Immunogen sequence: the fourth tier of AIDS vaccine design

References

• (WHO) AIDS epidemic update. Geneva, Switzerland (2002).
   Google Scholar
• McMichael A, Rowland-Jones S. Cellular immune responses to HIV Nature 410, 980–987 (2001).
   Google Scholar
• Graham BS. Clinical trials of HIV vaccines.Ann. Rev Merl 53, 207–221 (2002).
   PubMedGoogle Scholar
• Koup RA, Safrit JT, Cao Y et al Temporal association of cellular immune responses with the initial control of viremia in primary human immunodeficiency virus type 1 syndrome. J. Vim!. 68,4650-4655 (1994).
   Google Scholar
• Parren PWHI, Moore J, Burton DR, Sattentau QJ. The neutralizing antibody responses to HIV-1: viral evasion and escape from humoral immunity. AIDS13, S137—S162 (1999).
   Google Scholar
• Montefiori DC, Altfeld M, Lee PK et al. Viremia control despite escape from a rapid and potent autologous neutralizing antibody response after therapy cessation in an HIV-1-infected individual. j Immunol 170, 3906–3914 (2003).
   PubMedGoogle Scholar
• Burton DR. A vaccine for HIV type 1: the antibody perspective. Proc. Nail Acad. Sc]. USA 94, 10018–10023 (1997).
   Google Scholar
• Wei X, Decker JM, Wang S et al Antibody neutralization and escape by HIV-1. Nature 422, 307–312 (2003).
   PubMed Web of Science ®Google Scholar
• •Provides evidence for an evolving glycan shield' mechanism of neutralization escape.
   Google Scholar
• Richman DD, Wrin T, Little SJ, Petropoulos CJ. Rapid evolution of the neutralizing antibody response to HIV type 1 infection. Proc. Natl Acad. Sc]. USA 100, 4144–4149 (2003).
   Google Scholar
• •Illustrates potent neutralizing antibody responses that are generated early after infection in most patients. Plasma virus continually evolved to escape neutralization.
   Google Scholar
• Shibata R, Igarashi T, Haigwood N et al. Neutralizing antibody directed against the HIV-1 envelope glycoprotein can completely block HIV-1/SIV chimeric virus infections of macaque monkeys. Nature Merl 5,204–210 (1999).
   PubMed Web of Science ®Google Scholar
• Mascola JR. Defining the protective antibody response for HIV-1. CU17: Mal Merl 3, 209–216 (2003).
   Google Scholar
• Burton DR Antibodies, viruses and vaccines.Nature Rev Immunol 2, 706–713 (2002).
   Google Scholar
• Borrow P, Lewicki H, Hahn BH, Shaw GM, Oldstone MB. Virus-specific CD8+ cytotoxic T-lymphocyte activity associated with control of viremia in primary human immunodeficiency virus type 1 infection.j Viral 68, 6103–6110 (1994).
   Google Scholar
• Musey L, Hughes J, Schacker T, Shea T, Corey L, McElrath MJ. Cytotoxic-T-cell responses, viral load, and disease progression in early human immunodeficiency virus type 1 infection. N. Engl. Merl 337, 1267–1274 (1997).
   Google Scholar
• Harrer T, Harrer E, Kalams SA et al. Cytotoxic T-lymphocytes in asymptomaticlong-term nonprogressing HIV-1 infection. Breadth and specificity of the response and relation to in vivoviral quasispecies in a person with prolonged infection and low viral load. J. Immunol 156, 2616–2623 (1996).
   Google Scholar
• Ogg GS, Jin X, Bonhoeffer S et al. Quantitation of HIV-1-specific T-lymphocytes and plasma viral load of viral RNA. Science 279, 2103–2106 (1998).
   PubMed Web of Science ®Google Scholar
• Klein MR, Miedema F. Long-term survivors in HIV-1 infection. 7iencls Nlicrobiol 10, 386–391 (1995).
   Google Scholar
• Propato A, Schiaffella E, Vicenzi E et al. Spreading of HIV-specific CD8* T-cell repertoire in long-term nonprogressors and its role in the control of viral load and disease activity. Hum. Immunol 62, 561–576 (2001).
   Google Scholar
• Schmitz JE, Kuroda MJ, Santra S et al Control of viremia in simian immunodeficiency virus infection by CD8* lymphocytes. Science283, 857–860 (1999).
   PubMed Web of Science ®Google Scholar
• Jin X, Bauer DE, Tuttleton SE et al Dramatic rise in plasma viremia after CD8* T-cell depletion in simian immunodeficiency virus-infected macaques.EAp. Merl 189, 991–998 (1999).
