1887

Abstract

In human immunodeficiency virus type 1 (HIV-1) infection, the presence of divergent nucleotide sequences within a quasispecies has been associated with double infections or samples from different times or from different tissue compartments. The authors analysed HIV-1 proviral quasispecies from PBMC of three untreated Spanish patients displaying highly divergent nucleotide sequences without evidence of double infection. The origin of these nucleotide sequences was determined by phylogenetic analysis and by dating of the different groups using a genetic divergence versus sampling year plot from a set of Spanish samples. By their short genetic distance to the node of the patient's HIV-1 phylogenetic tree and by their early date of origin, close to the seroconversion time, some groups of sequences were considered ancestral. The presence within HIV-1 quasispecies of ancestral sequences, dated up to 10 years earlier than present ones, has important consequences for viral evolution, in the pathogenesis and treatment of HIV-1 infection.

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2004-02-01
2024-03-29
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References

  1. Bagnarelli P., Mazzola F., Menzo S., Montroni M., Butini L., Clementi M. 1999; Host-specific modulation of the selective constraints driving human immunodeficiency virus type 1 env gene evolution. J Virol 73:3764–3777
    [Google Scholar]
  2. Boom R., Sol C. J. A., Salimans M. M. M., Jansen C. L., Wertheim-van Dillen P. M. E., Van der Noordaa J. 1990; Rapid and simple method for purification of nucleic acids. J Clin Microbiol 283:495–503
    [Google Scholar]
  3. Casado C., Urtasun I., Martin-Walther M. V., Garcia S., Rodriguez C., del Romero J., Lopez-Galindez C. 2000; Genetic analysis of HIV-1 samples from Spain. J Acquir Immune Defic Syndr 23:68–74
    [Google Scholar]
  4. Casado C., Garcia S., Rodriguez C., del Romero J., Bello G., Lopez-Galindez C. 2001; Different evolutionary patterns are found within human immunodeficiency virus type 1-infected patients. J Gen Virol 82:2495–2508
    [Google Scholar]
  5. CDC 1992; Revised classification system for HIV infection and expanded surveillance case definition for AIDS among adolescents and adults. Morbid Mortal Wkly Rep 41 (no. RR-17:
    [Google Scholar]
  6. Cheynier R., Henrichwark S., Hadida F., Pelletier E., Oksenhendler E., Autran B., Wain-Hobson S. 1994; HIV and T cell expansion in splenic white pulps is accompanied by infiltration of HIV-specific cytotoxic T lymphocytes. Cell 78:373–387
    [Google Scholar]
  7. Cheynier R., Gratton S., Halloran M., Stahmer I., Letvin N. L., Wain-Hobson S. 1998; Antigenic stimulation by BCG vaccine as an in vivo driving force for SIV replication and dissemination. Nat Med 4:421–427
    [Google Scholar]
  8. Delwart E. L., Pan H., Sheppard H. W., Wolpert D., Neumann A. U., Korber B., Mullins J. I. 1997; Slower evolution of human immunodeficiency virus type 1 quasispecies during progresion to AIDS. J Virol 71:7498–7508
    [Google Scholar]
  9. Delwart E. L., Mullins J. I., Gupta P., Learn J. G. H., Holodniy M., Katzenstein D., Walker B. D., Singh M. K. 1998; Human immunodeficiency virus type 1 populations in blood and semen. J Virol 72:617–623
    [Google Scholar]
  10. Diaz R. S., Sabino E. C., Mayer A., Mosley J. W., Busch M. P. 1995; Dual human immunodeficiency virus type 1 infection and recombination in a dually exposed transfusion recipient. The Transfusion Safety Study Group. J Virol 69:3273–3281
    [Google Scholar]
  11. Domingo E., Holland J. J. 1988; High error rates, population equilibrium and evolution of RNA replication systems. In RNA Genetics , In RNA Genetics edn pp  3–56 Edited by Domingo E., Holland J. J., Ahlquist P. Boca Raton, FL: CRC Press;
    [Google Scholar]
  12. Eigen M., Biebricher C. K. 1988; Sequence space and quasispecies distribution. In RNA Genetics pp  211–245 Edited by Domingo E., Holland J. J., Ahlquist P. Boca Raton, FL: CRC Press;
    [Google Scholar]
  13. Fauci A. S. 1996; Host factors and the pathogenesis of HIV-induced disease. Nature 384:529–534
    [Google Scholar]
  14. Felsenstein J. 1993 PHYLIP (Phylogeny Interference Package), 3.5c ed. Department of Genetics, University of Washington; Seattle: Distributed by the author
    [Google Scholar]
  15. Finzi D., Hermankova M., Pierson T. 12 other authors 1997; Identification of a reservoir for HIV-1 in patients on highly active antiretroviral therapy. Science 278:1295–1300
    [Google Scholar]
  16. Gunthard H. F., Frost S. D., Leigh-Brown A. J. 9 other authors 1999; Evolution of envelope sequences of human immunodeficiency virus type 1 in cellular reservoirs in the setting of potent antiviral therapy. J Virol 73:9404–9412
    [Google Scholar]
  17. Halapi E., Leitner T., Jansson M. 7 other authors 1997; Correlation between HIV sequence evolution, specific immune response and clinical outcome in vertically infected infants. Aids 11:1709–1717
    [Google Scholar]
