Skip to main content

Some NLM-NCBI services and products are experiencing heavy traffic, which may affect performance and availability. We apologize for the inconvenience and appreciate your patience. For assistance, please contact our Help Desk at info@ncbi.nlm.nih.gov.

Journal of Virology logoLink to Journal of Virology
. 1995 Jan;69(1):263–271. doi: 10.1128/jvi.69.1.263-271.1995

Genetic diversity of the envelope glycoprotein from human immunodeficiency virus type 1 isolates of African origin.

J Louwagie 1, W Janssens 1, J Mascola 1, L Heyndrickx 1, P Hegerich 1, G van der Groen 1, F E McCutchan 1, D S Burke 1
PMCID: PMC188572  PMID: 7983718

Abstract

The genetic diversity of the envelope glycoprotein of human immunodeficiency virus type 1 (HIV-1) isolates was studied. HIV-1 isolates were obtained from eight countries in Africa: Djibouti, Gabon, Kenya, Senegal, Somalia, Uganda, Zaire, and Zambia. The DNA sequences encoding the complete HIV-1 envelope protein were PCR amplified and sequenced. Phylogenetic relationships among the 21 sequences from this study and the 32 previously published full-length env HIV-1 sequences were determined. Twenty of the newly sequenced African isolates could be assigned to envelope subtypes A, C, D, and G. One isolate, collected in Zambia, did not belong to any of the eight previously described subtypes and may represent a prototype sequence of its envelope subtype. The phylogenetic classification of these isolates was strongly supported by bootstrapping and the congruence of trees generated by either distance methods or maximum parsimony analysis. The data presented in this study confirm the existence of several genetic subtypes within the global HIV epidemic and broaden the genetic variability previously observed for envelope subtypes. The geographic spread of different subtypes was shown to be substantial, and the notion of cocirculation of subtypes was reinforced.

Full Text

The Full Text of this article is available as a PDF (496.8 KB).

