Skip to main content
NCBI home page
Journal of Virology logoLink to Journal of Virology
. 1994 Oct;68(10):6340–6346. doi: 10.1128/jvi.68.10.6340-6346.1994

Identification of human immunodeficiency virus type 1 envelope genes recombinant between subtypes B and F in two epidemiologically linked individuals from Brazil.

E C Sabino 1, E G Shpaer 1, M G Morgado 1, B T Korber 1, R S Diaz 1, V Bongertz 1, S Cavalcante 1, B Galvão-Castro 1, J I Mullins 1, A Mayer 1
PMCID: PMC237055  PMID: 8083973

Abstract

Sequence analysis of a human immunodeficiency virus type 1 env gene PCR amplified from a Brazilian woman's peripheral blood mononuclear cell DNA (sample RJIO1) showed that it was likely to have been derived from a double recombination event between human immunodeficiency virus type 1 subtypes B and F. The major portion of the gp120 coding sequence belonged to the B lineage, but a segment of the C2 to V3 region (approximately 135 nucleotides) clearly associated with sequences of the F lineage. The subtype F-like segment had 15 noncontiguous signature nucleotides in common with Brazilian subtype F sequences that were not found, or were rare, in subtype B sequences. In contrast, this same segment had only 3 signature nucleotides shared with subtype B sequences and not present in the Brazilian subtype F sequences. Phylogenetic analysis, amino acid signature pattern analysis, and the pattern of synonymous mutations all supported the hypothesis of a recombinational origin of the RJIO1 sequence. Related recombinant genes were also detected in peripheral blood mononuclear cell DNA obtained from the woman's recent sexual partner, indicating that the recombination event probably occurred at some previous time in the chain of virus transmission. Divergent viral sequences in the V3 region were found in the male sexual partner, while a relatively homogeneous viral population was detected in the woman, consistent with her recent infection.

