........f 0.8μ§0η1 ............NT....... DU368(C)..........................[" .....25..... ""35"" ......62....... .....<20...... 27........ ........<20 ......<20 ........<20 ......23........f <20 ...........NT...........Γ 2.3μ^πι1 .............NT....... S021(C)...............................r '"<20..... "<20" ......33...... .....<20...... <20...... .........<20" .......<20"" ........'<20"" <20 i <20'...... ..........NT..........]" 8.3jigiml .............NT........ SOSO(C)...............................Γ .....24..... ....37.... ......70...... ......41........Γ 40 ........<20 .......<20 ........<20 .......52....... <20 ..........NT..........f 3.4jig/ml ............NT........ 93ZR001(D) P 275 144 126 114 154 306 .......195 .........129 ......173.....f" 191 ...........NT 1" ......NT Γ"" ..........693 — cm244:;e) | '35 43 64 ND 46 31 25 27 ......25........[ 26....... ...........NT..........[' NT ............693....... *MT-2 Assay; All other HIV isolates were tested in the M7-luciferase assay. HIV-1 isolates QH0692, ΞΞ1196, SF162, 6101, BX08, BG1168, EAL were assayed with post-injection 5 serum; other HI V-1 isolates were assayed with post-injection 4 serum. ND = not done. HIV+ sera was either HIV-1+ human serum (LEH3) or an anti-gpl20 guinea pig serum (if) with known neutralizing activity for HIV-1 isolate SSI 196. GMT = geometric mean titer of fou5 iiimals per group. Neutralizing titers reported are after subtraction of any background neutralization in prgljlgejJ sera. 4=TriMsib2 = a mixture of human rt$)s.2F5, bl2,2G12. 38 2017200429 20 Jan 2017

CONCLUSIONS

The production of an artificial HIV-1 Group M consensus env genes (encoding sequences) (CON6 and Con-S) have been described that encodes a functional Env protein that is capable of utilizing the CCR5 co-receptor for mediating viral entry. Importantly, these 5 Group M consensus envelope genes could induce T and B cell responses that recognized epitopes of subtype B and C HIV-1 primary isolates. In addition, Con-S induces antibodies that strongly neutralize Subtype-C and A HIV-1 strains (see Table 3).

The correlates of protection to HIV-1 are not conclusively known. Considerable data from animal models and studies in HIV-1-infected patients suggest the goal of HIV-1 vaccine 10 development should be the induction of broadly-reactive CD4+ and CD8+ anti-HIV-1 T cell responses (Letvin etal, Annu. Rev. Immunol. 20:73-99 (2002)) and high levels of antibodies that neutralize HIV-1 primary isolates of multiple subtypes (Mascola etal, J. Virol. 73:4009-4018 (1999), Mascola etal, Nat. Med. 6:270-210 (2000)).

The high level of genetic variability of HIV-1 has made it difficult to design immuno-15 gens capable of inducing immune responses of sufficient breadth to be clinically useful.

Epitope based vaccines for T and B cell responses (McMichael etal, Vaccine 20:1918-1921 (2002), Sbai etal, Curr. Drug Targets Infect, Disord. 1:303-313 (2001), Haynes, Lancet 348:933-937 (1996)), constrained envelopes reflective of fusion intermediates (Fouts etal,

Proc. Natl. Acad. Sci. USA 99:11842-22847 (2002)), as well as exposure of conserved high-20 order structures for induction of anti-HIV-1 neutralizing antibodies have been proposed to overcome HIV-1 variability (Roben etal, J. Virol. 68:4821-4828 (1994), Saphire etal, Science 293:1155-1159 (2001)). However, with the ever-increasing diversity and rapid evolution of HIV-1, the virus is a rapidly moving complex target, and the extent of complexity of HIV-1 variation makes all of these approaches problematic. The current most common approach to 25 HIV-1 immunogen design is to choose a wild-type field HTV-1 isolate that may or may not be from the region in which the vaccine is to be tested. Polyvalent envelope immunogens have been designed incorporating multiple envelope immunogens (Bartlett et al, AIDS 12:1291-1300 (1998), Cho etal, J. Virol. 75:2224-2234 (2001)).

The above-described study tests a new strategy for HIV-1 immunogen design by genera-30 ting a group M consensus env gene (CON6) with decreased genetic distance between this candidate immunogen and wild-type field virus strains. The CON6 env gene was generated for all subtypes by choosing the most common amino acids at most positions (Gaschen et al, Science 296:2354-2360 (2002), Korber et al, Science 288:1789-1796 (2000)). Since only the most common amino acids were used, the majority of antibody and T cell epitopes were well 39 2017200429 20 Jan 2017 preserved. Importantly, the genetic distances between the group M consensus env sequence and any subtype env sequences was about 15%, which is only half of that between wild-type subtypes (30%) (Gaschen etal, Science 296:2354-2360 (2002)). This distance is approximately the same as that among viruses within the same subtype. Further, the group M consensus env 5 gene was also about 15% divergent from any recombinant viral env gene, as well, since CRFs do not increase the overall genetic divergence among subtypes.