   Google Scholar
• Castro BA, Nepomuceno M, Lerche NW, Eichberg JW, Levy JA. Persistent infection of baboons and rhesus monkeys with different strains of HIV-2. Virology184, 219–226 (1991).
   Google Scholar
• Mullins JI. Curtailing the AIDS pandemic.Science 276, 1955–1957 (Letter) (1997).
   Google Scholar
• Warren J. Preclinical AIDS vaccine research: survey of SW, SHIV, and HIV challenge studies in vaccinated nonhuman primates. Merl Primatol 31, 237–256 (2002).
   Google Scholar
• Berman PW, Gray AM, Wrin T et al. Genetic and immunologic characterization of viruses infecting MN-rgp120-vaccinated volunteers. Infect. Dis. 176, 384–397 (1997).
   Google Scholar
• Connor RI, Korber BT, Graham BS et al Immunological and virological analyses of persons infected by human immunodeficiency virus type 1 while participating in trials of recombinant gp120 subunit vaccines. Viral 72, 1552–1576 (1998).
   PubMed Web of Science ®Google Scholar
• Graham BS, McElrath MJ, Connor RI et al Analysis of intercurrent human immunodeficiency virus type 1 infections in Phase I and II trials of candidate AIDS vaccines. AIDS Vaccine Evaluation Group, and the Correlates of HIV Immune Protection Group. J Infect. Dis. 177, 310–319 (1998).
   Google Scholar
• Jost S, Bernard MC, Kaiser L et al. A patient with HIV-1 superinfection. N Engl J. Merl 347, 731–736 (2002).
   Google Scholar
• Altfeld M, Allen TM, Yu XG et al. HIV-1 superinfection despite broad CD8+ T-cell responses containing replication of the primary virus. Nature 420, 434–439 (2002).
   PubMed Web of Science ®Google Scholar
• Nabel GJ. HIV vaccine strategies. Vaccine 20, 1945–1947 (2002).
   PubMedGoogle Scholar
• Shankarappa R, Margolick JB, Gange SJ et al Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection.Vim!. 73, 10489–10502 (1999).
   Google Scholar
• Myers G, Korber B, Wain-Hobson S, Smith RF, Pavlakis GN. Human retroviruses and AIDS. A compilation and analysis of nucleic acid and amino acid sequences (1993).
   Google Scholar
• Anderson JP, Rodrigo AG, Learn GH et al Substitution model of sequence evolution for the human immunodeficiency virus type 1 subtype B gp120 gene over the C2-V5 region. J Mal Eval. 53, 55–62 (2001).
   Google Scholar
• Nabel G, Makgoba W, Esparza J. HIV-1 diversity and vaccine development. Science 296, 2335 (2002).
   Google Scholar
• Francis DP, Gregory T, McElrath MJ et al Advancing AIDSVAX to Phase III. Safety, immunogenicity, and plans for Phase III. AIDS Res. Hum. Retroviruses 14 Suppl. 3, S325-331 (1998).
   Google Scholar
• Esparza J, Osmanov S, Pattou-Markovic C, Toure C, Chang ML, Nixon S. Past, present and future of HIV vaccine trials in developing countries. Vaccine 20, 1897–1898 (2002).
   Google Scholar
• Alcorn K. Vaxgen announces second Phase III trial failure in its AIDSVAX programme www.aidsmap.com/news/newsdisplay2.asp? newsId=2411 (2003).
   Google Scholar
• Wagner R, Deml L, Wolf H. Polyvalent, recombinant HIV-1 virus-like particles: novel HIV-1 vaccine strategies. Antibiot. Chemother. 46, 48–61 (1994).
   Google Scholar
• Fomsgaard A. HIV-1 DNA vaccines.Immunol Lett. 65, 127–131 (1999).
   PubMed Web of Science ®Google Scholar
• Cho MW, Kim YB, Lee MK et al Polyvalent envelope glycoprotein vaccine elicits a broader neutralizing antibody response but is unable to provide sterilizing protection against heterologous simian/human immunodeficiency virus infection in pigtailed macaques. J Viral 75, 2224–2234 (2001).
   PubMed Web of Science ®Google Scholar
• Slobod KS, Lockey TD, Howlett N et al Subcutaneous administration of a recombinant vaccinia virus vaccine expressing multiple envelopes of HIV-1. Eur. j Orin. Nlicmbiol. Infect. Dis. 23, 106–110 (2004).