Full text

PDF
6340

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Coffin J. M. Genetic diversity and evolution of retroviruses. Curr Top Microbiol Immunol. 1992;176:143–164. doi: 10.1007/978-3-642-77011-1_10. [DOI] [PubMed] [Google Scholar]
  2. Delassus S., Cheynier R., Wain-Hobson S. Evolution of human immunodeficiency virus type 1 nef and long terminal repeat sequences over 4 years in vivo and in vitro. J Virol. 1991 Jan;65(1):225–231. doi: 10.1128/jvi.65.1.225-231.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Delwart E. L., Shpaer E. G., Louwagie J., McCutchan F. E., Grez M., Rübsamen-Waigmann H., Mullins J. I. Genetic relationships determined by a DNA heteroduplex mobility assay: analysis of HIV-1 env genes. Science. 1993 Nov 19;262(5137):1257–1261. doi: 10.1126/science.8235655. [DOI] [PubMed] [Google Scholar]
  4. Dumitrescu O., Kalish M. L., Kliks S. C., Bandea C. I., Levy J. A. Characterization of human immunodeficiency virus type 1 isolates from children in Romania: identification of a new envelope subtype. J Infect Dis. 1994 Feb;169(2):281–288. doi: 10.1093/infdis/169.2.281. [DOI] [PubMed] [Google Scholar]
  5. Faulkner D. V., Jurka J. Multiple aligned sequence editor (MASE). Trends Biochem Sci. 1988 Aug;13(8):321–322. doi: 10.1016/0968-0004(88)90129-6. [DOI] [PubMed] [Google Scholar]
  6. Groenink M., Andeweg A. C., Fouchier R. A., Broersen S., van der Jagt R. C., Schuitemaker H., de Goede R. E., Bosch M. L., Huisman H. G., Tersmette M. Phenotype-associated env gene variation among eight related human immunodeficiency virus type 1 clones: evidence for in vivo recombination and determinants of cytotropism outside the V3 domain. J Virol. 1992 Oct;66(10):6175–6180. doi: 10.1128/jvi.66.10.6175-6180.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Hillis D. M., Allard M. W., Miyamoto M. M. Analysis of DNA sequence data: phylogenetic inference. Methods Enzymol. 1993;224:456–487. doi: 10.1016/0076-6879(93)24035-s. [DOI] [PubMed] [Google Scholar]
  8. Hillis D. M., Huelsenbeck J. P. Signal, noise, and reliability in molecular phylogenetic analyses. J Hered. 1992 May-Jun;83(3):189–195. doi: 10.1093/oxfordjournals.jhered.a111190. [DOI] [PubMed] [Google Scholar]
  9. Hu W. S., Temin H. M. Retroviral recombination and reverse transcription. Science. 1990 Nov 30;250(4985):1227–1233. doi: 10.1126/science.1700865. [DOI] [PubMed] [Google Scholar]
  10. 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]
  11. Kusumi K., Conway B., Cunningham S., Berson A., Evans C., Iversen A. K., Colvin D., Gallo M. V., Coutre S., Shpaer E. G. Human immunodeficiency virus type 1 envelope gene structure and diversity in vivo and after cocultivation in vitro. J Virol. 1992 Feb;66(2):875–885. doi: 10.1128/jvi.66.2.875-885.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Li W. H., Tanimura M., Sharp P. M. Rates and dates of divergence between AIDS virus nucleotide sequences. Mol Biol Evol. 1988 Jul;5(4):313–330. doi: 10.1093/oxfordjournals.molbev.a040503. [DOI] [PubMed] [Google Scholar]
  13. Louwagie J., Delwart E. L., Mullins J. I., McCutchan F. E., Eddy G., Burke D. S. Genetic analysis of HIV-1 isolates from Brazil reveals presence of two distinct genetic subtypes. AIDS Res Hum Retroviruses. 1994 May;10(5):561–567. doi: 10.1089/aid.1994.10.561. [DOI] [PubMed] [Google Scholar]
  14. Meyerhans A., Vartanian J. P., Wain-Hobson S. DNA recombination during PCR. Nucleic Acids Res. 1990 Apr 11;18(7):1687–1691. doi: 10.1093/nar/18.7.1687. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Morgado M. G., Sabino E. C., Shpaer E. G., Bongertz V., Brigido L., Guimaraes M. D., Castilho E. A., Galvão-Castro B., Mullins J. I., Hendry R. M. V3 region polymorphisms in HIV-1 from Brazil: prevalence of subtype B strains divergent from North American/European prototype and detection of subtype F. AIDS Res Hum Retroviruses. 1994 May;10(5):569–576. doi: 10.1089/aid.1994.10.569. [DOI] [PubMed] [Google Scholar]
  16. Murphy E., Korber B., Georges-Courbot M. C., You B., Pinter A., Cook D., Kieny M. P., Georges A., Mathiot C., Barré-Sinoussi F. Diversity of V3 region sequences of human immunodeficiency viruses type 1 from the central African Republic. AIDS Res Hum Retroviruses. 1993 Oct;9(10):997–1006. doi: 10.1089/aid.1993.9.997. [DOI] [PubMed] [Google Scholar]
  17. Nei M., Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol. 1986 Sep;3(5):418–426. doi: 10.1093/oxfordjournals.molbev.a040410. [DOI] [PubMed] [Google Scholar]
  18. Potts K. E., Kalish M. L., Lott T., Orloff G., Luo C. C., Bernard M. A., Alves C. B., Badaro R., Suleiman J., Ferreira O. Genetic heterogeneity of the V3 region of the HIV-1 envelope glycoprotein in Brazil. Brazilian Collaborative AIDS Research Group. AIDS. 1993 Sep;7(9):1191–1197. doi: 10.1097/00002030-199309000-00007. [DOI] [PubMed] [Google Scholar]
  19. 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]
  20. 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]
  21. 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]
  22. 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]
  23. 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]

Articles from Journal of Virology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES