Population dynamics of HIV-1 inferred from gene sequences

Genetics

Volumn 151, Issue 2, 1999, Pages 427-438

  Grassly, Nicholas C ^a,b   Harvey, Paul H ^a   Holmes, Edward C ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DRUG RESISTANCE; GENE MUTATION; GENE SEQUENCE; GENETIC DRIFT; GENETIC RECOMBINATION; GENETIC SELECTION; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; PHYLOGENY; POPULATION GENETICS; POPULATION MODEL; POPULATION STRUCTURE; PRIORITY JOURNAL;

GENES, VIRAL; GENOME, VIRAL; HIV-1; HUMANS; MUTATION; PHYLOGENY; POPULATION DYNAMICS; VARIATION (GENETICS);

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 0032912338     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (81)

1. ANDERSON, R. M., and R. M. MAY, 1988 Epidemiological parameters of HIV transmission. Nature 333: 514-519.
2. ANDERSON, R. M., R. M. MAY, T. W. NG and J. T. ROWLEY, 1992 Age-dependent choice of sexual partners and the transmission dynamics of HIV in sub-Saharan Africa. Philos. Trans. R. Soc. Lond. B Biol. Sci. 336: 135-155.
3. ARAKI, H., and H. TACHIDA, 1997 Bottleneck effect on evolutionary rate in the nearly neutral mutation model. Genetics 147: 907-914.
4. BIRKY, C. W., and J. B. WALSH, 1988 Effects of linkage on rates of molecular evolution. Proc. Natl. Acad. Sci. USA 85: 6414-6418.
5. BLOWER, S. M., D. HARTEL, H. DOWLATABADI, R. M. ANDERSON and R. M. MAY, 1991 Drugs, sex and HIV: a mathematical model for New York City. Philos. Trans. R. Soc. Lond. B Biol. Sci. 331: 171-187.
6. BONHOEFFER, S., and M. A. NOWAK, 1997 Pre-existence and emergence of drug resistance in HIV-1 infection. Proc. R. Soc. Lond. Ser. B Biol. Sci. 264: 631-637.
7. BONHOEFFER, S., R. M. MAY, G. M. SHAW and M. A. NOWAK, 1997 Virus dynamics and drug therapy. Proc. Natl. Acad. Sci. USA 94: 6971-6976.
8. CHARLESWORTH, B., M. T. MORGAN and D. CHARLESWORTH, 1993 The effect of deleterious mutations on neutral molecular variation. Genetics 134: 1289-1303.
9. CONLON, C. P., P. KLENERMAN, A. EDWARDS, B. A. LARDER and R. E. PHILLIPS, 1994 Heterosexual transmission of human immunodeficiency virus type-1 variants associated with zidovudine resistance. J. Infect. Dis. 169: 411-415.
10. CORNELISSEN, M., R. VAN DEN BURG, F. ZORGDRAGER, V. LUKASHOV and J. GOUDSMIT, 1997 pol gene diversity of five human immunodeficiency virus type 1 subtypes: evidence for naturally occurring mutations that contribute to drug resistance, limited recombination patterns, and common ancestry for subtypes B and D. J. Virol. 71: 6348-6358.
11. DEAN, M., M. CARRINGTON, C. WINKLER, G. A. HUTTLEY, M. W. SMITH et al., 1996 Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Science 273: 1856-1862.
12. DIAZ, R. S., E. C. SABINO, A. MAYER, J. W. MOSLEY and M. P. BUSCH, 1995 Dual Human Immunodeficiency Virus type-1 infection and recombination in a dually exposed transfusion recipient. J. Virol. 69: 3273-3281.
13. EDWARDS, A. W. F., 1992 Livelihood. Extended Edition. The Johns Hopkins University Press, London.
14. EIGEN, M., and K. NIESELT-STRUWE, 1990 How old is the immunodeficiency virus? AIDS 4: S85-S93.
15. FELSENSTEIN, J., 1974 The evolutionary advantage of recombination. Genetics 78: 737-756.
16. FELSENSTEIN, J., 1981 Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17: 368-376.
17. FELSENSTEIN, J., 1992 Estimating effective population-size from samples of sequences - inefficiency of pairwise and segregating sites as compared to phylogenetic estimates. Genet. Res. 59: 139-147.