Selected References

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

  1. Alizon M., Wain-Hobson S., Montagnier L., Sonigo P. Genetic variability of the AIDS virus: nucleotide sequence analysis of two isolates from African patients. Cell. 1986 Jul 4;46(1):63–74. doi: 10.1016/0092-8674(86)90860-3. [DOI] [PubMed] [Google Scholar]
  2. Barré-Sinoussi F., Chermann J. C., Rey F., Nugeyre M. T., Chamaret S., Gruest J., Dauguet C., Axler-Blin C., Vézinet-Brun F., Rouzioux C. Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS). Science. 1983 May 20;220(4599):868–871. doi: 10.1126/science.6189183. [DOI] [PubMed] [Google Scholar]
  3. Benn S., Rutledge R., Folks T., Gold J., Baker L., McCormick J., Feorino P., Piot P., Quinn T., Martin M. Genomic heterogeneity of AIDS retroviral isolates from North America and Zaire. Science. 1985 Nov 22;230(4728):949–951. doi: 10.1126/science.2997922. [DOI] [PubMed] [Google Scholar]
  4. Bruce C., Clegg C., Featherstone A., Smith J., Oram J. Sequence analysis of the gp120 region of the env gene of Ugandan human immunodeficiency proviruses from a single individual. AIDS Res Hum Retroviruses. 1993 Apr;9(4):357–363. doi: 10.1089/aid.1993.9.357. [DOI] [PubMed] [Google Scholar]
  5. Burke D. S., Fowler A. K., Redfield R. R., Dilworth S., Oster C. N. Isolation of HIV-1 from the blood of seropositive adults: patient stage of illness and sample inoculum size are major determinants of a positive culture. The Walter Reed Retroviral Research Group. J Acquir Immune Defic Syndr. 1990;3(12):1159–1167. [PubMed] [Google Scholar]
  6. 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]
  7. Dubay J. W., Roberts S. J., Brody B., Hunter E. Mutations in the leucine zipper of the human immunodeficiency virus type 1 transmembrane glycoprotein affect fusion and infectivity. J Virol. 1992 Aug;66(8):4748–4756. doi: 10.1128/jvi.66.8.4748-4756.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Goodenow M., Huet T., Saurin W., Kwok S., Sninsky J., Wain-Hobson S. HIV-1 isolates are rapidly evolving quasispecies: evidence for viral mixtures and preferred nucleotide substitutions. J Acquir Immune Defic Syndr. 1989;2(4):344–352. [PubMed] [Google Scholar]
  9. Guo H. G., Reitz M. S., Gallo R. C., Ko Y. C., Chang K. S. A new subtype of HIV-1 gag sequence detected in Taiwan. AIDS Res Hum Retroviruses. 1993 Sep;9(9):925–927. doi: 10.1089/aid.1993.9.925. [DOI] [PubMed] [Google Scholar]
  10. Gürtler L. G., Hauser P. H., Eberle J., von Brunn A., Knapp S., Zekeng L., Tsague J. M., Kaptue L. A new subtype of human immunodeficiency virus type 1 (MVP-5180) from Cameroon. J Virol. 1994 Mar;68(3):1581–1585. doi: 10.1128/jvi.68.3.1581-1585.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Hahn B. H., Shaw G. M., Taylor M. E., Redfield R. R., Markham P. D., Salahuddin S. Z., Wong-Staal F., Gallo R. C., Parks E. S., Parks W. P. Genetic variation in HTLV-III/LAV over time in patients with AIDS or at risk for AIDS. Science. 1986 Jun 20;232(4757):1548–1553. doi: 10.1126/science.3012778. [DOI] [PubMed] [Google Scholar]
  12. Helseth E., Olshevsky U., Furman C., Sodroski J. Human immunodeficiency virus type 1 gp120 envelope glycoprotein regions important for association with the gp41 transmembrane glycoprotein. J Virol. 1991 Apr;65(4):2119–2123. doi: 10.1128/jvi.65.4.2119-2123.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Higgins D. G., Bleasby A. J., Fuchs R. CLUSTAL V: improved software for multiple sequence alignment. Comput Appl Biosci. 1992 Apr;8(2):189–191. doi: 10.1093/bioinformatics/8.2.189. [DOI] [PubMed] [Google Scholar]
  14. Janssens W., Heyndrickx L., Fransen K., Motte J., Peeters M., Nkengasong J. N., Ndumbe P. M., Delaporte E., Perret J. L., Atende C. Genetic and phylogenetic analysis of env subtypes G and H in central Africa. AIDS Res Hum Retroviruses. 1994 Jul;10(7):877–879. doi: 10.1089/aid.1994.10.877. [DOI] [PubMed] [Google Scholar]
  15. Laure F., Leonard R., Mbayo K., Lurhuma Z., Kayembe N., Brechot C., Sarin P. S., Sarngadharan M., Wong-Staal F., Gallo R. C. Genomic diversity of Zairian HIV isolates: biological characteristics and clinical manifestation of HIV infection. AIDS Res Hum Retroviruses. 1987;3(4):343–353. doi: 10.1089/aid.1987.3.343. [DOI] [PubMed] [Google Scholar]
  16. 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]
  17. Louwagie J., McCutchan F. E., Peeters M., Brennan T. P., Sanders-Buell E., Eddy G. A., van der Groen G., Fransen K., Gershy-Damet G. M., Deleys R. Phylogenetic analysis of gag genes from 70 international HIV-1 isolates provides evidence for multiple genotypes. AIDS. 1993 Jun;7(6):769–780. doi: 10.1097/00002030-199306000-00003. [DOI] [PubMed] [Google Scholar]
