Immunogen sequence: The fourth tier of AIDS vaccine design

Expert Review of Vaccines

Volumn 3, Issue 4 SUPPL., 2004, Pages

  Mullins, James I ^a   Nickle, David C ^a   Heath, Laura ^a   Rodrigo, Allen G ^b   Learn, Gerald H ^a  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF AUCKLAND   (New Zealand)

Author keywords

Ancestral state reconstruction; Center of tree; Maximum likelihhod; Maximum parsimony; Most recent common ancestor; Phylogeny; Sequence concensus

Indexed keywords

AMINO ACID; ANTIGEN; ANTIVIRUS AGENT; EPITOPE; HUMAN IMMUNODEFICIENCY VIRUS VACCINE; IMMUNOLOGICAL ADJUVANT; NUCLEOTIDE;

DEVELOPING COUNTRY; DRUG DESIGN; GLYCOSYLATION; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMORAL IMMUNITY; IMMUNIZATION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; REVIEW; SYSTEMATIC REVIEW; TECHNIQUE; VACCINATION; VIRAL GENETICS;

AIDS VACCINES; ANIMALS; COMPUTER SIMULATION; DRUG DESIGN; EVOLUTION, MOLECULAR; HIV ANTIGENS; HIV-1; HUMANS; SEQUENCE ANALYSIS;

EID: 4344657035     PISSN: 14760584     EISSN: None     Source Type: Journal    
DOI: 10.1586/14760584.3.4.S151     Document Type: Review

References (82)