18. FISHER, R. A., 1921 On the 'probable error' of a coefficient of correlation deduced from a small sample. Metron 1: part 4, 3-32.
19. FISHER, R. A., 1930 The Genetical Theory of Natural Selection. Clarendon Press, Oxford.
20. FU, Y. X., 1994 A phylogenetic estimator of effective population size or mutation rate. Genetics 136: 685-692.
21. FU, Y. X., and W. H. LI, 1993 Maximum likelihood estimation of population parameters. Genetics 134: 1261-1270.
22. GAO, F., D. L. ROBINSON, S. G. MORRISON, H. X. HUI, S. CRAIG et al., 1996 The heterosexual human immunodeficiency virus type 1 epidemic in Thailand is caused by an intersubtype (A/E) recombinant of African origin. J. Virol. 70: 7013-7029.
23. GOUDSMIT, J., A. DE RONDE, D. D. HO and A. S. PERELSON, 1996 Human immunodeficiency virus fitness in vivo: calculations based on a single zidovudine resistance mutation at codon 215 of reverse transcriptase. J. Virol. 70: 5662-5664.
24. GOUDSMIT, J., A. DE RONDE, E. DE ROOIJ and R. DE BOER, 1997 Broad spectrum of in vivo fitness of human immunodeficiency virus type 1 subpopulations differing at reverse transcriptase codons 41 and 215. J. Virol. 71: 4479-4484.
25. GRASSLY, N. C., and E. C. HOLMES, 1998 The use of Monte Carlo simulation to infer population dynamic history from DNA sequence data, pp. 91-112 in Proceedings of the Trinational Workshop on Molecular Evolution, edited by M. K. UYENOYAMA, A. VON HAESELER and N. TAKAHATA. Duke University Publications Group, Durham, NC.
26. GREENHALGH, D., 1996 Effects of heterogeneity on the spread of HIV AIDS among intravenous drug users in 'shooting galleries'. Math. Biosci. 136: 141-186.
27. GRIFFITHS, R. C., and S. TAVARE, 1994a Ancestral inference in population genetics. Stat. Sci. 9: 307-319.
28. GRIFFITHS, R. C., and S. TAVARE, 1994b Sampling theory for neutral alleles in a varying environment. Philos. Trans. R. Soc. Lond. B Biol. Sci. 344: 403-410.
29. GRIFFITHS, R. C., and S. TAVARE, 1996 Monte Carlo inference methods in population genetics. Math. Comp. Mod. 23: 141-158.
30. GUPTA, S., M. C. J. MAIDEN, I. M. FEAVERS, S. NEE, R. M. MAY et al., 1996 The maintenance of strain structure in populations of recombining infectious agents. Nat. Med. 2: 437-442.
31. HEY, J., 1997 Mitochondria and nuclear genes present conflicting portraits of human origins. Mol. Biol. Evol. 14: 166-172.
32. HO, D., A. NEUMANN, A. PERELSON, W. CHEN, J. LEONARD et al., 1995 Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection. Nature 373: 123-126.
33. HOLMES, E. C., L. Q. ZHANG, P. SIMMONDS, C. A. LUDLAM and A. J. LEIGH BROWN, 1992 Convergent and divergent sequence evolution in the surface envelope glycoprotein of human immunodeficiency virus type 1 within a single infected patient. Proc. Natl. Acad. Sci. USA 89: 4835-4839.
34. HUDSON, R. R., 1987 Estimating the recombination parameter of a finite population-model without selection. Genet. Res. 50: 245-250.
35. JANSSENS, W., A. BUVE and J. N. NKENGASONG, 1997 The puzzle of HIV-1 subtypes in Africa. AIDS 11: 705-712.
36. KAPLAN, E. H., 1989 Needles that kill: modelling human immunodeficiency virus transmission via shared drug injection equipment in shooting galleries. Rev. Infect. Dis. 11: 289-298.
37. KINGMAN, J. F. C., 1982a The coalescent. Stoch. Process. Appl. 13: 235-248.
38. KINGMAN, J. F. C., 1982b On the genealogy of large populations. J. Appl. Probab. 19A: 27-43.
39. KINGMAN, J. F. C., 1982c Exchangeability and the evolution of large populations, pp. 97-112 in Exchangeability in Probability and Statistics, edited by G. KOCH and F. SPIZZICHINO. North-Holland, Amsterdam.
