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. 1994 Sep;68(9):5918–5924. doi: 10.1128/jvi.68.9.5918-5924.1994

Analysis of a rape case by direct sequencing of the human immunodeficiency virus type 1 pol and gag genes.

J Albert 1, J Wahlberg 1, T Leitner 1, D Escanilla 1, M Uhlén 1
PMCID: PMC236997  PMID: 7520096

Abstract

Transmission of human immunodeficiency virus type 1 (HIV-1) from a male accused of rape and deliberate transmission of HIV-1 was investigated by sequencing of the HIV-1 pol and gag genes from virus obtained from the male and from the female victim. Parts of the reverse transcriptase and p17gag genes were amplified and directly sequenced from uncultured peripheral blood mononuclear cells. The sequences were compared with sequences from 21 unrelated HIV-1-infected controls from the same geographic area (Stockholm, Sweden). Bootstrap analysis of phylogenetic trees demonstrated that the sequences from the female were significantly more closely related to the sequences from the male than to sequences from the controls. Furthermore, we found that the male and female shared two distinct genetic variants of HIV-1. In p17gag the major variant had an unusual, out-of-frame deletion of 3 nucleotides which the minor variant lacked. These results indicated that the male had transmitted more than one infectious unit to the female. From this study we concluded that it was highly likely that the HIV-1 strains carried by the male and female were closely epidemiologically linked.