1. (WHO) AIDS epidemic update. Geneva, Switzerland (2002).
2. McMichael A, Rowland-Jones S. Cellular immune responses to HIV. Nature 410, 980-987 (2001).
3. Graham BS. Clinical trials of HIV vaccines. Ann. Rev. Med. 53, 207-221 (2002).
4. 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. Virol. 68, 4650-4655 (1994).
5. Parren PWHI, Moore J, Burton DR, Sattentau QJ. The neutralizing antibody responses to HIV-1: viral evasion and escape from humoral immunity. AIDS 13, S137-S162 (1999).
6. 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).
7. Burton DR. A vaccine for HIV type 1: the antibody perspective. Proc. Natl Acad. Sci. USA 94, 10018-10023 (1997).
8. Wei X, Decker JM, Wang S et al. Antibody neutralization and escape by HIV-1. Nature 422, 307-312 (2003). Provides evidence for an evolving 'glycan shield' mechanism of neutralization escape.
9. Richman DD, Wrin T, Little SJ, Petropoulos CJ. Rapid evolution of the neutralizing antibody response to HIV type 1 infection. Proc. Natl Acad. Sci. USA 100, 4144-4149 (2003). Illustrates potent neutralizing antibody responses that are generated early after infection in most patients. Plasma virus continually evolved to escape neutralization,
10. 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 Med. 5, 204-210 (1999).
11. Mascola JR. Defining the protective antibody response for HIV-1. Curr. Mol. Med. 3, 209-216 (2003).
12. Burton DR. Antibodies, viruses and vaccines. Nature Rev. Immunol. 2, 706-713 (2002).
13. 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. Virol. 68, 6103-6110 (1994).
14. 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. J. Med. 337, 1267-1274 (1997).
15. Harrer T, Harrer E, Kalams SA et al. Cytotoxic T-lymphocytes in asymptomatic long-term nonprogressing HIV-1 infection. Breadth and specificity of the response and relation to in vivo viral quasispecies in a person with prolonged infection and low viral load. J. Immunol. 156, 2616-2623 (1996).
16. 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).
17. Klein MR, Miedema F. Long-term survivors in HIV-1 infection. Trends Microbiol. 10, 386-391 (1995).
18. + 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).
19. + lymphocytes. Science 283, 857-860 (1999).
20. + T-cell depletion in simian immunodeficiency virus-infected macaques. J. Exp. Med. 189, 991-998 (1999).
21. Castro BA, Nepomuceno M, Lerche NW, Eichberg JW, Levy JA. Persistent infection of baboons and rhesus monkeys with different strains of HIV-2. Virology 184, 219-226 (1991).
22. Mullins JI. Curtailing the AIDS pandemic. Science 276, 1955-1957 (Letter) (1997).
23. Warren J. Preclinical AIDS vaccine research: survey of SIV, SHIV, and HIV challenge studies in vaccinated nonhuman primates. J. Med. Primatol. 31, 237-256 (2002).
24. Berman PW, Gray Am, Wrin T et al. Genetic and immunologic characterization of viruses infecting MN-rgp120-vaccinated volunteers. J. Infect. Dis. 176, 384-397 (1997).
25. 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. J. Virol. 72, 1552-1576 (1998).
26. 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).
27. Jost S, Bernard MC, Kaiser L et al. A patient with HIV-1 superinfection. N. Engl. J. Med. 347, 731-736 (2002).
28. 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).
29. Nabel GJ. HIV vaccine strategies. Vaccine 20, 1945-1947 (2002).
30. Shankarappa R, Margolick JB, Gange SJ et al. Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J. Virol. 73, 10489-10502 (1999).
31. 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).
32. 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. Mol. Evol. 53, 55-62 (2001).
33. Nabel G, Makgoba W, Esparza J. HIV-1 diversity and vaccine development. Science 296, 2335 (2002).
34. 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).
35. Esparza J, Osmanov S, Pattou-Markovic C, Toute C, Chang ML, Nixon S. Past, present and future of HIV vaccine trials in developing countries. Vaccine 20, 1897-1898 (2002).
36. Alcorn K. Vaxgen announces second Phase III trial failure in its AIDSVAX programme www.aidsmap.com/news/newsdisplay2.asp?newsId=2411 (2003).
37. Wagner R, Deml L, Wolf H. Polyvalent, recombinant HIV-1 virus-like particles: novel HIV-1 vaccine strategies. Antibiot. Chemother. 46, 48-61 (1994).
38. Fomsgaard A. HIV-1 DNA vaccines. Immunol. Lett. 65, 127-131 (1999).
39. 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. Virol. 75, 2224-2234 (2001).
40. Slobod KS, Lockey TD, Howlett N et al. Subcutaneous administration of a recombinant vaccinia virus vaccine expressing multiple envelopes of HIV-1. Eur. J. Clin. Microbiol. Infect. Dis. 23, 106-110 (2004).
41. Takahashi H, Nakagawa Y, Pendleton CD et al. Induction of broadly cross-reactive cytotoxic T-cells recognizing an HIV-1 envelope determinant. Science 255, 333-336 (1992).
42. 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). Illustrates the design of a vaccine immunogen that strings together 25 partially overlapping cytotoxic T-cell (CTL) epitopes from Gag, Pol, Env and Nef.