Infectivity of CON6-Env pseudovirions was confirmed using a single-round infection system, although the infectivity was compromised, indicating the artificial envelope was not in an “optimal” functional conformation, but yet was able to mediate virus entry. That the CON6 10 envelope used CCR5 (R5) as its coreceptor is important, since majority of HIV-1 infected patients are initially infected with R5 viruses. BIAcore analysis showed that both CON6 gpl20 and gpl40CF bound sCD4 and a number of mabs that bind to wild-type HIV-1 Env proteins. The expression of the CON6 gpl20 and 140CF proteins that are similar antigenically to wild-type HIV-1 envelopes is an 15 important step in HIV-1 immunogen development. However, many wild-type envelope proteins express the epitopes to which potent neutralizing human mabs bind, yet when used as immunogens themselves, do not induce broadly neutralizing anti-HIV-1 antibodies of the specificity of the neutralizing human mabs.

The neutralizing antibody studies were encouraging in that both CON6 gpl20, CON6 20 gpl40CF and Con-S gpl40CFI induced antibodies that neutralized select subtype B, C and D HIV-1 primary isolates, with Con-S gpl40CFI inducing the most robust neutralization of nonsubtype B primary HIV isolates. However, it is clear that the most difficult-to-neutralize primary isolates (PAVO, 6101, BG1168, 92RW020, CM244) were either only weakly or not neutralized by anti-CON6 gpl20 or gpl40 sera (Table 4b). Nonetheless, the Con-S envelope 25 immunogenicity for induction of neutralizing antibodies is promising, given the breadth of responses generated with the Con-S subunit gpl40CFI envelope protein for non-subtype B HIV isolates. Previous studies with poxvirus constructs expressing gpl20 and gpl60 have not generated high levels of neutralizing antibodies (Evans etal, J. Infect. Dis. 180:290-298 (1999), Polacino etal, J. Virol. 73:618-630 (1999), Ourmanov etal, J. Virol. 74:2960-2965 (2000), Pal 30 et al, J. Virol 76:292-302 (2002), Excler and Plotkin, AIDS 1 l(Suppl A):S127-137 (1997). rVV expressing secreted CON6 gpl20 and gpl40 have been constructed and antibodies that neutralize HIV-1 primary isolates induced. An HIV neutralizing antibody immunogen can be a combination of Con-S gpl40CFI, or subunit thereof, with immunogens that neutralize most subtype B isolates. 40 2017200429 20 Jan 2017

The structure of an oligomeric gpl40 protein is critical when evaluating protein immunogenicity. In this regard, study of purified CON6 gpl40CF proteins by fast performance liquid chromatography (FPLC) and analytical ultracentrifiguration has demonstrated that the purified gpl40 peak consists predominantly of trimers with a small component of dimers. 5 Thus, centralized envelopes such as CON6, Con-S or 2003 group M or subtype consensus or ancestral encoding sequences described herein, are attractive candidates for preparation of various potentially “enhanced” envelope immunogens including CD4-Env complexes, constrained envelope structures, and trimeric oligomeric forms. The ability of CON6-induced T and B cell responses to protect against HIV-1 infection and/or disease in 10 SHIV challenge models will be studied in non-human primates.

The above study has demonstrated that artificial centralized HIV-1 genes such as group M consensus env gene (CON6) and Con-S can also induce T cell responses to T cell epitopes in wild-type subtype B and C Env proteins as well as to those on group M consensus Env proteins (Figure 5). While the DNA prime and rVV boost regimen with CON6 gpl40CF immunogen 15 clearly induced IFN-( producing T cells that recognized subtype B and C epitopes, further studies are needed to determine if centralized sequences such as are found in the CON6 envelope are significantly better at inducing cross-clade T cell responses than wild-type HIV-1 genes (Ferrari etal, Proc. Natl. Acad. Sci. USA 94:1396-1401 (1997), Ferrari etal, AIDS Res. Hum. Retroviruses 16:1433-1443 (2000)). However, the fact that CON6 (and Con-S env 20 encoding sequence) prime and boosted splenocyte T cells recognized HIV-1 subtype B and C T cell epitopes is an important step in demonstration that CON6 (and Con-S) can induce T cell responses that might be clinically useful.

Three computer models (consensus, ancestor and center of the tree (COT)) have been proposed to generate centralized HIV-1 genes (Gaschen etal, Science 296:2354-2360 (2002), 25 Gao etal, Science 299:1517-1518 (2003), Nickle etal, Science 299:1515-1517 (2003), Korber etal, Science 288:1789-1796 (2000). They all tend to locate at the roots of the star-like phylogenetic trees for most HIV-1 sequences within or between subtypes. As experimental vaccines, they all can reduce the genetic distances between immunogens and field virus strains. However, consensus, ancestral and COT sequences each have advantages and disadvantages 30 (Gaschen et al, Science 296:2354-2360 (2002), Gao etal, Science 299:1517-1518 (2003), Nickle etal, Science 299:1515-1517 (2003). Consensus and COT represent the sequences or epitopes in sampled current wild-type viruses and are less affected by outliers HIV-1 sequences, while ancestor represents ancestral sequences that can be significantly affected by outlier 41 2017200429 20 Jan 2017 sequences. However, at present, it is not known which centralized sequence can serve as the best immunogen to elicit broad immune responses against diverse HIV-1 strains, and studies are in progress to test these different strategies.

