A statistical characterization of consistent patterns of human immunodeficiency virus evolution within infected patients

Molecular Biology and Evolution

Volumn 22, Issue 3, 2005, Pages 456-468

  Williamson, Scott ^a,b   Perry, Steven M ^b   Bustamante, Carlos D ^a   Orive, Maria E ^b   Stearns, Miles N ^b   Kelly, John K ^b  

^a Department of Molecular Biology and Genetics   (United States)

^b UNIVERSITY OF KANSAS   (United States)

Author keywords

Divergence rate; HIV; Longitudinal study

Indexed keywords

CD4 ANTIGEN; VIRUS DNA; VIRUS RNA;

ACQUIRED IMMUNE DEFICIENCY SYNDROME; ARTICLE; DISEASE COURSE; DNA SEQUENCE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; LEUKOCYTE COUNT; LONGITUDINAL STUDY; MAXIMUM LIKELIHOOD METHOD; MOLECULAR EVOLUTION; NONHUMAN; STATISTICAL ANALYSIS;

ACQUIRED IMMUNODEFICIENCY SYNDROME; EVOLUTION, MOLECULAR; GENOME, VIRAL; HIV; HUMANS; MODELS, GENETIC;

EID: 14544287462     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msi029     Document Type: Article

References (62)

1. Anderson, J. P., A. G. Rodrigo, G. H. Learn, Y. Wang, H. Weinstock, M. L. Kalish, K. E. Robbins, L. Hood, and J. I. Mullins. 2001. Substitution model of sequence evolution for the human immunodeficiency virus type 1 subtype B gp120 gene over the C2-V5 region. J. Mol. Evol. 53:55-62.
2. Anisimova, M., R. Nielsen, and Z. Yang. 2003. Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164:1229-1236.
3. Balfe, P., P. Simmonds, C. A. Ludlam, J. O. Bishop, and A. J. Brown. 1990. Concurrent evolution of human immunodeficiency virus type 1 in patients infected from the same source: rate of sequence change and low frequency of inactivating mutations. J. Virol. 64:6221-6233.
4. Barton, N. H., and A. M. Etheridge. 2004. The effect of selection on genealogies. Genetics 166:1115-1131.
5. Bonhoeffer, S., E. C. Holmes, and M. A. Nowak. 1995. Causes of HIV diversity. Nature 376:125.
6. Davison, A. C., and D. V. Hinkley. 1997. Bootstrap methods and their application. Cambridge University Press, Cambridge, UK.
7. + T cells. Nature 417:95-98.
8. Drummond, A. J., G. K. Nicholls, A. G. Rodrigo, and W. Solomon. 2002. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161:1307-1320.
9. Durbin, J., and S. J. Koopman. 2001. Time series analysis by state space methods. Oxford University Press, New York.
10. Finzi, D., J. Blankson, J. D. Silicano et al. (16 co-authors). 1999. Latent infection of CD4 T cells provides a mechanism for lifelong persistence of HIV-1, even in patients on effective combination therapy. Nat. Med. 5:512-517.
11. Finzi, D., M. Hermankova, T. Pierson et al. (15 co-authors). 1997. Identification of a reservoir for HIV-1 in patients on highly active antiretroviral therapy. Science 278:1295-1300.
12. Fu, Y.-X. 2001. Estimating mutation rate and generation time from longitudinal samples of DNA sequences. Mol. Biol. Evol. 18:620-626.
13. 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.
14. Goulder, P. J. R., C. Brander, Y. Tang et al. (19 co-authors). 2001. Evolution and transmission of stable CTL escape mutations in HIV infection. Nature 412:334-338.
15. Graur, D., and W.-H. Li. 2000. Fundamentals of molecular evolution. Sinauer Associates, Sunderland, Mass.
16. Harvey, A. C. 1989. Forecasting, structural time series models and the Kalman filter. Cambridge University Press, Cambridge, UK.
17. Hillis, D. M., J. P. Huelsenbeck, and C. W. Cunningham. 1994. Application and accuracy of molecular phylogenies. Science 264:671-677.
18. Holmes, E. C., L. Q. Zhang, P. Simmonds, C. A. Ludlam, and A. J. 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.