  18. Itescu S., Simonelli P. F., Winchester R. J., Ginsberg H. S. 1994; Human immunodeficiency virus type 1 strains in the lungs of infected individuals evolve independently from those in peripheral blood and are highly conserved in the C-terminal region of the envelope V3 loop. Proc Natl Acad Sci U S A 91:11378–11382
    [Google Scholar]
  19. Korber B., Theiler J., Wolinsky S. 1998; Limitations of a molecular clock applied to considerations of the origin of HIV-1. Science 280:1868–1871
    [Google Scholar]
  20. Korber B. T., Sharp P. M., Ho D. D. 1999; Dating the origin of HIV-1 subtypes. Nature 400:326
    [Google Scholar]
  21. Kumar S., Tamura K., Jakobsen I. B., Nei M. 2001; MEGA2: Molecular Evolutionary Genetics Analysis software. Bioinformatics 17:1244–1245
    [Google Scholar]
  22. Leitner T., Albert J. 1999; The molecular clock of HIV-1 unveiled through analysis of a known transmission history. Proc Natl Acad Sci U S A 96:10752–10757
    [Google Scholar]
  23. Lukashov V. V., 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
    [Google Scholar]
  24. Lukashov V. V., Goudsmit J. 2002; Recent evolutionary history of human immunodeficiency virus type 1 subtype B: reconstruction of epidemic onset based on sequence distances to the common ancestor. J Mol Evol 54:680–691
    [Google Scholar]
  25. Lukashov V. V., Kuiken C. L., Goudsmit J. 1995; Intrahost human immunodeficiency virus type 1 evolution is related to length of the immunocompetent period. J Virol 69:6911–6916
    [Google Scholar]
  26. Meyerhans A., Vartanian J. P., Wain-Hobson S. 1990; DNA recombination during PCR. Nucleic Acids Res 18:1687–1691
    [Google Scholar]
  27. Nijhuis M., Schuurman R., de Jong D., Erickson J., Gustchina E., Albert J., Schipper P., Gulnik S., Boucher C. A. 1999; Increased fitness of drug resistant HIV-1 protease as a result of acquisition of compensatory mutations during suboptimal therapy. Aids 13:2349–2359
    [Google Scholar]
  28. Ostrowski M. A., Krakauer D. C., Li Y., Justement S. J., Learn G., Ehler L. A., Stanley S. K., Nowak M., Fauci A. S. 1998; Effect of immune activation on the dynamics of human immunodeficiency virus replication and on the distribution of viral quasispecies. J Virol 72:7772–7784
    [Google Scholar]
  29. Plikat U., Nielsen-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
    [Google Scholar]
  30. Poss M., Rodrigo A. G., Gosink J. J., Learn G. H., de Vange Panteleeff D., Martin H. L., Bwayo J. Jr, Kreiss J. K., Overbaugh J. 1998; Evolution of envelope sequences from the genital tract and peripheral blood of women infected with clade A human immunodeficiency virus type 1. J Virol 72:8240–8251
    [Google Scholar]
  31. Rodrigo A. G., Goracke P. C., Rowhanian K., Mullins J. I. 1997; Quantitation of target molecules from polymerase chain reaction-based limiting dilution assays. AIDS Res Hum Retrovir 13:737–742
    [Google Scholar]
  32. Ryzhova E. V., Crino P., Shawver L., Westmoreland S. V., Lackner A. A., Gonzalez-Scarano F. 2002; Simian immunodeficiency virus encephalitis: analysis of envelope sequences from individual brain multinucleated giant cells and tissue samples. Virology 297:57–67
    [Google Scholar]
  33. Sala M., Zambruno M., Vartanian J. P., Marconi A., Bertazoni U., Wain-Hobson S. 1994; Spatial discontinuities in human immunodeficiency virus type 1 quasispecies derived from epidermal Langerhans cells of a patient with AIDS and evidence for double infection. J Virol 68:217–222
    [Google Scholar]
  34. Shankarappa R., Margolick J. B., Gange S. J. 9 other authors 1999; Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J Virol 73:10489–10502
    [Google Scholar]
  35. Simmonds P., Zhang L. Q., McOmish F., Balfe P., Ludlam C. A., Brown A. J. L. 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. J Virol 65:6266–6276
    [Google Scholar]
  36. Thompson J., Higgins D., Gibson T. 1994; CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680
    [Google Scholar]
  37. Wolinsky S. M., Korber B. T. M., Neuman A. U. 8 other authors 1996; Adaptative evolution of human immunodeficiency virus type 1 during the natural course of infection. Science 272:537–542
    [Google Scholar]
  38. Wong J. K., Hezareh M., Günthard H. F., Havlir D. V., Ignacio C. C., Spina C. A., Richman D. D. 1997a; Recovery of replication-competent HIV despite prolonged suppression of plasma viremia. Science 278:1291–1295
    [Google Scholar]
  39. Wong J. K., Ignacio C. C., Torriani F., Havlir D., Fitch N. J. S., Richman D. D. 1997b; In vivo compartmentalization of human immunodeficiency virus: evidence from the examination of pol sequences from autopsy tissues. J Virol 71:2059–2071
    [Google Scholar]
  40. Zhu T., Wang N., Carr A., Wolinsky S., Ho D. D. 1995; Evidence for coinfection by multiple strains of human immunodeficiency virus type 1 subtype B in an acute seroconvertor. J Virol 69:1324–1327
    [Google Scholar]
  41. Zhu T., Korber B. T., Nahmias A. J., Hooper E., Sharp P. M., Ho D. D. 1998; An African HIV-1 sequence from 1959 and implications for the origin of the epidemic. Nature 391:594–597
    [Google Scholar]
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