  18. Louwagie J., McCutchan F., Van der Groen G., Peeters M., Fransen K., Piot P., Gershy-Damet G. M., Roelants G., Van Heuverswyn H., Eddy G. Genetic comparison of HIV-1 isolates from Africa, Europe, and North America. AIDS Res Hum Retroviruses. 1992 Aug;8(8):1467–1469. doi: 10.1089/aid.1992.8.1467. [DOI] [PubMed] [Google Scholar]
  19. Mascola J. R., Louwagie J., McCutchan F. E., Fischer C. L., Hegerich P. A., Wagner K. F., Fowler A. K., McNeil J. G., Burke D. S. Two antigenically distinct subtypes of human immunodeficiency virus type 1: viral genotype predicts neutralization serotype. J Infect Dis. 1994 Jan;169(1):48–54. doi: 10.1093/infdis/169.1.48. [DOI] [PubMed] [Google Scholar]
  20. McCutchan F. E., Hegerich P. A., Brennan T. P., Phanuphak P., Singharaj P., Jugsudee A., Berman P. W., Gray A. M., Fowler A. K., Burke D. S. Genetic variants of HIV-1 in Thailand. AIDS Res Hum Retroviruses. 1992 Nov;8(11):1887–1895. doi: 10.1089/aid.1992.8.1887. [DOI] [PubMed] [Google Scholar]
  21. McCutchan F. E., Ungar B. L., Hegerich P., Roberts C. R., Fowler A. K., Hira S. K., Perine P. L., Burke D. S. Genetic analysis of HIV-1 isolates from Zambia and an expanded phylogenetic tree for HIV-1. J Acquir Immune Defic Syndr. 1992;5(5):441–449. [PubMed] [Google Scholar]
  22. McKeating J. A., Moore J. P., Ferguson M., Marsden H. S., Graham S., Almond J. W., Evans D. J., Weiss R. A. Monoclonal antibodies to the C4 region of human immunodeficiency virus type 1 gp120: use in topological analysis of a CD4 binding site. AIDS Res Hum Retroviruses. 1992 Apr;8(4):451–459. doi: 10.1089/aid.1992.8.451. [DOI] [PubMed] [Google Scholar]
  23. Meyerhans A., Cheynier R., Albert J., Seth M., Kwok S., Sninsky J., Morfeldt-Månson L., Asjö B., Wain-Hobson S. Temporal fluctuations in HIV quasispecies in vivo are not reflected by sequential HIV isolations. Cell. 1989 Sep 8;58(5):901–910. doi: 10.1016/0092-8674(89)90942-2. [DOI] [PubMed] [Google Scholar]
  24. 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]
  25. Oram J. D., Downing R. G., Roff M., Serwankambo N., Clegg J. C., Featherstone A. S., Booth J. C. Sequence analysis of the V3 loop regions of the env genes of Ugandan human immunodeficiency proviruses. AIDS Res Hum Retroviruses. 1991 Jul;7(7):605–614. doi: 10.1089/aid.1991.7.605. [DOI] [PubMed] [Google Scholar]
  26. Ou C. Y., Kwok S., Mitchell S. W., Mack D. H., Sninsky J. J., Krebs J. W., Feorino P., Warfield D., Schochetman G. DNA amplification for direct detection of HIV-1 in DNA of peripheral blood mononuclear cells. Science. 1988 Jan 15;239(4837):295–297. doi: 10.1126/science.3336784. [DOI] [PubMed] [Google Scholar]
  27. Ou C. Y., Takebe Y., Luo C. C., Kalish M., Auwanit W., Bandea C., de la Torre N., Moore J. L., Schochetman G., Yamazaki S. Wide distribution of two subtypes of HIV-1 in Thailand. AIDS Res Hum Retroviruses. 1992 Aug;8(8):1471–1472. doi: 10.1089/aid.1992.8.1471. [DOI] [PubMed] [Google Scholar]
  28. Ou C. Y., Takebe Y., Weniger B. G., Luo C. C., Kalish M. L., Auwanit W., Yamazaki S., Gayle H. D., Young N. L., Schochetman G. Independent introduction of two major HIV-1 genotypes into distinct high-risk populations in Thailand. Lancet. 1993 May 8;341(8854):1171–1174. doi: 10.1016/0140-6736(93)91001-3. [DOI] [PubMed] [Google Scholar]
  29. 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]
  30. 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]
  31. Shaw G. M., Hahn B. H., Arya S. K., Groopman J. E., Gallo R. C., Wong-Staal F. Molecular characterization of human T-cell leukemia (lymphotropic) virus type III in the acquired immune deficiency syndrome. Science. 1984 Dec 7;226(4679):1165–1171. doi: 10.1126/science.6095449. [DOI] [PubMed] [Google Scholar]
  32. Starcich B. R., Hahn B. H., Shaw G. M., McNeely P. D., Modrow S., Wolf H., Parks E. S., Parks W. P., Josephs S. F., Gallo R. C. Identification and characterization of conserved and variable regions in the envelope gene of HTLV-III/LAV, the retrovirus of AIDS. Cell. 1986 Jun 6;45(5):637–648. doi: 10.1016/0092-8674(86)90778-6. [DOI] [PubMed] [Google Scholar]
  33. Stewart C. B. The powers and pitfalls of parsimony. Nature. 1993 Feb 18;361(6413):603–607. doi: 10.1038/361603a0. [DOI] [PubMed] [Google Scholar]
  34. Vanden Haesevelde M., Decourt J. L., De Leys R. J., Vanderborght B., van der Groen G., van Heuverswijn H., Saman E. Genomic cloning and complete sequence analysis of a highly divergent African human immunodeficiency virus isolate. J Virol. 1994 Mar;68(3):1586–1596. doi: 10.1128/jvi.68.3.1586-1596.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Wong-Staal F., Shaw G. M., Hahn B. H., Salahuddin S. Z., Popovic M., Markham P., Redfield R., Gallo R. C. Genomic diversity of human T-lymphotropic virus type III (HTLV-III). Science. 1985 Aug 23;229(4715):759–762. doi: 10.1126/science.2992084. [DOI] [PubMed] [Google Scholar]

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

RESOURCES