1887

Abstract

The intra-host evolution of 73 human immunodeficiency virus type 1 quasispecies was analysed by split decomposition analysis. Non-synonymous and synonymous nucleotide substitutions were counted along the shortest path connecting all sequences and compared with the numbers expected under the assumption of a random model of mutation. For the majority of substitutions, drift and negative selection seemed to prevail.

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2001-07-01
2019-09-18
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References

  1. Ball, J. K., Holmes, E. C., Whitwell, H. & Desselberger, U. ( 1994; ). Genomic variation of human immunodeficiency virus type 1 (HIV-1): molecular analyses of HIV-1 in sequential blood samples and various organs obtained at autopsy. Journal of General Virology 75, 867-879.[CrossRef]
    [Google Scholar]
  2. Bandelt, H. J. & Dress, A. W. ( 1992; ). Split decomposition: a new and useful approach to phylogenetic analysis of distance data. Molecular Phylogenetics and Evolution 1, 242-252.[CrossRef]
    [Google Scholar]
  3. Brown, A. J. & Cleland, A. ( 1996; ). Independent evolution of the env and pol genes of HIV-1 during zidovudine therapy. AIDS 10, 1067-1073.
    [Google Scholar]
  4. Brown, A. J., Lobidel, D., Wade, C. M., Rebus, S., Phillips, A. N., Brettle, R. P., France, A. J., Leen, C. S., McMenamin, J., McMillan, A., Maw, R. D., Mulcahy, F., Robertson, J. R., Sankar, K. N., Scott, G., Wyld, R. & Peutherer, J. F. ( 1997; ). The molecular epidemiology of human immunodeficiency virus type 1 in six cities in Britain and Ireland. Virology 235, 166-177.[CrossRef]
    [Google Scholar]
  5. Cheynier, R., Kils-Hütten, L., Meyerhans, A. & Wain-Hobson, S. ( 2001; ). Insertion/deletion frequencies match those of point mutations in the hypervariable regions of the simian immunodeficiency virus surface envelope gene. Journal of General Virology 82, 1613-1619.
    [Google Scholar]
  6. Delassus, S., Cheynier, R. & Wain-Hobson, S. ( 1991; ). Evolution of human immunodeficiency virus type 1 nef and long terminal repeat sequences over 4 years in vivo and in vitro. Journal of Virology 65, 225-231.
    [Google Scholar]
  7. Donaldson, Y. K., Bell, J. E., Holmes, E. C., Hughes, E. S., Brown, H. K. & Simmonds, P. ( 1994; ). In vivo distribution and cytopathology of variants of human immunodeficiency virus type 1 showing restricted sequence variability in the V3 loop. Journal of Virology 68, 5991-6005.
    [Google Scholar]
  8. Dopazo, J., Dress, A. W. M. & von Haeseler, A. ( 1993; ). Split decomposition: a technique to analyze viral evolution. Proceedings of the National Academy of Sciences, USA 90, 10320-10324.[CrossRef]
    [Google Scholar]
  9. Gojobori, T., Moriyama, E. N. & Kimura, M. ( 1990; ). Molecular clock of viral evolution, and the neutral theory. Proceedings of the National Academy of Sciences, USA 87, 10015-10018.[CrossRef]
    [Google Scholar]
  10. Holmes, E. C., Zhang, L. Q., Simmonds, P., Ludlam, C. A. & Brown, A. J. ( 1992; ). Convergent and divergent sequence evolution in the surface envelope glycoprotein of human immunodeficiency virus type 1 within a single infected patient. Proceedings of the National Academy of Sciences, USA 89, 4835-4839.[CrossRef]
    [Google Scholar]
  11. Holmes, E. C., Zhang, L. Q., Robertson, P., Cleland, A., Harvey, E., Simmonds, P. & Leigh Brown, A. J. ( 1995; ). The molecular epidemiology of human immunodeficiency virus type 1 in Edinburgh. Journal of Infectious Diseases 171, 45-53.[CrossRef]
    [Google Scholar]
  12. Hughes, E. S., Bell, J. E. & Simmonds, P. ( 1997; ). Investigation of the dynamics of the spread of human immunodeficiency virus to brain and other tissues by evolutionary analysis of sequences from the p17gag and env genes. Journal of Virology 71, 1272-1280.
    [Google Scholar]
  13. Huson, D. H. ( 1998; ). SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 14, 68-73.[CrossRef]
    [Google Scholar]
  14. Jetzt, A. E., Yu, H., Klarmann, G. J., Ron, Y., Preston, B. D. & Dougherty, J. P. ( 2000; ). High rate of recombination throughout the human immunodeficiency virus type 1 genome. Journal of Virology 74, 1234-1240.[CrossRef]
    [Google Scholar]
