HIV evolution: CTL escape mutation and reversion after transmission (original) (raw)

• Koenig, S. et al. Transfer of HIV-1-specific cytotoxic T lymphocytes to an AIDS patient leads to selection for mutant HIV variants and subsequent disease progression. Nat. Med. 1, 330–336 (1995).
  Article CAS Google Scholar
• Borrow, P. et al. Antiviral pressure exerted by HIV-1-specific cytotoxic T lymphocytes (CTLs) during primary infection demonstrated by rapid selection of CTL escape virus. Nat. Med. 3, 205–211 (1997).
  Article CAS Google Scholar
• Goulder, P.J. et al. Late escape from an immunodominant cytotoxic T-lymphocyte response associated with progression to AIDS. Nat. Med. 3, 212–217 (1997).
  Article CAS Google Scholar
• Barouch, D.H. et al. Eventual AIDS vaccine failure in a rhesus monkey by viral escape from cytotoxic T lymphocytes. Nature 415, 335–339 (2002).
  Article CAS Google Scholar
• Klenerman, P., Wu, Y. & Phillips, R. HIV: current opinion in escapology. Curr. Opin. Microbiol. 5, 408–413 (2002).
  Article CAS Google Scholar
• Evans, D.T. et al. Virus-specific cytotoxic T-lymphocyte responses select for amino-acid variation in simian immunodeficiency virus Env and Nef. Nat. Med. 5, 1270–1276 (1999).
  Article CAS Google Scholar
• Allen, T.M. et al. Tat-specific cytotoxic T lymphocytes select for SIV escape variants during resolution of primary viraemia. Nature 407, 386–390 (2000).
  Article CAS Google Scholar
• Phillips, R.E. et al. Human immunodeficiency virus genetic variation that can escape cytotoxic T cell recognition. Nature 354, 453–459 (1991).
  Article CAS Google Scholar
• Moore, C.B. et al. Evidence of HIV-1 adaptation to HLA-restricted immune responses at a population level. Science 296, 1439–1443 (2002).
  Article CAS Google Scholar
• Goulder, P.J. et al. Evolution and transmission of stable CTL escape mutations in HIV infection. Nature 412, 334–338 (2001).
  Article CAS Google Scholar
• Kaslow, R.A. et al. Influence of combinations of human major histocompatibility complex genes on the course of HIV-1 infection. Nat. Med. 2, 405–411 (1996).
  Article CAS Google Scholar
• Migueles, S.A. et al. HLA B*5701 is highly associated with restriction of virus replication in a subgroup of HIV-infected long term nonprogressors. Proc. Natl. Acad. Sci. USA 97, 2709–2714 (2000).
  Article CAS Google Scholar
• O'Brien, S.J., Gao, X. & Carrington, M. HLA and AIDS: a cautionary tale. Trends Mol. Med. 7, 379–381 (2001).
  Article CAS Google Scholar
• Goulder, P.J. et al. Novel, cross-restricted, conserved, and immunodominant cytotoxic T lymphocyte epitopes in slow progressors in HIV type 1 infection. AIDS Res. Hum. Retroviruses 12, 1691–1698 (1996).
  Article CAS Google Scholar
• Tang, J. et al. Favorable and unfavorable HLA class I alleles and haplotypes in Zambians predominantly infected with clade C human immunodeficiency virus type 1. J. Virol. 76, 8276–8284 (2002).
  Article CAS Google Scholar
• Yu, X.G. et al. Consistent patterns in the development and immunodominance of human immunodeficiency virus type 1 (HIV-1)-specific CD8+ T-cell responses following acute HIV-1 infection. J. Virol. 76, 8690–8701 (2002).
  Article CAS Google Scholar
• Novitsky, V. et al. Magnitude and frequency of cytotoxic T-lymphocyte responses: identification of immunodominant regions of human immunodeficiency virus type 1 subtype C. J. Virol. 76, 10155–10168 (2002).
  Article CAS Google Scholar
• Addo, M.M. et al. Comprehensive epitope analysis of human immunodeficiency virus type 1 (HIV-1)-specific T-cell responses directed against the entire expressed HIV-1 genome demonstrate broadly directed responses, but no correlation to viral load. J. Virol. 77, 2081–2092 (2003).
  Article CAS Google Scholar
• Altfeld, M.E.A. Influence of HLA-B57 on clinical presentation and viral control during acute HIV-1 infection. AIDS 17, 2581–2591 (2003).
  Article CAS Google Scholar
• Yang, Z. Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A. J. Mol. Evol. 51, 423–432 (2000).
  Article CAS Google Scholar
• McMichael, A. & Klenerman, P. HIV/AIDS. HLA leaves its footprints on HIV. Science 296, 1410–1411 (2002).
  Article CAS Google Scholar
• Frahm, N. et al. Identification of highly immunodominant regions in HIV by comprehensive CTL screening of ethnically diverse populations. J. Virol. (in the press).
• Barber, L.D. et al. Polymorphism in the α1 helix of the HLA-B heavy chain can have an overriding influence on peptide-binding specificity. J. Immunol. 158, 1660–1669 (1997).