40. KORBER, B. T. M., C. BRANDER, B. D. WALKER, R. KOUP, J. P. MOORE et al. (Editors), 1996 HIV-1 Molecular Immunology Database. Los Alamos National Laboratory, Los Alamos, NM.
41. KOZAL, M. J., N. SHAH, N. P. SHEN, R. YANG, R. FUCINI et al., 1996 Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays. Nat. Med. 2: 753-759.
42. KUHNER, M. K., J. YAMATO and J. FELSENSTEIN, 1995 Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics 140: 1421-1430.
43. KUHNER, M. K., J. YAMATO and J. FELSENSTEIN, 1998 Maximum likelihood estimation of population growth rates based on the coalescent. Genetics 149: 429-434.
44. LANAVE, C., G. PREPARATA, C. SACCONE and G. SERIO, 1984 A new method for calculating evolutionary substitution rates. J. Mol. Evol. 20: 86-93.
45. LEIGH BROWN, A. J., 1997 Analysis of HIV-1 env gene sequences reveals evidence for a low effective number in the viral population. Proc. Natl. Acad. Sci. USA 94: 1862-1865.
46. LEIGH BROWN, A. J., and D. D. RICHMAN, 1997 HIV-1: gambling on the evolution of drug resistance? Nat. Med. 3: 268-271.
47. LEITNER, T., S. KUMAR and J. ALBERT, 1997 Tempo and mode of nucleotide substitutions in gag and env gene fragments in human immunodeficiency virus type 1 populations with a known transmission history. J. Virol. 71: 4761-4770.
48. LI, W.-H., M. TANIMURA and P. M. SHARP, 1988 Rates and dates of divergence between AIDS virus nucleotide sequences. Mol. Biol. Evol. 5: 313-330.
49. LOUWAGIE, J., F. E. MCCUTCHAN, M. PEETERS, T. P. BRENNAN, E. SANDERS-BUELL et al. 1993 Phylogenetic analysis of gag genes from 70 international HIV-1 isolates provides evidence for multiple genotypes. AIDS 7: 769-780.
50. LUNDSTROM, R., S. TAVARE and R. H. WARD, 1992 Estimating substitution rates from molecular data using the coalescent. Proc. Natl. Acad. Sci. USA 89: 5961-5965.
51. MAY, R. M., and R. M. ANDERSON, 1989 The transmission dynamics of human immunodeficiency virus (HIV). Biomath. 18: 263-311.
52. MCCUTCHAN, F. E., M. O. SALMINEN, J. K. CARR and D. S. BURKE, 1996 HIV-1 genetic diversity. AIDS 10 (Suppl. 3): S13-S20.
53. MICHAEL, N. L., G. CHANG, L. G. LOUIE, J. R. MASCOLA, D. DONDERO et al., 1997 The role of viral phenotype and CCR-5 gene defects in HIV-1 transmission and disease progression. Nat. Med. 3: 338-340.
54. MORAN, P. A. P., 1958 Random processes in genetics. Proc. Camb. Philos. Soc. 54: 60-71.
55. MOUTOUH, L., J. CORBEIL and D. D. RICHMAN, 1996 Recombination leads to the rapid emergence of HIV-1 dually resistant mutants under selective drug pressure. Proc. Natl. Acad. Sci. USA 93: 6106-6111.
56. MYERS, G., B. KORBER, J. A. BERZOFSKY, T. F. SMITH and G. N. PAVLAKIS (Editors), 1991 Human Retrovirus and AIDS 1991. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM.
57. MYERS, G., B. KORBER, B. FOLEY, K.-T. JEANG, J. W. MELLORS et al. (Editors), 1996 Human Retrovirus and AIDS 1996. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM.
58. NAJERA, I., A. HOLGUIN, M. E. QUINONESMATEU, M. A. MUNOZFERNANDEZ, R. NAJERA et al., 1995 pol gene quasi-species of human immunodeficiency virus: mutations associated with drug resistance in virus from patients undergoing no drug-therapy. J. Virol. 69: 23-31.