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Selected References

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  1. Albert J., Fenyö E. M. Simple, sensitive, and specific detection of human immunodeficiency virus type 1 in clinical specimens by polymerase chain reaction with nested primers. J Clin Microbiol. 1990 Jul;28(7):1560–1564. doi: 10.1128/jcm.28.7.1560-1564.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Albert J., Wahlberg J., Lundeberg J., Cox S., Sandström E., Wahren B., Uhlén M. Persistence of azidothymidine-resistant human immunodeficiency virus type 1 RNA genotypes in posttreatment sera. J Virol. 1992 Sep;66(9):5627–5630. doi: 10.1128/jvi.66.9.5627-5630.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Boucher C. A., O'Sullivan E., Mulder J. W., Ramautarsing C., Kellam P., Darby G., Lange J. M., Goudsmit J., Larder B. A. Ordered appearance of zidovudine resistance mutations during treatment of 18 human immunodeficiency virus-positive subjects. J Infect Dis. 1992 Jan;165(1):105–110. doi: 10.1093/infdis/165.1.105. [DOI] [PubMed] [Google Scholar]
  4. Brinchmann J. E., Albert J., Vartdal F. Few infected CD4+ T cells but a high proportion of replication-competent provirus copies in asymptomatic human immunodeficiency virus type 1 infection. J Virol. 1991 Apr;65(4):2019–2023. doi: 10.1128/jvi.65.4.2019-2023.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Erice A., Mayers D. L., Strike D. G., Sannerud K. J., McCutchan F. E., Henry K., Balfour H. H., Jr Brief report: primary infection with zidovudine-resistant human immunodeficiency virus type 1. N Engl J Med. 1993 Apr 22;328(16):1163–1165. doi: 10.1056/NEJM199304223281605. [DOI] [PubMed] [Google Scholar]
  6. Hein J. Unified approach to alignment and phylogenies. Methods Enzymol. 1990;183:626–645. doi: 10.1016/0076-6879(90)83041-7. [DOI] [PubMed] [Google Scholar]
  7. Holmes E. C., Zhang L. Q., Simmonds P., Ludlam C. A., Brown A. J. 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 U S A. 1992 Jun 1;89(11):4835–4839. doi: 10.1073/pnas.89.11.4835. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Holmes E. C., Zhang L. Q., Simmonds P., Rogers A. S., Brown A. J. Molecular investigation of human immunodeficiency virus (HIV) infection in a patient of an HIV-infected surgeon. J Infect Dis. 1993 Jun;167(6):1411–1414. doi: 10.1093/infdis/167.6.1411. [DOI] [PubMed] [Google Scholar]
  9. Hultman T., Bergh S., Moks T., Uhlén M. Bidirectional solid-phase sequencing of in vitro-amplified plasmid DNA. Biotechniques. 1991 Jan;10(1):84–93. [PubMed] [Google Scholar]
  10. Hultman T., Ståhl S., Hornes E., Uhlén M. Direct solid phase sequencing of genomic and plasmid DNA using magnetic beads as solid support. Nucleic Acids Res. 1989 Jul 11;17(13):4937–4946. doi: 10.1093/nar/17.13.4937. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Korber B., Myers G. Signature pattern analysis: a method for assessing viral sequence relatedness. AIDS Res Hum Retroviruses. 1992 Sep;8(9):1549–1560. doi: 10.1089/aid.1992.8.1549. [DOI] [PubMed] [Google Scholar]
  12. Kwok S., Higuchi R. Avoiding false positives with PCR. Nature. 1989 May 18;339(6221):237–238. doi: 10.1038/339237a0. [DOI] [PubMed] [Google Scholar]
  13. Larder B. A., Kemp S. D. Multiple mutations in HIV-1 reverse transcriptase confer high-level resistance to zidovudine (AZT). Science. 1989 Dec 1;246(4934):1155–1158. doi: 10.1126/science.2479983. [DOI] [PubMed] [Google Scholar]
  14. Leitner T., Halapi E., Scarlatti G., Rossi P., Albert J., Fenyö E. M., Uhlén M. Analysis of heterogeneous viral populations by direct DNA sequencing. Biotechniques. 1993 Jul;15(1):120–127. [PubMed] [Google Scholar]
  15. Ou C. Y., Ciesielski C. A., Myers G., Bandea C. I., Luo C. C., Korber B. T., Mullins J. I., Schochetman G., Berkelman R. L., Economou A. N. Molecular epidemiology of HIV transmission in a dental practice. Science. 1992 May 22;256(5060):1165–1171. doi: 10.1126/science.256.5060.1165. [DOI] [PubMed] [Google Scholar]
  16. Palker T. J., Clark M. E., Langlois A. J., Matthews T. J., Weinhold K. J., Randall R. R., Bolognesi D. P., Haynes B. F. Type-specific neutralization of the human immunodeficiency virus with antibodies to env-encoded synthetic peptides. Proc Natl Acad Sci U S A. 1988 Mar;85(6):1932–1936. doi: 10.1073/pnas.85.6.1932. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Rusche J. R., Javaherian K., McDanal C., Petro J., Lynn D. L., Grimaila R., Langlois A., Gallo R. C., Arthur L. O., Fischinger P. J. Antibodies that inhibit fusion of human immunodeficiency virus-infected cells bind a 24-amino acid sequence of the viral envelope, gp120. Proc Natl Acad Sci U S A. 1988 May;85(9):3198–3202. doi: 10.1073/pnas.85.9.3198. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Rüther U. pUR 250 allows rapid chemical sequencing of both DNA strands of its inserts. Nucleic Acids Res. 1982 Oct 11;10(19):5765–5772. doi: 10.1093/nar/10.19.5765. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987 Jul;4(4):406–425. doi: 10.1093/oxfordjournals.molbev.a040454. [DOI] [PubMed] [Google Scholar]