Taken together, the data have shown that the HIV-1 artificial CON6 and Con-S 5 envelope can induce T cell responses to wild-type HIV-1 epitopes, and can induce antibodies that neutralize HIV-1 primary isolates, thus demonstrating the feasibility and promise of using artificial centralized HIV-1 sequences in HIV-1 vaccine design. EXAMPLE 2

HIV-1 Subtype C Ancestral and Consensus Envelope Glycoproteins 10 EXPERIMENTAL DETAILS HIV-1 subtype C ancestral and consensus env genes were obtained from the Los Alamos HIV Molecular Immunology Database (http://hiv-web.lanl.gov/immunology), codon-usage optimized for mammalian cell expression, and synthesized (Fig. 6). To ensure optimal expression, a Kozak sequence (GCCGCCGCC) was inserted immediately upstream of the 15 initiation codon. In addition to the full-length genes, two truncated env genes were generated by introducing stop codons immediately after the gp41 membrane-spanning domain (IVNR) and the gpl20/gp41 cleavage site (REKR), generating gpl40 and gpl20 form of the glycoproteins, respectively (Fig. 8).

Genes were tested for integrity in an in vitro transcription/translation system and /0 expressed in mammalian cells. To determine if the ancestral and consensus subtype C envelopes were capable of mediating fusion and entry, gpl60 and gpl40 genes were cotransfected with an HIV-l/SG3Ae«v provirus and the resulting pseudovirions tested for infectivity using the JC53-BL cell assay (Fig. 7). Co-receptor usage and envelope neutralization sensitivity were also determined with slight modifications of the JC53-BL assay. Codon-usage 25 optimized and rev-dependent 96ZAM651 env genes were used as contemporary subtype C controls.

RESULTS

Codon-optimized subtype C ancestral and consensus envelope genes (gpl60, gpl40, gpl20) express high levels of env glycoprotein in mammalian cells (Fig. 9). 30 Codon-optimized subtype C gpl60 and gpl40 glycoproteins are efficiently incorporated into virus particles. Western Blot analysis of sucrose-purified pseudovirions reveals ten-fold higher levels of virion incorporation of the codon-optimized envelopes compared to that of a rev-dependent contemporary envelope controls (Fig. 10A). 2017200429 20 Jan 2017 42

Virions pseudotyped with either the subtype C consensus gpl60 or gpl40 envelope were more infectious than pseudovirions containing the corresponding gpl60 and gpl40 ancestral envelopes. Additionally, gpl60 envelopes were consistently more infectious than their respective gpl40 counterparts (Fig. 10B). 5 Both subtype C ancestral and consensus envelopes utilize CCR5 as a co-receptor to mediate virus entry (Fig. 11).

The infectivity of subtype C ancestral and consensus gp!60 containing pseudovirions was neutralized by plasma from subtype C infected patients. This suggests that these artificial envelopes possess a structure that is similar to that of native HIV-1 env glycoproteins and that 10 common neutralization epitopes are conserved. No significant differences in neutralization potential were noted between subtype C ancestral and consensus env glycoproteins (gpl60) (Fig. 12).

CONCLUSIONS HIV-1 subtype C viruses are among the most prevalent circulating isolates, representing 15 approximately fifty percent of new infections worldwide. Genetic diversity among globally circulating HIV-1 strains poses a challenge for vaccine design. Although HIV-1 Env protein is highly variable, it can induce both humoral and cellular immune responses in the infected host. By analyzing 70 HIV-1 complete subtype C env sequences, consensus and ancestral subtype C env genes have been generated. Both sequences are roughly equidistant from contemporary 20 subtype C strains and thus expected to induce better cross-protective immunity. A reconstructed ancestral or consensus sequence derived-immunogen minimizes the extent of genetic differences between the vaccine candidate and contemporary isolates. However, consensus and ancestral subtype C env genes differ by 5% amino acid sequences. Both consensus and ancestral sequences have been synthesized for analyses. Codon-optimized subtype C ancestral 25 and consensus envelope genes have been constructed and the in vitro biological properties of the expressed glycoproteins determined. Synthetic subtype C consensus and ancestral env genes express glycoproteins that are similar in their structure, function and antigenicity to contemporary subtype C wild-type envelope glycoproteins. 43 2017200429 20 Jan 2017 EXAMPLE 3

Codon-Usage Optimization of Consensus of Subtype C gag and nef Genes (C.con.gag and C.con.nef)

Subtype C viruses have become the most prevalent viruses among all subtypes of Group 5 M viruses in the world. More than 50% of HIV-1 infected people are currently carrying HIV-1 subtype C viruses. In addition, there is considerable intra-subtype C variability: different subtype C viruses can differ by as much as 10%, 6%, 17% and 16% of their Gag, Pol, Env and Nef proteins, respectively. Most importantly, the subtype C viruses from one country can vary as much as the viruses isolated from other parts of the world. The only exceptions are HTV-1 10 strains from India/China, Brazil and Ethiopia/Djibouti where subtype C appears to have been introduced more recently. Due to the high genetic variability of subtype C viruses even within a single country, an immunogen based on a single virus isolate may not elicit protective immunity against other isolates circulating in the same area.

