Selection in context: Patterns of natural selection in the glycoprotein 120 region of human immunodeficiency virus 1 within infected individuals

Genetics

Volumn 167, Issue 4, 2004, Pages 1547-1561

  Templeton, Alan R ^a   Reichert, Rebecca A ^a,c   Weisstein, Anton E ^a,d   Yu, Xiao Fang ^b   Markham, Richard B ^b  

^a WASHINGTON UNIVERSITY   (United States)

^b JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

^c NEWTON WELLESLEY HOSPITAL   (United States)

^d BELOIT COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLYCOPROTEIN GP 120;

ACQUIRED IMMUNE DEFICIENCY SYNDROME; ADULT; AMINO ACID SUBSTITUTION; ANTIBODY TITER; ARTICLE; CLINICAL ARTICLE; EVOLUTION; FEMALE; GENE SEQUENCE; GENETIC RECOMBINATION; GENETIC SELECTION; HAPLOTYPE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; IMMUNE SYSTEM; MALE; NATURAL SELECTION; NONHUMAN; NONSYNCYTIUM INDUCING STRAIN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PRIORITY JOURNAL; STRAIN DIFFERENCE; SYNCYTIUM INDUCING STRAIN; VIRUS DETECTION; VIRUS GENE; VIRUS STRAIN;

ACQUIRED IMMUNODEFICIENCY SYNDROME; CD4 LYMPHOCYTE COUNT; CD8-POSITIVE T-LYMPHOCYTES; DEMOGRAPHY; HAPLOTYPES; HIV ENVELOPE PROTEIN GP120; HIV SEROPOSITIVITY; HIV-1; HUMANS; LYMPHOCYTE COUNT; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; SELECTION (GENETICS);

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

EID: 4644278569     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.103.023945     Document Type: Article

References (53)

