Positive in vivo selection of the HIV-1 envelope protein gp120 occurs at surface-exposed regions

Journal of Infectious Diseases

Volumn 196, Issue 2, 2007, Pages 313-320

  Joos, Beda ^a   Fischer, Marek ^a   Schweizer, Andreas ^a   Kuster, Herbert ^a   Böni, Jürg ^b   Wong, Joseph K ^c   Weber, Rainer ^a   Trkola, Alexandra ^a   Günthard, Huldrych F ^a  

^a UNIVERSITY HOSPITAL ZURICH   (Switzerland)

^b Swiss National Center for Retroviruses   (Switzerland)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIRETROVIRUS AGENT; GLYCOPROTEIN GP 120; HUMAN IMMUNODEFICIENCY VIRUS VACCINE; VIRUS GLYCOPROTEIN; VIRUS RNA;

ARTICLE; CLINICAL ARTICLE; CRYSTAL STRUCTURE; HIGHLY ACTIVE ANTIRETROVIRAL THERAPY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN STRUCTURE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; UNINDEXED SEQUENCE; VIRUS ENVELOPE;

ANTI-RETROVIRAL AGENTS; DRUG ADMINISTRATION SCHEDULE; EVOLUTION, MOLECULAR; HIV ENVELOPE PROTEIN GP120; HIV INFECTIONS; HIV-1; HUMANS; LONGITUDINAL STUDIES; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ANALYSIS, PROTEIN;

EID: 34447278063     PISSN: 00221899     EISSN: None     Source Type: Journal    
DOI: 10.1086/518935     Document Type: Article

References (30)

1. Ho DD, Neumann AU, Perelson AS, Chen W, Leonard JM, Markowitz M. Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection. Nature 1995; 373:123-6.
2. Rambaut A, Posada D, Crandall KA, Holmes EC. The causes and consequences of HIV evolution. Nat Rev Genet 2004; 5:52-61.
3. 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 1999; 73:10489-502.
4. Yamaguchi-Kabata Y, Gojobori T. Reevaluation of amino acid variability of the human immunodeficiency virus type 1 gp120 envelope glycoprotein and prediction of new discontinuous epitopes. J Virol 2000; 74:4335-50.
5. Yang W, Bielawski JP, Yang Z. Widespread adaptive evolution in the human immunodeficiency virus type 1 genome. J Mol Evol 2003; 57: 212-21.
6. Choisy M, Woelk CH, Guegan JF, Robertson DL. Comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes. J Virol 2004; 78:1962-70.
7. Cocchi F, DeVico AL, Garzino-Demo A, Cara A, Gallo RC, Lusso P. The V3 domain of the HIV-1 gp120 envelope glycoprotein is critical for chemokine-mediated blockade of infection. Nat Med 1996; 2:1244-7.
8. Edinger AL, Amedee A, Miller K, et al. Differential utilization of CCR5 by macrophage and T cell tropic simian immunodeficiency virus strains. Proc Natl Acad Sci USA 1997; 94:4005-10.
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 2003; 100:4144-9.
10. Wei X, Decker JM, Wang S, et al. Antibody neutralization and escape by HIV-1. Nature 2003; 422:307-12.
11. Joos B, Trkola A, Fischer M, et al. Low human immunodeficiency virus envelope diversity correlates with low in vitro replication capacity and predicts spontaneous control of plasma viremia after treatment interruptions. J Virol 2005; 79:9026-37.
12. Fagard C, Oxenius A, Gunthard H, et al. A prospective trial of structured treatment interruptions in human immunodeficiency virus infection. Arch Intern Med 2003; 163:1220-6.
13. Fischer M, Hafner R, Schneider C, et al. HIV RNA in plasma rebounds within days during structured treatment interruptions. AIDS 2003; 17: 195-9.
14. Fischer M, Joos B, Hirschel B, Bleiber G, Weber R, Gunthard HF. Cellular viral rebound after cessation of potent antiretroviral therapy predicted by levels of multiply spliced HIV-1 RNA encoding nef. J Infect Dis 2004; 190:1979-88.
15. Trkola A, Kuster H, Leemann C, et al. Humoral immunity to HIV-1: kinetics of antibody responses in chronic infection reflects capacity of immune system to improve viral set point. Blood 2004; 104:1784-92.
16. + T-cell responses do not predict viral growth and clearance rates during structured intermittent antiretroviral therapy. J Virol 2002; 76:10169-76.
17. Joos B, Trkola A, Kuster H, et al. Selection pressure by neutralizing antibodies results in higher adaptive mutation rates in gp120. Antiviral Therapy 2004; 9:S75.
18. Kumar S, Tamura K, Nei M. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 2004; 5:150-63.
19. Williamson S. Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression. Mol Biol Evol 2003; 20:1318-25.
20. Kosakovsky Pond SL, Frost SD, Muse SV. HyPhy: hypothesis testing using phylogenies. Bioinformatics 2005; 21:676-9.
21. Kosakovsky Pond SL, Frost SD. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol 2005; 22:1208-22.
22. Kosakovsky Pond SL, Frost SD. Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 2005; 21:2531-3.
23. Collaborative computational project, number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 1994; 50:760-3.
24. Lee B, Richards FM. The interpretation of protein structures: estimation of static accessibility. J Mol Biol 1971; 55:379-400.
25. Ahmad S, Gromiha MM, Sarai A. Real value prediction of solvent accessibility from amino acid sequence. Proteins 2003; 50:629-35.
26. Huang CC, Tang M, Zhang MY, et al. Structure of a V3-containing HIV-1 gp120 core. Science 2005; 310:1025-8.
27. Derdeyn CA, Decker JM, Bibollet-Ruche F, et al. Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission. Science 2004; 303:2019-22.
28. Pantophlet R, Burton DR. gp120: target for neutralizing HIV-1 antibodies. Annu Rev Immunol 2006; 24:739-69.
29. 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 1997; 337:1267-74.
30. Ross HA, Rodrigo AG. Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration. J Virol 2002; 76:11715-20.