Thus gag and nef gene sequences of subtype C viruses were gathered to generate 15 consensus sequences for both genes by using a 50% consensus threshold. To avoid a potential bias toward founder viruses, only one sequence was used from India/China, Brazil and Ethiopia/Djibouti, respectively, to generate the subtype C consensus sequences (C.con.gag and C.con.nef). The codons of both C.con.gag and C.con.nef genes were optimized based on the codon usage of highly expressed human genes. The protein expression following transfection /0 into 293T cells is shown in Figure 13. As can be seen, both consensus subtype C Gag and Nef proteins were expressed efficiently and recognized by Gag- and Nef-specific antibodies. The protein expression levels of both C.con.gag and C.con.nef genes are comparible to that of native subtype env gene (96ZM651). EXAMPLE 4 25 Synthesis of a Full Length “Consensus of the Consensus env Gene with Consensus Variable

Regions” (CON-S)

In the synthesized “consensus of the consensus” env gene (CON6), the variable regions were replaced with the corresponding regions from a contemporary subtype C virus (98CN006). A further con/con gene has been designed that also has consensus variable regions 30 (CON-s). The codons of the Con-S env gene were optimized based on the codon usage of highly expressed human genes. (See Figs. 14A and 14B for amino acid sequences and nucleic acid sequences, respectfully.) 44 2017200429 20 Jan 2017

Paired oligonucleotides (80-mers) which overlap by 20 bp at their 3’ ends and contain invariant sequences at their 5’ and 3’ ends, including the restriction enzyme sites EcoRI and Bbsl as well as BsmBI and BamHI, respectively, were designed. Bbsl and BamHI are Type II restriction enzymes that cleave outside of their recognition sequences. They have been 5 positioned in the oligomers in such a way that they cleave the first four resides adjacent to the 18 bp invariant region, leaving 4 base 5’ overhangs at the end of each fragment for the following ligation step. 26 paired oligomers were linked individually using PCR and primers complimentary to the 18 bp invariant sequences. Each pair was cloned into pGEM-T (Promega) using the T/A cloning method and sequenced to confirm the absence of inadvertent 10 mutations/deletions. pGEM-T subclones containing the proper inserts were then digested, run on a 1% agarose gel, and gel purified (Qiagen). Four individual 108-mers were ligated into pcDNA3.1 (Invitrogen) in a multi-fragment ligation reaction. The four-way ligations occurred among groups of fragments in a stepwise manner from the 5’ to the 3’ end of the gene. This process was repeated until the entire gene was reconstructed in the pcDNA3.1 vector. 15 A complete Con-S gene was constructed by ligating the codon usage optimized oligo pairs together. To confirm its open reading frame, an in vitro transcription and translation assay was performed. Protein products were labeled by ^-methionine during the translation step, separated on a 10% SDS-PAGE, and detected by radioautography. Expected size of the expressed Con-S gpl60 was identified in 4 out of 7 clones (Fig. 14C). 20 CONs Env protein expression in the mammalian cells after transfected into 293T cells using a Western blot assay (Figure 15). The expression level of Con-S Env protein is very similar to what was observed from the previous CON6 env clone that contains the consensus conservative regions and variable loops from 98CN006 virus isolate.

The Env-pseudovirons was produced by cotransfecting Con-S env clone and env-25 deficient SG3 proviral clone into 293T cells. Two days after transfection, the pseudovirions were harvested and infected into JC53BL-13 cells. The infectious units (IU) were determined by counting the blue cells after staining with X-gal in three independent experiments. When compared with CON6 env clone, Con-S env clones produce similar number of IU in JC53BL-13 cells (Figure 16). The IU titers for both are about 3 log higher than the SG3 backbone clone 30 control (No Env). However, the titers are also about 2 log lower than the positive control (the native HIV-1 env gene, NL4-3 or YU2). These data suggest that both consensus group M env clones are biologically functional. Their functionality, however, has been compromised. The functional consensus env genes indicate that these Env proteins fold correctly, preserve the 45 2017200429 20 Jan 2017 basic conformation of the native Env proteins, and are able to be developed as universal Env immunogens.

It was next determined what coreceptor Con-S Env uses for its entry into JC53-BL cells. When treated with CXCR4 blocking agent AMD3100, the infectivity of NL4-3 Env-5 pseudovirons was blocked while the infectivity of YU2, Con-S or CON6 Env-pseudovirons was not inhibited. In contrast, when treated with CCR5 blocking agent TAK.779, the infectivity of NL4-3 Env-pseudovirons was not affected, while the infectivity of YU2, Con-S or CON6 Env-pseudovirons was inhibited. When treated with both blocking agents, the infectivity of all pseudovirions was inhibited. Taken together, these data show that the Con-S as well as CON6 10 envelope uses the CCR5 but not CXCR4 co-receptor for its entry into target cells.