  CAS Google Scholar
• Kelleher, A.D. et al. Clustered mutations in HIV-1 gag are consistently required for escape from HLA-B27-restricted cytotoxic T lymphocyte responses. J. Exp. Med. 193, 375–386 (2001).
  Article CAS Google Scholar
• Richman, D.D., Wrin, T., Little, S.J. & Petropoulos, C.J. Rapid evolution of the neutralizing antibody response to HIV type 1 infection. Proc. Natl. Acad. Sci. USA 100, 4144–4149 (2003).
  Article CAS Google Scholar
• Cohen, J. HIV. Escape artist par excellence. Science 299, 1505–1508 (2003).
  Article CAS Google Scholar
• Migueles, S.A. et al. The differential ability of HLA B*5701+ long-term nonprogressors and progressors to restrict human immunodeficiency virus replication is not caused by loss of recognition of autologous viral gag sequences. J. Virol. 77, 6889–6898 (2003).
  Article CAS Google Scholar
• Coffin, J.M. HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science 267, 483–489 (1995).
  Article CAS Google Scholar
• Greene, W.C. & Peterlin, B.M. Charting HIV's remarkable voyage through the cell: basic science as a passport to future therapy. Nat. Med. 8, 673–680 (2002).
  Article CAS Google Scholar
• Novitsky, V. et al. Human immunodeficiency virus type 1 subtype C molecular phylogeny: consensus sequence for an AIDS vaccine design? J. Virol. 76, 5435–5451 (2002).
  Article CAS Google Scholar
• Singh, A.R., Hill, R.L. & Lingappa, J.R. Effect of mutations in Gag on assembly of immature human immunodeficiency virus type 1 capsids in a cell-free system. Virology 279, 257–270 (2001).
  Article CAS Google Scholar
• Furuta, R.A. et al. HIV-1 capsid mutants inhibit the replication of wild-type virus at both early and late infection phases. FEBS Lett. 415, 231–234 (1997).
  Article CAS Google Scholar
• Krogstad, P. et al. Human immunodeficiency virus nucleocapsid protein polymorphisms modulate the infectivity of RNA packaging mutants. Virology 294, 282–288 (2002).
  Article CAS Google Scholar
• Forshey, B.M., von Schwedler, U., Sundquist, W.I. & Aiken, C. Formation of a human immunodeficiency virus type 1 core of optimal stability is crucial for viral replication. J. Virol. 76, 5667–5677 (2002).
  Article CAS Google Scholar
• Braaten, D., Franke, E.K. & Luban, J. Cyclophilin A is required for the replication of group M human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus SIV(CPZ)GAB but not group O HIV-1 or other primate immunodeficiency viruses. J. Virol. 70, 4220–4227 (1996).
  CAS PubMed Central Google Scholar
• Braaten, D., Franke, E.K. & Luban, J. Cyclophilin A is required for an early step in the life cycle of human immunodeficiency virus type 1 before the initiation of reverse transcription. J. Virol. 70, 3551–3560 (1996).
  CAS PubMed Central Google Scholar
• Yoo, S. et al. Molecular recognition in the HIV-1 capsid/cyclophilin A complex. J. Mol. Biol. 269, 780–795 (1997).
  Article CAS Google Scholar
• Goulder, P.J. et al. Substantial differences in specificity of HIV-specific cytotoxic T cells in acute and chronic HIV infection. J. Exp. Med. 193, 181–194 (2001).
  Article CAS Google Scholar
• Bunce, M. et al. Phototyping: comprehensive DNA typing for HLA-A, B, C, DRB1, DRB3, DRB4, DRB5 & DQB1 by PCR with 144 primer mixes utilizing sequence-specific primers (PCR-SSP). Tissue Antigens 46, 355–367 (1995).
  Article CAS Google Scholar
• Goulder, P.J. et al. Rapid definition of five novel HLA-A*3002-restricted human immunodeficiency virus-specific cytotoxic T-lymphocyte epitopes by Elispot and intracellular cytokine staining assays. J. Virol. 75, 1339–1347 (2001).
  Article CAS Google Scholar
• Ross, H.A. & Rodrigo, A.G. Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration. J. Virol. 76, 11715–11720 (2002).
  Article CAS Google Scholar
• Yang, Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555–556 (1997).
  CAS Google Scholar
• Swofford, D.L. in PAUP*. Phylogenetic Analysis Using Parsimony (* and other methods) 4th edn. (Sinauer Associates, Sunderland, Massachusetts, 2002).
  Google Scholar
• Hayman, A. et al. Phylogenetic analysis of multiple heterosexual transmission events involving subtype B of HIV type 1. AIDS Res. Hum. Retroviruses 17, 689–695 (2001).
  Article CAS Google Scholar
• Kasper, P. et al. The genetic diversification of the HIV type 1 gag p17 gene in patients infected from a common source. AIDS Res. Hum. Retroviruses 11, 1197–1201 (1995).
  Article CAS Google Scholar