  20. Scarlatti G., Leitner T., Halapi E., Wahlberg J., Marchisio P., Clerici-Schoeller M. A., Wigzell H., Fenyö E. M., Albert J., Uhlén M. Comparison of variable region 3 sequences of human immunodeficiency virus type 1 from infected children with the RNA and DNA sequences of the virus populations of their mothers. Proc Natl Acad Sci U S A. 1993 Mar 1;90(5):1721–1725. doi: 10.1073/pnas.90.5.1721. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Simmonds P., Balfe P., Peutherer J. F., Ludlam C. A., Bishop J. O., Brown A. J. Human immunodeficiency virus-infected individuals contain provirus in small numbers of peripheral mononuclear cells and at low copy numbers. J Virol. 1990 Feb;64(2):864–872. doi: 10.1128/jvi.64.2.864-872.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Simmonds P., Zhang L. Q., McOmish F., Balfe P., Ludlam C. A., Brown A. J. 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. 1991 Nov;65(11):6266–6276. doi: 10.1128/jvi.65.11.6266-6276.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. St Clair M. H., Martin J. L., Tudor-Williams G., Bach M. C., Vavro C. L., King D. M., Kellam P., Kemp S. D., Larder B. A. Resistance to ddI and sensitivity to AZT induced by a mutation in HIV-1 reverse transcriptase. Science. 1991 Sep 27;253(5027):1557–1559. doi: 10.1126/science.1716788. [DOI] [PubMed] [Google Scholar]
  24. Wahlberg J., Albert J., Lundeberg J., Cox S., Wahren B., Uhlén M. Dynamic changes in HIV-1 quasispecies from azidothymidine (AZT)-treated patients. FASEB J. 1992 Jul;6(10):2843–2847. doi: 10.1096/fasebj.6.10.1634047. [DOI] [PubMed] [Google Scholar]
  25. Wahlberg J., Albert J., Lundeberg J., Von Gegerfelt A., Broliden K., Utter G., Fenyö E. M., Uhlén M. Analysis of the V3 loop in neutralization-resistant human immunodeficiency virus type 1 variants by direct solid-phase DNA sequencing. AIDS Res Hum Retroviruses. 1991 Dec;7(12):983–990. doi: 10.1089/aid.1991.7.983. [DOI] [PubMed] [Google Scholar]
  26. Wahlberg J., Fiore J., Angarano G., Uhlén M., Albert J. Apparent selection against transmission of zidovudine-resistant human immunodeficiency virus type 1 variants. J Infect Dis. 1994 Mar;169(3):611–614. doi: 10.1093/infdis/169.3.611. [DOI] [PubMed] [Google Scholar]
  27. Wolfs T. F., Zwart G., Bakker M., Goudsmit J. HIV-1 genomic RNA diversification following sexual and parenteral virus transmission. Virology. 1992 Jul;189(1):103–110. doi: 10.1016/0042-6822(92)90685-i. [DOI] [PubMed] [Google Scholar]
  28. Wolfs T. F., Zwart G., Bakker M., Valk M., Kuiken C. L., Goudsmit J. Naturally occurring mutations within HIV-1 V3 genomic RNA lead to antigenic variation dependent on a single amino acid substitution. Virology. 1991 Nov;185(1):195–205. doi: 10.1016/0042-6822(91)90767-6. [DOI] [PubMed] [Google Scholar]
  29. Wolinsky S. M., Wike C. M., Korber B. T., Hutto C., Parks W. P., Rosenblum L. L., Kunstman K. J., Furtado M. R., Muñoz J. L. Selective transmission of human immunodeficiency virus type-1 variants from mothers to infants. Science. 1992 Feb 28;255(5048):1134–1137. doi: 10.1126/science.1546316. [DOI] [PubMed] [Google Scholar]
  30. Zhang L. Q., MacKenzie P., Cleland A., Holmes E. C., Brown A. J., Simmonds P. Selection for specific sequences in the external envelope protein of human immunodeficiency virus type 1 upon primary infection. J Virol. 1993 Jun;67(6):3345–3356. doi: 10.1128/jvi.67.6.3345-3356.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Zhang L. Q., Simmonds P., Ludlam C. A., Brown A. J. Detection, quantification and sequencing of HIV-1 from the plasma of seropositive individuals and from factor VIII concentrates. AIDS. 1991 Jun;5(6):675–681. doi: 10.1097/00002030-199106000-00006. [DOI] [PubMed] [Google Scholar]
  32. Zhu T., Mo H., Wang N., Nam D. S., Cao Y., Koup R. A., Ho D. D. Genotypic and phenotypic characterization of HIV-1 patients with primary infection. Science. 1993 Aug 27;261(5125):1179–1181. doi: 10.1126/science.8356453. [DOI] [PubMed] [Google Scholar]

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