19. Hudson, R. R. 1983. Properties of a neutral allele model with intragenic recombination. Theor. Popul. Biol. 23:183-201.
20. Jung A, R. Maier, J. P. Vartanian, G. Bocharov, V. Jung, U. Fischer, E. Meese, S. Wain-Hobson, and A. Meyerhans. 2002. Multiply infected spleen cells in HIV patients. Nature 418:144.
21. 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.
22. Kelly, J. K. 1996. Replication rate and evolution in the human immunodeficiency virus. J. Theor. Biol. 180:359-364
23. Kelly, J. K. 2003. Deleterious mutations and the genetic variance of male fitness components in Mimulus guttatus. Genetics 164:1071-1085.
24. Kelly, J. K., and H. S. Arathi. 2003. Inbreeding and the genetic variance in floral traits of Mimulus guttatus. Heredity 90: 77-83.
25. Kelly, J. K., S. Williamson, M. E. Orive, M. S. Smith, and R. D. Holt. 2003. Linking dynamical and population genetic models of persistent viral infection. Am. Nat. 162:14-28.
26. Kingman, J. F. C. 1982. The coalescent. Stoch. Proc. Appl. 13:235-248.
27. Larder, B. A., G. Darby, and D. D. Richman. 1989. HIV with reduced sensitivity to zidovudine (AZT) isolated during prolonged therapy. Science 243:1731-1734.
28. 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.
29. Markham, R. B., W.-C. Wang, A. E. Weisstein et al. (11 co-authors) 1998. Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proc. Natl. Acad. Sci. USA 95:12568-12573.
30. Mayer-Hamblett, N, and S. Self. 2001. A regression modelling approach for describing patterns of HIV genetic variation. Biometrics 57:449-460.
31. McMichael, A. J., and R. E. Phillips. 1997. Escape of human immunodeficiency virus from immune control. Annu. Rev. Immunol. 15:271-296.
32. Moriyama, E. N., Y. Ina, K. Ikeo, N. Shimizu, and T. Gojobori. 1991. Mutation pattern of human immunodeficiency virus gene. J. Mol. Evol. 32:360-363.
33. Neuhauser, C., and S. M. Krone. 1997. The genealogy of samples in models with selection. Genetics 145:519-534.
34. n in the HIV-1 env gene. Mol. Biol. Evol. 16:711-714.
35. Nielsen, R., and Z. Yang. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929-936.
36. Nowak, M. A., R. M. Anderson, A. R. McLean, T. F. Wolfs, J. Goudsmit, and R. M. May. 1991. Antigenic diversity thresholds and the development of AIDS. Science 254:963-969.
37. Richman, D. D., T. Wrin, S. J. Little, and C. J. Petropoulos. 2003. Rapid evolution of the neutralizing antibody response to HIV type 1 infection. Proc. Natl. Acad. Sci. USA 100:4144-4149.
38. Rodrigo, A. G., and J. Felsenstein. 1999. Coalescent approaches to HIV population genetics. Pp. 233-272 in K. A. Crandall, ed. The evolution of HIV. John Hopkins University Press, Baltimore.
39. Rodrigo, A. G., E. G. Shaper, E. L. Delwart, A. K. Iversen, M. V. Gallo, J. Brojatsch, M. S. Hirsch, B. D. Walker, and J. I. Mullins. 1999. Coalescent estimates of HIV-1 generation time in vivo. Proc. Natl. Acad. Sci. USA 96:2187-2191.
40. + T cell responses associated with control of viremia. Science 278:1447-1450.
41. Ross, H. A., and A. G. Rodrigo. 2002. Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration. J. Virol. 76: 11715-11720.
42. Schierup, M. H., and J. Hein. 2000. Consequences of recombination on traditional phylogenetic analysis. Genetics 156:879-891.
43. Schuitemaker, H., M. Koot, N. A. Kootstra, M. W. Dercksen, R. E. de Goede, R. P. van Steenwijk, J. M. Lange, J. K. Schattenkerk, F. Miedema, and M. Tersmette. 1992. Biological phenotype of human immunodeficiency virus type 1 clones at different stages of infection: progression of disease is associated with a shift from monocytotropic to T-cell-tropic virus population. J. Virol. 66:1354-1360.