1. BLANCO, J. B., J. BARRETINA, C. CABRERA, A. GUTIERREZ and B. CLOTET, 2001 CD4+ and CD8+ T cell death during human immunodeficiency virus infection in vitro. Virology 285: 356-365.
2. BONHOEFFER, S., and M. A. NOWAK, 1994 Mutation and the evolution of virulence. Proc. R. Soc. Lond. Ser. B 258: 133-140.
3. BONHOEFFER, S., E. C. HOLMES and M. A. NOWAK, 1995 Causes of HIV diversity. Nature 376: 125.
4. BRIGGS, D. R., D. L. TUFFLE, J. W. SLEASMAN and M. M. GOODENOW, 2000 Envelope V3 amino acid sequence predicts HIV-1 pheno-type (co-receptor usage and tropism for macrophages). AIDS 14: 2937-2939.
5. CALLAWAY, D. S., R. M. RIBEIRO and M. A. NOWAK, 1999 Virus phenotype switching and disease progression in HIV-1 infection. Proc. R. Soc. Lond. Ser. B 266: 2523-2530.
6. CARRIERI, M. P., M. A. CHESNEY, B. SPIRE, A. LOUNDOU, A. SOBEL et al., 2003 Failure to maintain adherence to HAART in a cohort of French HIV-positive injecting drug users. Int. J. Behav. Med. 10: 1-14.
7. CASTELLOE, J., and A. R. TEMPLETON, 1994 Root probabilities for intraspecific gene trees under neutral coalescent theory. Mol. Phylogenet. Evol. 3: 102-113.
8. COFFIN, J. M., 1995 HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science 267: 483-489.
9. COFFIN, J. M., 1999 Molecular biology of HIV, pp. 3-40 in The Evolution of HIV, edited by K. A. CRANDALL. The Johns Hopkins University Press, Baltimore.
10. CRANDALL, K. A., 1994 Intraspecific cladogram estimation: accuracy at higher levels of divergence. Syst. Biol. 43: 222-235.
11. CRANDALL, K. A., and A. R. TEMPLETON, 1996 Applications of intra-specific phylogenetics, pp. 81-99 in New Uses for New Phytogenies, edited by P. HARVEY, A. J. L. BROWN, J. M. SMITH and S. NEE. Oxford University Press, Oxford.
12. CRANDALL, K. A., and A. R. TEMPLETON, 1999 Statistical approaches to detecting recombination, pp. 153-176 in TheEvolution of HIV, edited by K. A. CRANDALL. The Johns Hopkins University Press, Baltimore.
13. DE JONG, J. J., A. DERONDE, W. KEULEN, M. TERSMETTE and J. GOUDSMIT, 1992 Minimal requirements for the human-immunodeficiency-virus type-1 V3 domain to support the syncytium-inducing phenotype: analysis by single amino-acid substitution. J. Virol. 66: 6777-6780.
14. DITTMAR, M. T., A. MCKNIGHT, G. SIMMONS, P. R. CLAPHAM, R. A. WEISS et al., 1997 HIV-1 tropism and co-receptor use. Nature 385: 495-496.
15. ENDO, T., K. IKEO and T. GOJOBORI, 1996 Large-scale search for genes on which positive selection may operate. Mol. Biol. Evol. 13: 685-690.
16. FIENBERG, S. E., 1977 The Analysis of Cross-Classified Categorical Data. The MlT Press, Cambridge, MA.
17. FU, Y. X., and W. H. LI, 1993 Statistical tests of neutrality of mutations. Genetics 133: 693-709.
18. GANESHAN, S., R. E. DICKOVER, B. T. M. KORBER, Y. J. BRYSON and S. M. WOLINSKY, 1997 Human immunodeficiency virus type 1 genetic evolution in children with different rates of development of disease. J. Virol. 71: 663-677.
19. GOUDSMIT, J., 1997 Viral Sex: The Nature of AIDS. Oxford University Press, New York.
20. HERBEIN, G., U. MAHLKNECHT, F. BATLIWALLA, P. GREGERSEN, T. PAPPAS et al., 1998 Apoptosis of CD8+ T cells is mediated by macrophages through interaction of HIV gp120 with chemokine receptor CXCR4. Nature 395: 189-194.
21. HETTMANSPERGER, T. P., 1984 Statistical Inference Based on flanks. John Wiley & Sons, New York.
22. HORIKOSHI, H., M. KINOMOTO, F. SASAO, T. MUKAI, R. B. LUFTIG et al., 2001 Differential susceptibility of resting CD4(+) T lymphocytes to a T-tropic and a macrophage (M)-tropic human immunodeficiency virus type 1 is associated with their surface expression of CD38 molecules. Virus Res. 73: 1-16.
23. KELLY, J. K., 1994 An application of population genetic theory to synonymous gene sequence evolution in the human immunodeficiency virus (HIV). Genet. Res. 64: 1-9.
24. KESTENS, L., G. VANHAM, C. VEREECKEN, M. VANDENBRUAENE, G. VERCAUTEREN et al., 1994 Selective increase of activation antigens HLA-DR and CD38 on CD4+ CD45RO+ T lymphocytes during HIV-1 infection. Clin. Exp. Immunol. 95: 436-441.
25. KIMURA, M., and T. OHTA, 1971 Protein polymorphism as a phase of molecular evolution. Nature 229: 467-469.
26. LEIGH BROWN, A. J., and E. C. HOLMES, 1994 Evolutionary biology of human immunodeficiency virus. Annu. Rev. Ecol. Syst. 25: 127-165.
27. LIU, S. L., T. SCHACKER, L. MUSEY, D. SHRINER, M. J. MCELRATH et al., 1997 Divergent patterns of progression to AIDS after infection from the same source: human immunodeficiency virus type 1 evolution and antiviral responses. J. Virol. 71: 4284-4295.
28. MARKHAM, R. B., W. WANG, A. E. WEISSTEIN, Z. WANG, A. MUNOZ et al., 1998 Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proc. Natl. Acad. Sci. USA 95: 12568-12573.