  15. Leitner, T., Kumar, S. & Albert, J. ( 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. Journal of Virology 71, 4761-4770.
    [Google Scholar]
  16. Liu, S. L., Schacker, T., Musey, L., Shriner, D., McElrath, M. J., Corey, L. & Mullins, J. I. ( 1997; ). Divergent patterns of progression to AIDS after infection from the same source: human immunodeficiency virus type 1 evolution and antiviral responses. Journal of Virology 71, 4284-4295.
    [Google Scholar]
  17. McDonald, R. A., Mayers, D. L., Chung, R. C., Wagner, K. F., Ratto-Kim, S., Birx, D. L. & Michael, N. L. ( 1997; ). Evolution of human immunodeficiency virus type 1 env sequence variation in patients with diverse rates of disease progression and T-cell function. Journal of Virology 71, 1871-1879.
    [Google Scholar]
  18. Mansky, L. M. & Temin, H. M. ( 1995; ). Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase. Journal of Virology 69, 5087-5094.
    [Google Scholar]
  19. Martins, L. P., Chenciner, N., Asjo, B., Meyerhans, A. & Wain-Hobson, S. ( 1991; ). Independent fluctuation of human immunodeficiency virus type 1 rev and gp41 quasispecies in vivo. Journal of Virology 65, 4502-4507.
    [Google Scholar]
  20. Michie, C. A., McLean, A., Alcock, C. & Beverley, P. C. ( 1992; ). Lifespan of human lymphocyte subsets defined by CD45 isoforms. Nature 360, 264-265.[CrossRef]
    [Google Scholar]
  21. Nei, M. & Gojobori, T. ( 1986; ). Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Molecular Biology and Evolution 3, 418-426.
    [Google Scholar]
  22. 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.
    [Google Scholar]
  23. Perelson, A. S., Neumann, A. U., Markowitz, M., Leonard, J. M. & Ho, D. D. ( 1996; ). HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time. Science 271, 1582-1586.[CrossRef]
    [Google Scholar]
  24. Perelson, A. S., Essunger, P., Cao, Y., Vesanen, M., Hurley, A., Saksela, K., Markowitz, M. & Ho, D. D. ( 1997; ). Decay characteristics of HIV-1-infected compartments during combination therapy. Nature 387, 188-191.[CrossRef]
    [Google Scholar]
  25. Plikat, U., Nieselt-Struwe, K. & Meyerhans, A. ( 1997; ). Genetic drift can dominate short-term human immunodeficiency virus type 1 nef quasispecies evolution in vivo. Journal of Virology 71, 4233-4240.
    [Google Scholar]
  26. Sala, M. & Wain-Hobson, S. ( 2000; ). Are RNA viruses adapting or merely changing? Journal of Molecular Evolution 51, 12-20.
    [Google Scholar]
  27. Simmonds, P., Zhang, L. Q., McOmish, F., Balfe, P., Ludlam, C. A. & Brown, A. J. ( 1991; ). Discontinuous sequence change of human immunodeficiency virus (HIV) type 1 env sequences in plasma viral and lymphocyte-associated proviral populations in vivo: implications for models of HIV pathogenesis. Journal of Virology 65, 6266-6276.
    [Google Scholar]
  28. Thompson, J. D., Higgins, D. G. & Gibson, T. J. ( 1994; ). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22, 4673-4680.[CrossRef]
    [Google Scholar]
  29. Wolfs, T. F., Zwart, G., Bakker, M., Valk, M., Kuiken, C. L. & Goudsmit, J. ( 1991; ). Naturally occurring mutations within HIV-1 V3 genomic RNA lead to antigenic variation dependent on a single amino acid substitution. Virology 185, 195-205.[CrossRef]
    [Google Scholar]
  30. Wolinsky, S. M., Korber, B. T., Neumann, A. U., Daniels, M., Kunstman, K. J., Whetsell, A. J., Furtado, M. R., Cao, Y., Ho, D. D. & Safrit, J. T. ( 1996; ). Adaptive evolution of human immunodeficiency virus-type 1 during the natural course of infection. Science 272, 537-542.[CrossRef]
    [Google Scholar]
  31. Yamaguchi-Kabata, Y. & Gojobori, T. ( 2000; ). Reevaluation of amino acid variability of the human immunodeficiency virus type 1 gp120 envelope glycoprotein and prediction of new discontinuous epitopes. Journal of Virology 74, 4335-4350.[CrossRef]
    [Google Scholar]
  32. Zanotto, P. M., Kallas, E. G., de Souza, R. F. & Holmes, E. C. ( 1999; ). Genealogical evidence for positive selection in the nef gene of HIV-1. Genetics 153, 1077-1089.
    [Google Scholar]
  33. Zhang, L., Diaz, R. S., Ho, D. D., Mosley, J. W., Busch, M. P. & Mayer, A. ( 1997; ). Host-specific driving force in human immunodeficiency virus type 1 evolution in vivo. Journal of Virology 71, 2555-2561.
    [Google Scholar]
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