   Google Scholar
• Takahashi H, Nakagawa Y, Pendleton CDet al Induction of broadly cross-reactive cytotoxic T-cells recognizing an HIV-1 envelope determinant. Science 255, 333–336 (1992).
   PubMed Web of Science ®Google Scholar
• Hanke T, McMichael AJ. Design and construction of an experimental HIV-1 vaccine for a year-2000 clinical trial in Kenya. Nature Med. 6, 951–955 (2000).
   PubMed Web of Science ®Google Scholar
• ••Illustrates the design of a vaccine immunogen that strings together 25 partially overlapping cytotoxic T-cell (cro epitopes from Gag, Pol, Env and Nef.
   Google Scholar
• Hanke T, McMichael AJ, Mwau M et al Development of a DNA—MVA/HIVA vaccine for Kenya. Vaccine 20, 1995–1998 (2002).
   PubMed Web of Science ®Google Scholar
• Hanke T, Barnfield C, Wee EG et al Construction and immunogenicity in a prime-boost regimen of a Semliki Forest virus-vectored experimental HIV clade A vaccine. J Gen. Vim!. 84, 361–368 (2003).
   PubMedGoogle Scholar
• Pantophlet R, Ollmann Saphire E, Poignard P, Parren PW, Wilson IA, Burton DR. Fine mapping of the interaction of neutralizing and nonneutralizing monoclonal antibodies with the CD4 binding site of human immunodeficiency virus type 1 gp120. Viral 77, 642–658 (2003).
   PubMed Web of Science ®Google Scholar
• ••Reports efforts to engineer gp120 suchthat antibody binding is restricted to those with broadly neutralizing capacity.
   Google Scholar
• Burton DR, Pyati J, Koduri R et al. Efficient neutralization of primary isolates of HIV-1 by a recombinant human monoclonal antibody. Science 266, 1024–1027 (1994).
   PubMed Web of Science ®Google Scholar
• Pantophlet R, Wilson IA, Burton DR. Hyperglycosylated mutants of human immunodeficiency virus (HIV) type 1 monomeric gp120 as novel antigens for HIV vaccine design. J Viral 77, 5889–5901 (2003).
   Google Scholar
• Delves PJ, Lund T, Roitt IM. Can epitope- focused vaccines select advantageous immune responses? Mal Merl Today 3, 55–60 (1997).
   Google Scholar
• Garrity RR, Rimmelzwaan G, Minassian A et al. Refocusing neutralizing antibody response by targeted dampening of an immunodominant epitope. I Immunol 159, 279–289 (1997).
   PubMed Web of Science ®Google Scholar
• •Suggests a strategy for reshaping humoral immune responses by redirecting immune response away from the V3 domain.
   Google Scholar
• Learn G, Mullins JI. The Use of an Inferred Epidemic Ancestral Sequence as a Vaccine Immunogen, Abstract at Seventh International Discussion Meeting on HIV Dynamics & Evolution, Seattle, WA (2000).
   Google Scholar
• Gaschen B, Taylor J, Yusim K et al Diversity considerations in HIV-1 vaccine selection. Science 296, 2354–2360 (2002).
   PubMed Web of Science ®Google Scholar
• Page RDM, Holmes EC. Molecular Evolution: a Phylogenetic Approach, Blackwell Science, Oxford (1998).
   Google Scholar
• Gao F, Bhattacharya T, Gaschen B et al Consensus and ancestral state HIV vaccines [author reply]. Science 299, 1517–1518 (2003).
   Google Scholar
• Chang BS, Donoghue MJ. Recreating ancestral proteins. Trench Era'. Evol 15, 109–114 (2000).
   Google Scholar
• Jermann TM, Opitz JG, Stackhouse J, Benner SA. Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily. Nature 374, 57–59 (1995).
   PubMed Web of Science ®Google Scholar
• Niclde DC, Jensen MA, Gottlieb GS et al. Consensus and ancestral state HIV vaccines. Science 299, 1515–1518; author reply 1515–1518 (2003).
   Google Scholar
• Zuckerkandl E, Pauling L. Molecules as documents of evolutionary history. J Theor. Biol. 8, 357–366 (1965).
   PubMed Web of Science ®Google Scholar
• Schultz TR, Cocroft RB, Churchill GA. The reconstruction of ancestral character states. Evolution 50, 504–511 (1996).
   Google Scholar
• Cunningham CW, Omland KE, Oakley TH. Reconstructing ancestral character states: a critical reappraisal. Trench Era'. Eva 13, 361–366 (1998).