43. Hanke T, McMichael AJ, Mwau M et al. Development of a DNA-MVA/HIVA vaccine for Kenya. Vaccine 20, 1995-1998 (2002).
44. 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. Virol. 84, 361-368 (2003).
45. 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. J. Virol. 77, 642-658 (2003). Reports efforts to engineer gp120 such that antibody binding is restricted to those with broadly neutralizing capacity.
46. 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).
47. 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. Virol. 77, 5889-5901 (2003).
48. Delves PJ, Lund T, Roitt IM. Can epitope-focused vaccines select advantageous immune responses? Mol. Med. Today 3, 55-60 (1997).
49. Garrity RR, Rimmelzwaan G, Minassian A et al. Refocusing neutralizing antibody response by targeted dampening of an immunodominant epitope. J. Immunol. 159, 279-289 (1997). Suggests a strategy for reshaping humoral immune responses by redirecting immune response away from the V3 domain.
50. 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).
51. Gaschen B, Taylor J, Yusim K et al. Diversity considerations in HIV-1 vaccine selection. Science 296, 2354-2360 (2002).
52. Page RDM, Holmes EC. Molecular Evolution: a Phylogenetic Approach, Blackwell Science, Oxford (1998).
53. Gao F, Bhattacharya T, Gaschen B et al. Consensus and ancestral state HIV vaccines [author reply]. Science 299, 1517-1518 (2003).
54. Chang BS, Donoghue MJ. Recreating ancestral proteins. Trends Ecol. Evol. 15, 109-114 (2000).
55. Jermann TM, Opitz JG, Stackhouse J, Benner SA. Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily. Nature 374, 57-59 (1995).
56. Nickle DC, Jensen MA, Gottlieb GS et al. Consensus and ancestral state HIV vaccines. Science 299, 1515-1518; author reply 1515-1518 (2003).
57. Zuckerkandl E, Pauling L. Molecules as documents of evolutionary history. J. Theor. Biol. 8, 357-366 (1965).
58. Schultz TR, Cocroft RB, Churchill GA. The reconstruction of ancestral character states. Evolution 50, 504-511 (1996).
59. Cunningham CW, Omland KE, Oakley TH. Reconstructing ancestral character states: a critical reappraisal. Trends Ecol. Evol. 13, 361-366 (1998).
60. Yang Z, Kumar S, M. Nei A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141, 1641-1650 (1995).
61. Huelsenbeck JP, Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755 (2001).
62. Huelsenbeck JP, Bollback JP Empirical and hierarchical Bayesian estimation of ancestral states. Syst. Biol. 50, 351-366 (2001).
63. Swofford DL. PAUP* 4.0: Phylogenetic Analysis Using Parsimony (*and Other Methods), Sinauer Associates, Inc., Sunderland, MA, USA (1999).
64. Mau B, Newton MA, Larget B. Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Biometrics 55, 1-12 (1999).
65. Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294, 2310-2314 (2001).
66. Hillis DM, Huelsenbeck JP. Signal, noise, and reliability in molecular phylogenetic analyses. J. Hered. 83, 189-195 (1992).
67. Kornfeld H, Riedel N, Viglianti GA, Hirsch V, Mullins JI. Cloning of HTLV-4 and its relation to simian and human immunodeficiency viruses. Nature 326, 610-613 (1987).
68. Edmonson P, Murphey-Corb M, Martin LN et al. Evolution of a simian immunodeficiency virus pathogen. J. Virol. 72, 405-414 (1998).
69. Doria-Rose N, Learn GH, Rodrigo AG et al. Ancestral HIV protein elicits neutralizing antibodies against primary HIV-1 virus isolates (Submitted).
70. Julenius K, Mlgaard A, Gupta R, Brunak S. Prediction, conservation analysis and structural characterization of mammalian mucin-type O-glycosylation sites. Glycobiology (Submitted) (2004).
71. 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).
72. 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).
73. Burton DR, Desrosiers RC, Doms RW et al. HIV vaccine design and the neutralizing antibody problem. Nature Immunol. 5, 233-236 (2004).
74. Reitter JN, Means RE, Desrosiers RC. A role for carbohydrates in immune evasion in AIDS. Nat. Med. 4, 679-684 (1998).
75. 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. J. Virol. 77, 9993-10003 (2003).
76. Pantophlet R, Burton DR. Immunofocusing: antigen engineering to promote the induction of HIV-neutralizing antibodies. Trends Mol. Med. 9, 468-473 (2003).
77. Klausner RD, Fauci AS, Corey L et al. The need for a global HIV vaccine enterprise. Science 300, 2036-2039 (2003).
78. Desrosiers RC. Prospects for an AIDS vaccine. Nature Med. 10, 221-223 (2004).
79. Zinkernagel RM. The challenges of an HIV vaccine enterprise. Science 303, 1294-1297; author reply 1294-1297 (2004).
80. 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. Virol. 69, 6609-6617 (1995).
81. 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. Sci. USA 94, 1396-1401 (1997).
82. 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 12, 1206-1213 (2004).