Widespread adaptive evolution in the human immunodeficiency virus type 1 genome

Journal of Molecular Evolution

Volumn 57, Issue 2, 2003, Pages 212-221

  Yang, Wa ^a   Bielawski, Joseph P ^a   Yang, Ziheng ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Epitopes; HIV 1; Physiochemical properties; Positive selection

Indexed keywords

EPITOPE; GAG PROTEIN; GLYCOPROTEIN GP 160; NEF PROTEIN; TRANSACTIVATOR PROTEIN; VIF PROTEIN; VPR PROTEIN; VPU PROTEIN;

AMINO ACID ANALYSIS; ARTICLE; ENVELOPE GENE; GENE SEQUENCE; GENETIC SELECTION; GENETIC VARIABILITY; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN TERTIARY STRUCTURE; STRUCTURAL GENE; VIRUS GENE; VIRUS GENOME;

AMINO ACID SEQUENCE; EPITOPE MAPPING; EVOLUTION, MOLECULAR; GENOME, VIRAL; HIV-1; HUMANS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; RECOMBINATION, GENETIC; SELECTION (GENETICS); SEQUENCE HOMOLOGY, AMINO ACID;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; RNA VIRUSES;

EID: 0041884768     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-003-2467-9     Document Type: Article

References (61)

1. Alff-Steinberger C (1969) The genetic code and error transmission. Proc Natl Acad Sci USA 64:584-591
2. Allen TM, O'Connor DH, Jing P, et al. (2000) Tat-specific cytotoxic T lymphocytes selected for SIV escape variants during resolution of primary viraemia. Nature 407:386-390
3. Altfeld M, Rosenberg ES, Shankarappa R, et al. (2001) Cellular immune responses and viral diversity in individuals treated during acute and early HIV-1 infection. J Exp Med 193:169-180
4. Anisimova M, Bielawski JP, Yang Z (2001) The accuracy and power of likelihood ratio tests to detect positive selection at amino acid sites. Mol Biol Evol 18:1585-1592
5. Anisimova M, Bielawski JP, Yang Z (2002) Accuracy and power of Bayesian prediction of amino acid sites under positive selection. Mol Biol Evol 19:950-958
6. Beaumont T, van Nuenen A, Broersen S, Blattner WA, Lukashov VV, Schuitemaker H (2001) Reversal of human immunodeficiency virus type 1 IIIB to a neutralization-resistant phenotype in an accidentally infected laboratory worker with a progressive clinical course. J Virol 75:2246-2252
7. Bondada S, Chelvarajan RL (1999) B lymphocytes. In: Encyclopedia of science 2001. Nature Publishing Group, London
8. Brander C, Goulder PJR (2000) The evolving field of HIV CTL epitope mapping: New approaches to the identification of novel epitopes. In: Korber B, Brander C, Haynes BF, Koup R, Kuiken C, Moure JP, Walker BD, Watkins DI (eds) HIV molecular immunology 2001. Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, NM.
9. Calarota S, Jansson M, Levi M, Broliden K, Libonatti O, Wigzell H. Wahren B (1996) Immunodominant glycoprotein 41 epitope identified by seroreactivity in HIV type 1-infected individuals. AIDS Res Hum Retroviruses 12:705-713
10. Crandall KA, Kelsey CR, Imamichi H, Lane HC, Salzman NP (1999) Parallel evolution of drug resistance in HIV: Failure of nonsynonymous/synonymous substitution rate ratio to detect selection. Mol Biol Evol 16:372-382
11. Domingo E, Holland JJ (1997) RNA virus mutations and fitness for survival. Annu Rev Microbiol 51:151-178
12. Evans DT, O'Connor DH, Jing PC, et al. (1999) Virus-specific cytotoxic T-lymphocyte responses select for amino-acid variation in simian immunodeficiency virus Env and Nef. Nature Med 5:1270-1276
13. Eyre-Walker A, Keightley PD (1999) High genomic deleterious mutation rates in hominids. Nature 397:344-347
14. Fares MA, Moya A, Escarmis C, Baranowski E, Domingo E, Barrio E (2001) Evidence for positive selection in the capsid protein-coding region of the foot-and-mouth disease virus (FMDV) subjected to experimental passage regimens. Mol Biol Evol 18:10-21