   Google Scholar
• Yang Z, Kumar S, M. Nei A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141, 1641–1650 (1995).
   Google Scholar
• Huelsenbeck JP, Ronquist E MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754–755 (2001).
   PubMed Web of Science ®Google Scholar
• Huelsenbeck JP, Bollback JP Empirical and hierarchical Bayesian estimation of ancestral states. Syst Biol. 50, 351–366 (2001).
   PubMed Web of Science ®Google Scholar
• Swofford DL. PAUP* 4.0: Phylogenetic Analysis Using Parsimony (*and Other Methods), Sinauer Associates, Inc., Sunderland, MA, USA (1999).
   Google Scholar
• Mau B, Newton MA, Larget B. Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Biometrics 55, 1–12 (1999).
   Google Scholar
• Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JR Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294, 2310–2314 (2001).
   PubMed Web of Science ®Google Scholar
• Hillis DM, Huelsenbeck JR Signal, noise, and reliability in molecular phylogenetic analyses. Hered. 83, 189–195 (1992).
   PubMed Web of Science ®Google Scholar
• Kornfeld H, Riedel N, Viglianti GA, Hirsch V, Mullins R. Cloning of HTLV-4 and its relation to simian and human immunodeficiency viruses. Nature 326, 610–613 (1987).
   Google Scholar
• Edmonson P, Murphey-Corb M, Martin LN et al Evolution of a simian immunodeficiency virus pathogen. J. Viral 72, 405–414 (1998).
   Google Scholar
• Doria-Rose N, Learn GH, Rodrigo AGet al Ancestral HIV protein elicits neutralizing antibodies against primary HIV-1 virus isolates (Submitted).
   Google Scholar
• Julenius K, Molgaard A, Gupta R, Brunak S. Prediction, conservation analysis and structural characterization of mammalian mucin-type 0-glycosylation sites. Glycobiology (Submitted) (2004).
   Google Scholar
• Ross HA, Nickle DC, Liu Y et al. An assessment of different methods of reconstructing ancestral human immunodeficiency virus type 1 sequences as potential synthetic vaccine candidates (Submitted) (2004).
   Google Scholar
• Nakamura Y, Gojobori T, Ikemura T. Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Res. 28, 292 (2000).
   Google Scholar
• Burton DR, Desrosiers RC, Doms RVV et al HIV vaccine design and the neutralizing antibody problem. Nature Immunol 5, 233–236 (2004).
   PubMed Web of Science ®Google Scholar
• Reitter JN, Means RE, Desrosiers RC. A role for carbohydrates in immune evasion in AIDS. Nat. Merl 4, 679–684 (1998).
   Google Scholar
• Johnson WE, Sanford H, Schwall L et al Assorted mutations in the envelope gene of simian immunodeficiency virus lead to loss of neutralization resistance against antibodies representing a broad spectrum of specificities.Viro1.77, 9993–10003 (2003).
   Google Scholar
• Pantophlet R, Burton DR. Immunofocusing: antigen engineering to promote the induction of HIV-neutralizing antibodies. Bends Md. Merl 9, 468–473 (2003).
   PubMed Web of Science ®Google Scholar
• Klausner RD, Fauci AS, Corey L et al The need for a global HIV vaccine enterprise. Science 300, 2036–2039 (2003).
   PubMed Web of Science ®Google Scholar
• Desrosiers RC. Prospects for an AIDS vaccine. Nature Merl 10, 221–223 (2004).
   PubMed Web of Science ®Google Scholar
• Zinkernagel RM. The challenges of an HIV vaccine enterprise. Science 303, 1294–1297; author reply 1294–1297 (2004).
   Google Scholar
• Trkola A, Pomales AB, Yuan H et al Cross- clade neutralization of primary isolates of human immunodeficiency virus type 1 by human monoclonal antibodies and tetrameric CD4-IgG. j Viral 69, 6609–6617 (1995).
   PubMed Web of Science ®Google Scholar
• Ferrari G, Humphrey G, McElrath MJ et al Clade B-based HIV-1 vaccines elicit cross-clade cytotoxic T-lymphocyte reactivities in uninfected volunteers. Proc. Natl. Acad. ScL USA 94, 1396–1401 (1997).
   Google Scholar
• Zhan X, Slobod KS, Surman S, Brown SA, Coleclough C, Hurwitz JL. Minor components of a multi-envelope HIV vaccine are recognized by type-specific T-helper cells. Vaccine 22, 1206–1213 (2004).
   PubMedGoogle Scholar