It was next determined whether CON6 or Con-S Env proteins could be equally efficiently incorporated in to the pseudovirions. To be able precisely compare how much Env proteins were incorporated into the pseudovirions, each pseudovirions is loaded on SDS-PAGE at the same concentraion: 5:g total protein for cell lysate, 25ng p24 for cell culture supernatant, 15 or 150ng p24 for purified virus stock (concentrated pseudovirions after super-speed centrifugation). There was no difference in amounts of Env proteins incorporated in CON6 or Con-S Env-pseudovirions in any preparations (cell lysate, cell culture supernatant or purified virus stock) (Figure 17). EXAMPLE 5 20 Synthesis of a Consensus Subtype A Full Length env (A.con.env) Gene

Subtype A viruses are the second most prevalent HIV-1 in the African continent where over 70% of HIV-1 infections have been documented. Consensus gag, env and nef genes for subtype C viruses that are the most prevalent viruses in Africa and in the world were previously generated. Since genetic distances between subtype A and C viruses are as high as 30% in the 25 env gene, the cross reactivity or protection between both subtypes will not be optimal. Two group M consensus env genes for all subtypes were also generated. However, to target any particular subtype viruses, the subtype specific consensus genes will be more effective since the genetic distances between subtype consensus genes and field viruses from the same subtype will be smaller than that between group M consensus genes and these same viruses. Therefore, 30 consensus genes need to be generated for development of subtype A specific immunogens. The codons of the A.con.env gene were optimized based on the codon usage of highly expressed human genes. (See Figs. 18A and 18B for amino acid and nucleic acid sequences, respectively.) 46 2017200429 20 Jan 2017

Each pair of the oligos has been amplified, cloned, ligated and sequenced. After the open reading frame of the A.con env gene was confirmed by an in vitro transcription and translation system, the A.con env gene was transfected into the 293T cells and the protein expression and specificity confirmed with the Western blot assay (Figure 18). It was then 5 determined whether A.con envelope is biologically functional. It was co-transfected with the c/m-defective SG3 proviral clone into 293T cells. The pseudotyped viruses were harvested and used to infect JC53BL cells. Blue cells were detected in JC53-BL cells infected with the A.con Env-pseudovirions, suggesting that A.con Env protein is biologically functional (Table 6). However, the infectious titer of A.con Env-psuedovirions was about 7-fold lower than that of 10 pseudovirions with wild-type subtype C envelope (Table 6). Taken together, the biological function A.con Env proteins suggests that it folds correctly and may induce linear and conformational T and B cell epitopes if used as an Env immunogen.

Table 6. Infectivity of pseudovirons with A.con env genes JC53BL13 (IU/ul) 3/31/03 4/7/03 4/25/03 non filtered supt. 0.22pm filtered 0.22pm filtered A.con +SG3 4 8.5 15.3 96ZM651 +SG3 87 133 104 SG3 backbone 0 0.07 0.03 Neg control 0 0.007 0 EXAMPLE 6

Design of Full Length "Consensus of the Consensus gag, pol and nef Genes" (M.con.gag, 15 M.con.pol and M.con.nef) and a Subtype C Consensus pol Gene (C.con.pol)

For the group M consensus genes, two different env genes were constructed, one with virus specific variable regions (CON6) and one with consensus variable regions (Con-S). However, analysis of T cell immune responses in immunized or vaccinated animals and humans shows that the env gene normally is not a main target for T cell immune response although it is 20 the only gene that will induce neutralizing antibody. Instead, HIV-1 Gag, Pol and Nef proteins are found to be important for inducing potent T cell immune responses. To generate a repertoire of immunogens that can induce both broader humoral and cellular immune responses for all subtypes, it may be necessary to construct other group M consensus genes other than env gene alone. "Consensus of the consensus" gag, pol and nef genes (M.con.gag., M. con.pol and 47 2017200429 20 Jan 2017 M.con.nef) have been designed. To generate a subtype consensus pol gene, the subtype C consensus pol gene (C.con.pol) was also designed. The codons of the M.con.gag., M.con.pol, M.con.nef and C. con.pol. genes were optimized based on the codon usage of highly expressed human genes. (See Fig. 19 for nucleic acid and amino acid sequences.) 5 EXAMPLE 7

Synthetic Subtype B Consensus gag and env Genes EXPERIMENTAL DETAILS

Subtype B consensus gag and env sequences were derived from 37 and 137 contemporary HIV-1 strains, respectively, codon-usage optimized for mammalian cell 10 expression, and synthesized (Figs. 20A and 20B). To ensure optimal expression, a Kozak sequence (GCCGCCGCC) was inserted immediately upstream of the initiation codon. In addition to the full-length env gene, a truncated env gene was generated by introducing a stop codon immediately after the gp41 membrane-spanning domain (IVNR) to create a gpl45 gene. Genes were tested for integrity in an in vitro transcription/translation system and expressed in 15 mammalian cells. (Subtype B consensus Gag and Env sequences are set forth in Figs. 20C and 20D, respectively.)

To determine if the subtype B consensus envelopes were capable of mediating fusion and entry, gp!60 and gp!45 genes were co-transfected with an HIV-l/SG3)env provirus and the resulting pseudovirions were tested for infectivity using the JC53-BL cell assay. JC53-BL cells 20 are a derivative of HeLa cells that express high levels of CD4 and the HIV-1 coreceptors CCR5 and CXCR4. They also contain the reporter cassettes of luciferase and 3-galactosidase that are each expressed from an HTV-1 LTR. Expression of the reporter genes is dependent on production of HTV-1 Tat. Briefly, cells are seeded into 24-well plates, incubated at 37°C for 24 hours and treated with DEAE-Dextran at 37°C for 30min. Virus is serially diluted in 1% 25 DMEM, added to the cells incubating in DEAE-dextran, and allowed to incubate for 3 hours at 37°C after which an additional 500pL of cell media is added to each well. Following a final 48-hour incubation at 37°C, cells are fixed, stained using X-Gal, and overlaid with PBS for microscopic counting of blue foci. Counts for mock-infected wells, used to determine background, are subtracted from counts for the sample wells. Co-receptor usage and envelope 30 neutralization sensitivity were also determined with slight modifications of the JC53-BL assay.