59. ROBERTSON, D., P. SHARP, F. MCCUTCHAN and B. HAHN, 1995 Recombination in HIV-1. Nature 374: 124-126.
60. RODRIGUEZ, F., J. L. OLIVER, A. MARIN and J. R. MEDINA, 1990 The general stochastic model of nucleotide substitution. J. Theor. Biol. 142: 485-501.
61. ROGERS, A. R., and H. HARPENDING, 1992 Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 9: 552-569.
62. SERVICE, S. K., and S. M. BLOWER, 1995 HIV transmission in sexual networks: an empirical analysis. Proc. R. Soc. Lond. Ser. B Biol. Sci. 260: 237-244.
63. SHAO, Y., and H. WOLF, 1995 Unpublished. Genbank accession numbers U20001-U20054.
64. SHARP, P. M., D. L. ROBERTSON, F. GAO and B. H. HAHN, 1994 Origins and diversity of human immunodeficiency viruses. AIDS 8 (Suppl. 1): S27-S42.
65. SIMON, F., P. MAUCLÉRE, P. ROQUES, I. LOUSSERT-AJAKA, M. C. MÜLLER-TRUTWIN et al., 1998 Identification of a new human immunodeficiency virus type 1 distinct from group M and group O. Nat. Med. 4: 1032-1037.
66. SIMONSEN, K. L., G. A. CHURCHILL and C. F. AQUADRO, 1995 Properties of statistical tests of neutrality for DNA polymorphism data. Genetics 141: 413-429.
67. SLATKIN, M., and R. R. HUDSON, 1991 Pairwise comparisons of mitochondrial-DNA sequences in stable and exponentially growing populations. Genetics 129: 555-562.
68. SULLIVAN, J., K. E. HOLSINGER and C. SIMON, 1996 The effect of topology on estimates of among-site rate variation. J. Mol. Evol. 42: 308-312.
69. SWOFFORD, D. L., G. J. OLSEN, P. J. WADDELL and D. M. HILLIS, 1996 Phylogenetic inference, pp. 407-514 in Molecular Systematics, Ed. 2, edited by D. M. HILLIS, C. MORITZ and B. MABLE. Sinauer Associates, Sunderland, MA.
70. TAJIMA, F., 1983 Evolutionary relationships of DNA sequences in finite populations. Genetics 105: 437-460.
71. UNAIDS, and WHO, 1998 Report on the global HIV/AIDS pandemic June 1998. http://www.unaids.org.
72. VARTANIAN, J. P., A. MEYERHANS, M. SALA and H. S. WAIN, 1994 G → A hypermutation of the human immunodeficiency virus type 1 genome: evidence for dCTP pool imbalance during reverse transcription. Proc. Natl. Acad. Sci. USA 91: 3092-3096.
73. WATTERSON, G. A., 1975 On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7: 256-276.
74. WEBER, J., E. M. FENYO, S. BEDDOWS, P. KALEEBU, A. BJORNDAI. et al., 1996 Neutralization serotypes of human immunodeficiency virus type-1 field isolates are not predicted by genetic subtype. J. Virol. 70: 7827-7832.
75. WEI, X., S. GHOSH, M. TAYLOR, V. JOHNSON, E. EMINI et al., 1995 Viral dynamics in human immunodeficiency virus type 1 infection. Nature 373: 117-122.
76. WEISS, G., and A. VON HAESKLER, 1998 Inference of population history using a likelihood approach. Genetics 149: 1539-1546.
77. WILKS, S. S., 1938 The large-sample distribution of the likelihood ratio for testing composite hypotheses. Ann. Math. Stat. 9: 60-62.
78. WRIGHT, S., 1931 Evolution in Mendelian populations. Genetics 16: 97-159.
79. YANG, Z., 1994 Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39: 306-314.
80. ZHANG, L. Q., P. MACKENZIE, A. CLELAND, E. C. HOLMES, A. J. L. BROWN et al., 1993 Selection for specific sequences in the external envelope protein of human immunodeficiency virus type-1 upon primary infection. J. Virol. 67: 3345-3356.
81. ZHU, T. F., N. WANG, A. CARR, S. WOLINSKY and D. D. HO, 1995 Evidence for coinfection by multiple strains of human immunodeficiency virus type-1 subtype-B in an acute seroconvertor. J. Virol. 69: 1324-1327.