15. Fomsgaard A (1999) HIV-1 DNA vaccines. Immunol Lett 65:127-131
16. Fu YX (2001) Estimating mutation rate and generation time from longitudinal samples of DNA sequences. Mol Biol Evol 18:620-626
17. Gojobori T, Moriyama EN, Kimura M (1990) Molecular clock of viral evolution and the neutral theory. Proc Natl Acad Sci USA 87:10015-10018
18. Goldman N, Yang Z (1994) A codon based model of nucleotide substitution for protein coding DNA sequences. Mol Biol Evol 11:725-736
19. Gotch FM (1998) T lymphocytes: Cytotoxic. In: Encyclopedia of science 2001. Nature Publishing Group, London
20. Grantham R (1974) Amino acid difference formula to help explain protein evolution. Science 185:862-864
21. Harcourt GC, Garrard S, Davenport MP, Edwards A, Philips RE (1998) HIV-1 variation diminishes CD4 T lymphocyte recognition. J Exp Med 188:1785-1793
22. Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22:160-174
23. Haydon DT, Lea S, Fry L, Knowles N, Samuel AR, Stuart D, Woolhouse MEJ (1998) Characterising sequence variation in the VP1 capsid proteins of foot and mouth disease virus (serotype 0) with respect to virion structure. J Mol Evol 46:465-475
24. Haydon DT, Bastos AD, Knowles NJ, Samuel AR (2001) Evidence of positive selection in foot-and-mouth disease virus capsid genes from field isolates. Genetics 157:7-15
25. Hughes AL (1992) Positive selection and interallelic recombination at the Merozoite surface antigen-1 (MSA-1) locus of Plasmodium falciparum. Mol Biol Evol 9:381-393
26. Hughes AL, Ota T, Nei M (1990) Positive Darwinian selection promotes charge profile diversity in the antigen-binding cleft of class I major-histocompatibility-complex molecules. Mol Biol Evol 7:515-524
27. Igarashi T, Kuwata T, Takehisa J, Ibuki K, Shibata R, Mukai R, Komatsu T, Adachi A, Ido E, Hayami M (1996) Genomic and biological alteration of a human immunodeficiency virus type 1 (HIV-1)-simian immunodeficiency virus strain mac chimera, with HIV-1 Env, recovered from a long-term carrier monkey. J Gen Virol 77:1649-1658
28. Jetzt AE, Yu H, Klarmann GJ, Ron Y, Preston BD, Dougherty JP (2000) High rate of recombination throughout the human immunodeficiency virus type 1 genome. J Virol 74:1234-1240
29. Korber B, Brander C, Haynes B, Koup R, Kuiken C, Moore JP, Walker BD, Watkins DI (eds) (2000) HIV molecular immunology 2000. Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, NM
30. Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157:105-132
31. Langedijk JPM, Zwart G, Goudsmit J, Meloen RH (1995) Fine specificity of antibody recognition may predict amino acid substitution in the 3rd variable region of GP120 during HIV type-1 infection. AIDS Res Hum Retroviruses: 11:1153-1162
32. Leigh Brown AJ (1997) Analysis of HIV-1 env gene reveals evidence for a low effective number in the viral population. Proc Natl Acad Sci USA 94:1862-1865
33. Lukashov VV, Goudsmit J (1997) Evolution of the human immunodeficiency virus type 1 subtype-specific V3 domain is confined to a sequence space with a fixed distance to the subtype consensus. J Virol 71:6332-6338
34. McClellan DA, McCracken KG (2001) Estimating the influence of selection on the variable amino acid sites of the cytochrome b protein functional domains. Mol Biol Evol 18:917-925
35. McLain L, Brown JL, Cheung L, Reading SA, Parry C, Jones TD, Cleveland SM, Dimmock NJ (2001) Different effects of a single amino acid substitution on three adjacent epitopes in the gp41 C-terminal tail of a neutralizing antibody escape mutant of human immunodeficiency virus type 1. Arch Virol 146:157-166
36. Metzgar D, Wills C (2000) Evolutionary changes in mutation rates and spectra and their influence on the adaptation of pathogens. Microbes Infect 2:1513-1522