To determine whether the subtype B consensus Gag protein was capable of producing virus-like particles (VLPs) that incorporated Env glycoproteins, 293T cells were co-transfected with subtype B consensus gag and env genes. 48-hours post-transfection, cell supernatants 2017200429 20 Jan 2017 48 containing VLPs were collected, clarified in a tabletop centrifuge, filtered through a 0.2mM filter, and pellet through a 20% sucrose cushion. The VLP pellet was resuspended in PBS and transferred onto a 20-60% continuous sucrose gradient. Following overnight centrifugation at 100,000 x g, 0.5 ml fractions were collected and assayed for p24 content. The refractive index 5 of each fraction was also measured. Fractions with the correct density for VLPs and containing the highest levels of p24 were pooled and pellet a final time. VLP-containing pellets were resuspended in PBS and loaded on a 4-20% SDS-PAGE gel. Proteins were transferred to a PVDF membrane and probed with serum from a subtype B HIV-1 infected individual.

RESULTS 10 Codon-usage optimized, subtype B consensus envelope (gp!60, gpl45) and gag genes express high levels of glycoprotein in mammalian cells (Fig. 21).

Subtype B gpl60 and gpl45 glycoproteins are efficiently incorporated into virus particles. Western Blot analysis of sucrose-purified pseudovirions suggests at least five-fold higher levels of consensus B envelope incorporation compared to incorporation of a rev-15 dependent contemporary envelope (Fig.23A). Virions pseudotyped with either the subtype B consensus gpl60 or gpl45 envelope are more infectious than pseudovirions containing a rev-dependent contemporary envelope (Fig. 23 B).

Subtype B consensus envelopes utilize CCR5 as the co-receptor to gain entry into CD4 bearing target cells (Fig. 22). 20 The infectivity of pseudovirions containing the subtype B consensus gpl60 envelope was neutralized by plasma from HIV-1 subtype B infected patients (Fig. 24C) and neutralizing monoclonal antibodies (Fig. 24A). This suggests that the subtype B synthetic consensus B envelopes is similar to native HIV-1 Env glycoproteins in its overall structure and that common neutralization epitopes remain intact. Figs. 24B and 24D show neutralization profiles of a 25 subtype B control envelope (NL4.3 Env).

Subtype B consensus Gag proteins are able to bud from the cell membrane and form virus-like particles (Fig. 25A). Co-transfection of the codon-optimized subtype B consensus gag and gpl60 genes produces VLPs with incorporated envelope (Fig. 25B). CONCLUSIONS 2017200429 20 Jan 2017 49

The synthetic subtype B consensus env and gag genes express viral proteins that are similar in their structure, function and antigenicity to contemporary subtype B Env and Gag proteins. It is contemplated that immunogens based on subtype B consensus genes will elicit CTL and neutralizing immune responses that are protective against a broad set of HIV-1 5 isolates. * * *

All documents and other information sources cited above are hereby incorporated in their entirety by reference. Also incorporated by reference is Liao et al, J. Virol. 78:5270 (2004)). 10 Any reference to publications cited in this specification is not an admission that the disclosures constitute common general knowledge in Australia.

The term “comprise” and variants of the term such as “comprises” or “comprising” are used herein to denote the inclusion of a stated integer or stated integers but not to exclude any other integer or any other integers, unless in the context or usage an exclusive interpretation of 15 the term is required.

Claims (96)