44. Searle, S. R., G. Casella, and C. E. McCulloch. 1992. Variance components. John Wiley and Sons, New York.
45. Seo, T.-K., J. L. Thorne, M. Hasegawa, and H. Kishino. 2002. Estimation of effective population size of HIV-1 within a host: a pseudomaximum-likelihood approach. Genetics 160: 1283-1293.
46. Shankarappa, R. 1999. Evolution of HIV-1 resistance to antiviral agents. Pp. 469-490 in K. A. Crandall, ed. The evolution of HIV. John Hopkins University Press, Baltimore.
47. Shankarappa, R., J. B. Margolick, S. J. Gange et al. (12 co-authors). 1999. Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J. Virol. 73:10489-10502.
48. Shriner, D., D. C. Nickle, M. A. Jensen, and J. I. Mullins. 2003. Potential impact of recombination on sitewise approaches for detecting positive natural selection. Genet. Res. 81:115-121.
49. Sokal, R. R., and F. J. Rohlf. 1995. Biometry, 3rd ed. W. H. Freeman and Company, New York.
50. Tersmette, M., R. A. Gruters, F. de Wolf, R. E. de Goede, J. M. Lange, P. T. Schellekens, J. Goudsmit, H. G. Huisman, and F. Miedema. 1989. Evidence for a role of virulent human immunodeficiency virus (HIV) variants in the pathogenesis of acquired immunodeficiency syndrome: studies on sequential HIV isolates. J. Virol. 63:2118-2125.
51. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24:4876-4882.
52. Viscidi, R. P. 1999. HIV evolution and disease progression via longitudinal studies. Pp. 346-389 in K. A. Crandall, ed. The evolution of HIV. John Hopkins University Press, Baltimore.
53. Wain-Hobson, S., C. Renoux-Elbé, J.-P. Vartanian, and A. Meyerhans. 2003. Network analysis of human and simian immunodeficiency virus sequence sets reveals massive recombination resulting in shorter pathways. J. Gen. Virol. 84: 885-895.
54. Williamson, S. 2003. Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression. Mol. Biol. Evol. 20:1318-1325.
55. Wodarz, D., P. Klenerman, and M. A. Nowak. 1998. Dynamics of cytotoxic T-lymphocyte exhaustion. Proc. R. Soc. Lond. B Biol. Sci. 265:191-203.
56. Wolfs, T. F., J. J. de Jong, H. Van den Berg, J. M. Tijnagel, W. J. Krone, and J. Goudsmit. 1990. Evolution of sequences encoding the principal neutralization epitope of human immunodeficiency virus 1 is host-dependent, rapid, and continuous. Proc. Natl. Acad. Sci. USA 87:9938-9942.
57. Wolinsky, S. M., B. T. M. Korber, A. U. Neumann et al. (11 co-authors). 1996. Adaptive evolution of human immunodeficiency virus-type 1 during the natural course of infection. Science 272:537-542.
58. Wolinsky, S. M., and G. H. Learn. 1999. Levels of diversity within and among host individuals. Pp. 275-314 in K. A. Crandall, ed. The evolution of HIV. John Hopkins University Press, Baltimore.
59. Wong, J. K., M. Hczareh, H. F. Günthard, D. V. Havlir, C. C. Ignacio, C. A. Spina, and D. D. Richman. 1997. Recovery of replication-competent HIV despite prolonged suppression of plasma viremia. Science 278:1391-1300.
60. Yamaguchi-Kabata, Y., and T. Gojobori 2000. Reevaluation of amino acid variability of the human immunodeficiency virus type 1 gp120 envelope glycoprotein and prediction of new discontinuous epitopes. J. Virol. 74:4335-4350.
61. Zanotto, P. M. A., E. G. Kallas, R. F. de Souza, and E. C. Holmes. 1999. Genealogical evidence for positive selection in the nef gene of HIV-1. Genetics 153:1077-1089.
62. Zhang, L. Q., P. MacKenzie, A. Cleland, E. C. Holmes, A. J. Brown, and P. Simmonds. 1993. Selection for specific sequences in the external envelope protein of human immunodeficiency virus type 1 upon primary infection. J. Virol. 67:3345-3356.