29. MAY, R. M., 1995 The co-evolutionary dynamics of viruses and their hosts, pp. 553-585 in Molecular Basis of Virus Evolution, edited by F. GARCÍA-ARENAL. Cambridge University Press, Cambridge, UK.
30. MC.DONALD, J. H., and M. KREITMAN, 1991 Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
31. MCDONALD, R. A., D. L. MAYERS, R. C.-Y. CHUNG, K. F. WAGNER, S. RATTO-KIM et al., 1997 Evolution of human immunodeficiency virus type 1 env sequence variation in patients with diverse rates of disease progression and T-cell function.J. Virol. 71: 1871-1879.
32. NIELSEN, R., 2001 Statistical tests of selective neutrality in the age of genomics. Heredity 86: 641-647.
33. NOWAK, M. A., R. M. MAY, R. E. PHILLIPS, S. ROWLAND-JONES, D. G. LALLOO et al., 1995 Antigenic oscillations and shifting immunodominance in HIV-1 infections. Nature 375: 606-611.
34. PAGE, R. D. M., and E. C. HOLMES, 1998 Molecular Evolution: A Phylogenetic Approach. Blackwell Science, Oxford.
35. PALEPU, A., M. TYNDALL, B. YIP, M. V. O'SHAUGHNESSY, R. S. HOGG et al., 2003 Impaired virologic response to highly active antiretroviral therapy associated with ongoing injection drug use. J. Acquir. Immune Defic. Syndr. 32: 522-526.
36. PERELSON, A. S., A. U. NEUMANN, M. MARKOWITZ, J. M. LEONARD and D. D. HO, 1996 HPV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time. Science 271: 1582-1586.
37. ROWLAND-JONES, S., S. PINHEIRO and R. KAUL, 2001 New insights into host factors in HIV-1 pathogenesis. Cell 104: 473-476.
38. SEIBERT, S. A., C. Y. HOWELL, M. K. HUGHES and A. L. HUGHES, 1995 Natural selection on the gag, pol, and env genes of human immunodeficiency virus 1 (HIV-1). Mol. Biol. Evol. 12: 803-813.
39. SEILLIER-MOISEIWITSCH, F., B. H. MARGOLIN and R. SWANSTROM, 1994 Genetic variability of the human immunodeficiency virus: statistical and biological issues. Annu. Rev. Genet. 28: 559-596.
40. SHANKARAPPA, R., P. GUPTA, G. H. LEARN, A. G. RODRIGO, J. C. R. RINALDO et al., 1998 Evolution of human immunodeficiency virus type 1 envelope sequences in infected individuals with differing disease progression profiles. Virology 241: 251-259.
41. SHANKARAPPA, R., J. B. MARGOLICK, S. J. GANGE, A. G. RODRIGO, D. UPCHURCH et al., 1999 Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J. Virol. 73: 10489-10502.
42. SHIINO, T., K. KATO, N. KODAKA, T. MIYAKUNI, Y. TAKEBE et al., 2000 A group of V3 sequences from human immunodeficiency virus type 1 subtype E non-syncytium-inducing, CCR5-using variants are resistant to positive selection pressure. J. Virol. 74: 1069-1078.
43. TEMPLETON, A. R., 1987 Genetic systems and evolutionary rates, pp. 218-234 in Rates of Evolution, edited by K. S. W. CAMPBELL and M. F. DAY. Allen & Unwin, London.
44. TEMPLETON, A. R., 1996 Contingency tests of neutrality using intra-interspecific gene trees: the rejection of neutrality for the evolution of the mitochondrial cytochrome oxidase II gene in the hominoid primates. Genetics 144: 1263-1270.
45. TEMPLETON, A. R., K. A. CRANDALL and C. F. SING, 1992 A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132: 619-633.
46. TEMPLETON, A. R., A. G. CLARK, K. M. WEISS, D. A. NICKERSON, J. STENGÅRD et al., 2000 Recombinational and mutational hotspots within the human lipoprotein lipase gene. Am. J. Hum. Genet. 66: 69-83.
47. VAN RIJ, R. P., H. BLAAK, J. A. VISSER, M. BROUWER, R. RIENTSMA et al., 2000 Differential coreceptor expression allows for independent evolution of non-syncytium-inducing and syncytium-inducing HIV-1. J. Clin. Invest. 106: 1039-1052.
48. VAN RIJ, R. P., M. HAZENBERG, B. VAN BENTHEM, S. OTTO, M. PRINS et al., 2003 Early viral load and CD4+ T cell count, but not percentage of CCR5+ or CXCR4+ CD4+ T cells, are associated with R5-to-X4 HIV type 1 virus evolution. AIDS Res. Hum. Retroviruses 19: 389-398.
49. WEI, X. P., S. K. GHOSH, M. E. TAYLOR, V. A. JOHNSON, E. A. EMINI et al., 1995 Viral dynamics in human-immunodeficiency-virus type-1 infection. Nature 373: 117-122.
50. WOLINSKY, S. M., B. T. M. KORBER, A. U. NEUMANN, M. DANIELS, K. J. KUNSTMAN et al., 1996 Adaptive evolution of human immunodeficiency virus-type 1 during the natural course of infection. Science 272: 537-542.
51. WOOD, E., J. S. G. MONTANER, B. YIP, M. W. TYNDALL, M. T. SCHECHTER et al., 2003 Adherence and plasma HIV RNA responses to highly active antiretroviral therapy among HIV-1 infected injection drug users. Can. Med. Assoc. J. 169: 656-661.
52. XIAO, H., C. NEUVEUT, H. L. TIFFANY, M. BENKIRANE, E. A. RICH et al., 2000 Selective CXCR4 antagonism by Tat: implications for in vivo expansion of coreceptor use by HIV-1. Proc. Natl. Acad. Sci. USA 97: 11466-11471.
53. YAMAGUCHI, Y., and T. GOJOBORI, 1997 Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within single hosts. Proc. Natl. Acad. Sci. USA 94: 1264-1269.