1. WHAT IS CLAIMED IS:

   1. An isolated protein comprising the sequence of amino acids set forth in Fig. 1A.
2. 2. A nucleic acid comprising a nucleotide sequence encoding CON6 HIV gpl60 protein, wherein said nucleotide sequence comprises codons optimized for expression in human cells.
3. 3. The nucleic acid according to claim 2 wherein said nucleic acid comprises the nucleotide sequence set forth in Fig. ID.
4. 4. A nucleic acid comprising a nucleotide sequence encoding subtype C ancestral HIV envelope protein, wherein said nucleotide sequence comprises codons optimized for expression in human cells.
5. 5. The nucleic acid according to claim 4 wherein said nucleic acid comprises the nucleotide sequence set forth in Fig. 6A.
6. 6. A nucleic acid comprising a nucleotide sequence encoding subtype C consensus HIV envelope protein, wherein said nucleotide sequence comprises codons optimized for expression in human cells.
7. 7. The nucleic acid according to claim 6 wherein said nucleic acid comprises the nucleotide sequence set forth in Fig. 6B .
8. 8. An isolated protein comprising the sequence of amino acids set forth in Fig. 6C or 6D.
9. 9. A nucleic acid comprising a nucleotide sequence encoding a subtype C consensus HIV gag protein, wherein said nucleotide sequence comprises codons optimized for expression in human cells.
10. 10. The nucleic acid according to claim 9 wherein said nucleic acid comprises the nucleotide sequence set forth in Fig. 13E.
11. 11. A nucleic acid comprising a nucleotide sequence encoding a subtype C consensus HIV nef protein, wherein said nucleotide sequence comprises codons optimized for expression in human cells.
12. 12. The nucleic acid according to claim 11 wherein said nucleic acid comprises the nucleotide sequence set forth in Fig. 13F.
13. 13. A nucleic acid comprising a nucleotide sequence encoding Group M consensus HIV envelope protein, wherein said nucleotide sequence comprises codons optimized for expression in human cells.
14. 14. The nucleic acid according to claim 13 wherein said nucleic acid comprises the nucleotide sequence set forth in Fig. 14B.
15. 15. A nucleic acid comprising a nucleotide sequence encoding subtype A consensus HIV envelope protein, wherein said nucleotide sequence comprises codons optimized for expression in human cells.
16. 16. The nucleic acid according to claim 15 wherein said nucleic acid comprises the nucleotide sequence set forth in Fig. 18B.
17. 17. A nucleic acid comprising a nucleotide sequence encoding Group M consensus HIV gag protein, wherein said nucleotide sequence comprises codons optimized for expression in human cells.
18. 18. The nucleic acid according to claim 17 wherein said nucleic acid comprises the nucleotide sequence set forth in Fig. 19A .
19. 19. A nucleic acid comprising a nucleotide sequence encoding Group M consensus HIV pol protein, wherein said nucleotide sequence comprises codons optimized for expression in human cells.
20. 20. The nucleic acid according to claim 19 wherein said nucleic acid comprises the nucleotide sequence set forth in Fig. 19B.
21. 21. A nucleic acid comprising a nucleotide sequence encoding Group M consensus HIV nef protein, wherein said nucleotide sequence comprises codons optimized for expression in human cells.
22. 22. The nucleic acid according to claim 21 wherein said nucleic acid comprises the nucleotide sequence set forth in Fig. 19C.
23. 23. A nucleic acid comprising a nucleotide sequence encoding subtype C consensus HIV pol protein, wherein said nucleotide sequence comprises codons optimized for expression in human cells.
24. 24. The nucleic acid according to claim 23 wherein said nucleic acid comprises the nucleotide sequence set forth in Fig. 19D.
25. 25. A nucleic acid comprising a nucleotide sequence encoding subtype B consensus HIV gag protein, wherein said nucleotide sequence comprises codons optimized for expression in human cells.
26. 26. The nucleic acid according to claim 25 wherein said nucleic acid comprises the nucleotide sequence set forth in Fig. 20A.
27. 27. A nucleic acid comprising a nucleotide sequence encoding subtype B consensus HIV envelope protein, wherein said nucleotide sequence comprises codons optimized for expression in human cells.
28. 28. The nucleic acid according to claim 27 wherein said nucleic acid comprises the nucleotide sequence set forth in Fig. 20B.
29. 29. An isolated protein comprising the sequence of amino acids set forth in Fig. 20C or 20D.
30. 30. An isolated protein comprising the sequence of amino acids set forth in Fig. 26A .
31. 31. A nucleic acid comprising a nucleotide sequence that encodes the protein according to claim 30.
32. 32. The nucleic acid according to claim 31 wherein said nucleic acid comprises the nucleotide sequence set forth in Fig. 26B.
33. 33. An isolated protein comprising the sequence of amino acids set forth in Fig. 28B.
34. 34. A nucleic acid comprising a nucleotide sequence encoding the protein according to claim 33.
35. 35. The nucleic acid sequence according to claim 34 wherein said nucleic acid comprises the nucleotide sequence set forth in Fig. 28C.
36. 36. An isolated protein comprising the sequence of amino acids set forth in Fig. 29B.
37. 37. A nucleic acid comprising a nucleotide sequence encoding the protein according to claim 36.
38. 38. The nucleic acid sequence according to claim 37 wherein said nucleic acid comprises the nucleotide sequence set forth in Fig. 29C.
39. 39. An isolated protein comprising the sequence of amino acids set forth in Fig. 30B.
40. 40. A nucleic acid comprising a nucleotide sequence encoding the protein according to claim 39.