37. Nicholas KB, Nicholas HB, Deerfield DW (1997) GeneDoc: Analysis and visualization of genetic variation. Version 2.5. EMBnew News 4:14
38. Nielsen R, Yang Z (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929-936
39. Norris PJ, Sumaroka M, Brander C, Moffett HF, Boswell SL, Nguyen T, Sykulev Y, Walker BD, Rosenberg ES (2001) Multiple effector functions mediated by human immunodeficiency virus-specific CD4(+) T-cell clones. J Virol 75:9771-9779
40. Peek AS, Souza V, Eguiarte LE, Gaut BS (2001) The interaction of protein structure, selection, and recombination on the evolution of the type-1 fimbrial major subunit (fimA) from Escherichia coli. J Mol Evol 52:193-204
41. + T cells: The great escape. Nature Med 7:777-778
42. Plikat U, Nieselt-Struwe K, Meyerhans A (1997) Genetic drift can dominate short-term human immunodeficiency virus type 1 nef quasispecies evolution in vivo. J Virol 71:4233-4240
43. Robertson DL, Anderson JP, Bradac JA, et al. (1999) HIV-1 nomenclature proposal. In: Kuiken CL, Foley B, Hahn B, Korber B, McCutchan F, Marx PA, Mellors JW, Mullins JI, Sodroski J, Wolinksy S (eds) Human retroviruses and AIDS 1999. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, pp 492-505
44. Rosenberg ES, Altfeld M, Poon SH, Phillips MN, Wilkes BM, Eldridge RL, Robbins GK, D'Aquila RT, Goulder PJR, Walker BD (2000) Immune control of HIV-1 after early treatment of acute infection. Nature 407:523-526
45. Ross HA, Rodrigo AG (2002) Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration. J Virol 76:11715-11720
46. Seibert SA, Howell CY, Hughes MK, Hughes AL (1995) Natural selection on the gag, pol and env genes of human immunodeficiency virus 1 (HIV-1). Mol Biol Evol 12:803-813
47. Siliciano RF (2001) Acquired immune deficiency syndrome (AIDS). In: Encyclopedia of life science 2001. Nature Publishing Group, London
48. Sharp PM (1997) In search of molecular Darwinism. Nature 385:111-112
49. Swanson WJ, Yang Z, Wolfner MF, Aquadro CF (2001) Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals. Proc Natl Acad Sci USA 98:2509-2514
50. Swofford DL (2000) PAUP*. Phylogenetic analysis using parsimony (* and other methods). Version 4. Sinauer Associates, Sunderland, MA
51. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876-4882
52. Walker BD, Goulder PJR (2000) AIDS - Escape from the immune system. Nature 407:313-314
53. Walther D (1997) WEBMOL, a Java based PDB viewer. Trends Biochem Sci 22:274-275
54. Williams EJB, Pal C, Hurst LD (2000) The molecular evolution of signal peptides. Gene 253:313-322
55. Xia X (2000) Data analysis in molecular biology and evolution. Kluwer Academic, Dordrecht
56. Yamaguchi-Kabata Y, Gojobori T (2000) Reevaluation of amino acid variability of the HIV-1 gp120 envelop glycoprotein and prediction of new discontinuous epitopes. J Virol 74:4335-4350
57. Yang Z (2000) Phylogenetic analysis by maximum likelihood (PAML). Version 3. University College London, London
58. Yang Z (2001) Maximum likelihood analysis of adaptive evolution in HIV-1 gp120 env gene. Pacific Symp Biocomput pp 226-237
59. Yang Z, Nielsen R, Goldman N, Pedersen AM (2000) Codon substitution models for heterogeneous selection pressure at amino acid sites. Genetics 15:1600-1611
60. Zanotto PMde A, Kallas EG, de Souza RF, Holmes EC (1999) Genealogical evidence for positive selection in the nef gene of HIV-1. Genetics 153:1077-1089
61. Zhang PF, Chen X, Fu DW, Margolick JB, Quinnan GV (1999) Primary virus envelope cross-reactivity of the broadening neutralizing antibody response during early chronic human immunodeficiency virus type 1 infection. J Virol 73:5225-5230