41. 41. The nucleic acid sequence according to claim 40 wherein said nucleic acid comprises the nucleotide sequence set forth in Fig. 30C.
42. 42. An isolated protein comprising the sequence of amino acids set forth in Fig. 3IB.
43. 43. A nucleic acid comprising a nucleotide sequence encoding the protein according to claim 42
44. 44. The nucleic acid sequence according to claim 43 wherein said nucleic acid comprises the nucleotide sequence set forth in Fig. 31C.
45. 45. An isolated protein comprising the sequence of amino acids set forth in Fig. 32B.
46. 46. A nucleic acid comprising a nucleotide sequence encoding the protein according to claim 45
47. 47. The nucleic acid sequence according to claim 46 wherein said nucleic acid comprises the nucleotide sequence set forth in Fig. 32C.
48. 48. An isolated protein comprising the sequence of amino acids set forth in Fig. 33B.
49. 49. A nucleic acid comprising a nucleotide sequence encoding the protein according to claim 48
50. 50. The nucleic acid sequence according to claim 49 wherein said nucleic acid comprises the nucleotide sequence set forth in Fig. 33C.
51. 51. An isolated protein comprising the sequence of amino acids set forth in Fig. 34B.
52. 52. A nucleic acid comprising a nucleotide sequence encoding the protein according to claim 51.
53. 53. The nucleic acid sequence according to claim 52 wherein said nucleic acid comprises the nucleotide sequence set forth in Fig. 34C.
54. 54. An isolated protein comprising the sequence of amino acids set forth in Fig. 35B.
55. 55. A nucleic acid comprising a nucleotide sequence encoding the protein according to claim 54.
56. 56. The nucleic acid sequence according to claim 55 wherein said nucleic acid comprises the nucleotide sequence set forth in Fig. 35C.
57. 57. An isolated protein comprising the sequence of amino acids set forth in Fig. 36B.
58. 58. A nucleic acid comprising a nucleotide sequence encoding the protein according to claim 57.
59. 59. The nucleic acid sequence according to claim 58 wherein said nucleic acid comprises the nucleotide sequence set forth in Fig. 36C.
60. 60. An isolated protein comprising the sequence of amino acids set forth in Fig. 37B.
61. 61. A nucleic acid comprising a nucleotide sequence encoding the protein according to claim 60
62. 62. The nucleic acid sequence according to claim 61 wherein said nucleic acid comprises the nucleotide sequence set forth in Fig. 37C.
63. 63. An isolated protein comprising the sequence of amino acids set forth in Fig. 38B.
64. 64. A nucleic acid comprising a nucleotide sequence encoding the protein according to claim 63.
65. 65. The nucleic acid sequence according to claim 64 wherein said nucleic acid comprises the nucleotide sequence set forth in Fig. 38C.
66. 66. An isolated protein comprising a CF or CFI form of the amino acid sequence set forth in any one of Figs. 39A-127A.
67. 67. A nucleic acid comprising the nucleotide sequence set forth in Fig. 39B.
68. 68. A nucleic acid comprising the nucleotide sequence set forth in Fig. 40B.
69. 69. A nucleic acid comprising the nucleotide sequence set forth in Fig. IB.
70. 70. A nucleic acid comprising the nucleotide sequence set forth in Fig. 42B.
71. 71. A nucleic acid comprising the nucleotide sequence set forth in Fig. 43B.
72. 72. A nucleic acid comprising the nucleotide sequence set forth in Fig. 44B.
73. 73. A nucleic acid comprising the nucleotide sequence set forth in Fig. 45B.
74. 74. A nucleic acid comprising the nucleotide sequence set forth in Fig. 46B.
75. 75. A nucleic acid comprising the nucleotide sequence set forth in Fig. 7B.
76. 76. A nucleic acid comprising the nucleotide sequence set forth in Fig. 48B.
77. 77. A nucleic acid comprising the nucleotide sequence set forth in Fig. 49B.
78. 78. A nucleic acid comprising the nucleotide sequence set forth in Fig. 50B.
79. 79. A nucleic acid comprising the nucleotide sequence set forth in Fig. 5IB.
80. 80. A nucleic acid comprising the nucleotide sequence set forth in Fig. 52B.
81. 81. A nucleic acid comprising the nucleotide sequence set forth in Fig. 53B.
82. 82. A nucleic acid comprising the nucleotide sequence set forth in Fig. 54B.
83. 83. A nucleic acid comprising the nucleotide sequence set forth in Fig. 55B.
84. 84. A nucleic acid comprising the nucleotide sequence set forth in Fig. 56B.
85. 85. A nucleic acid comprising the nucleotide sequence set forth in Fig. 57B.
86. 86. A nucleic acid comprising the nucleotide sequence set forth in- Fig. 58B.
87. 87. A nucleic acid comprising the nucleotide sequence set forth in Fig. 59B.
88. 88. A nucleic acid comprising the nucleotide sequence set forth· in Fig. 60B.
89. 89. A nucleic acid comprising the nucleotide sequence set forth in Fig. 61B.
90. 90. A nucleic acid comprising the nucleotide sequence set forth in Fig. 62B.
91. 91. A nucleic acid comprising the nucleotide sequence set forth in any one of Figs. 63B- 84B, 65D, 67D and 68D.
92. 92. A nucleic acid comprising the nucleotide sequence set forth in any one of Figs. 85B-106B, 88D, 90D and 92D.
93. 93. A nucleic acid comprising the nucleotide sequence set forth in any one of Figs. 107B-127B, 109D, HID and 112D.
94. 94. A vector comprising the nucleic acid according to any one of claims 2-7, 9-28, 31, 32, 34, 35, 37, 38, 40, 41, 43, 44, 46, 47, 49, 50, 52, 53, 55, 56, 58, 59, 61, 62, 64, 65 and 6793.
95. 95. A composition comprising at least one protein or nucleic acid according to any one of claims 1-93 and a carrier.
96. 96. A method of inducing an immune response in a mammal comprising administering to said mammal an amount of at least one protein and/or nucleic acid according to any one of claims 1-93 sufficient to effect said induction.