1887

Abstract

Recombination is one of several factors that contribute to the great genetic diversity of human immunodeficiency virus type 1 (HIV-1). In the current study, analysis of the full-length genome of a novel complex mosaic HIV-1 isolate (99GR303) from a Greek sailor who was possibly infected in Sierra Leone, Africa is presented. The 99GR303 isolate was found to comprise genomic regions belonging to subtypes A, G, J and K as well as of regions of a subtype that remains unclassified. For a partial region of as well as , no apparent similarity to the known HIV-1 subtypes or to any of the circulating recombinant forms was found. In fact, in the partial gene, including the C2-V3 region, the 99GR303 isolate formed a new clade, suggesting the existence of an additional HIV-1 subtype. Thus, novel recombinants embody partial genomic regions which may have originated either from subtypes that existed in the past and became extinct or from contemporary subtypes that are extremely rare.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/0022-1317-82-10-2509
2001-10-01
2019-10-14
Loading full text...

Full text loading...

/deliver/fulltext/jgv/82/10/0822509a.html?itemId=/content/journal/jgv/10.1099/0022-1317-82-10-2509&mimeType=html&fmt=ahah

References

  1. Candotti, D., Tareau, C., Barin, F., Joberty, C., Rosenheim, M., M’Pele, P., Huraux, J. M. & Agut, H. ( 1999; ). Genetic subtyping and V3 serotyping of HIV type 1 isolates in Congo. AIDS Research and Human Retroviruses 15, 309-314.[CrossRef]
    [Google Scholar]
  2. Ellenberger, D. L., Pieniazeek, D., Nkengasong, J., Luo, C. C., Devare, S., Maurice, C., Janini, M., Ramos, A., Fridlund, C., Hu, D. J., Coulibaly, I. M., Ekpini, E., Wiktor, S. Z., Greenberg, A. E., Schochetman, G. & Rayfield, M. A. ( 1999; ). Genetic analysis of human immunodeficiency virus in Abidjan, Ivory Coast reveals predominance of HIV type 1 subtype A and introduction of subtype G. AIDS Research and Human Retroviruses 15, 3-9.[CrossRef]
    [Google Scholar]
  3. Felsenstein, J. (1993). PHYLIP: Phylogeny Inference Package, version 3.5. University of Washington, Seattle, WA, USA.
  4. Gao, F., Robertson, D. L., Morrison, S. G., Hui, H., Craig, S., Decker, J., Fultz, P. N., Girard, M., Shaw, G. M., Hahn, B. H. & Sharp, P. M. ( 1996; ). The heterosexual human immunodeficiency virus type 1 epidemic in Thailand is caused by an intersubtype (A/E) recombinant of African origin. Journal of Virology 70, 7013-7029.
    [Google Scholar]
  5. Gao, F., Robertson, D. L., Carruthers, C. D., Li, Y., Bailes, E., Kostrikis, L. G., Salminen, M. O., Bibollet-Ruche, F., Peeters, M., Ho, D. D., Shaw, G. M., Sharp, P. M. & Hahn, B. H. ( 1998; ). An isolate of human immunodeficiency virus type 1 originally classified as subtype I represents a complex mosaic comprising three different group M subtypes (A, G, and I). Journal of Virology 72, 10234-10241.
    [Google Scholar]
  6. Heyndrickx, L., Janssens, W., Alary, M., Fransen, K., Vereecken, K., Coppens, S., Willems, B., Davo, N., Guèdèmè, A., Baganizi, E., Joly, J. & Van der Groen, G. ( 1996; ). Genetic variability of HIV type 1 in Bénin. AIDS Research and Human Retroviruses 12, 1495-1497.[CrossRef]
    [Google Scholar]
  7. Hu, W. S. & Temin, H. M. ( 1990; ). Retroviral recombination and reverse transcription. Science 250, 1227-1233.[CrossRef]
    [Google Scholar]
  8. Ishikawa, K., Janssens, W., Brandful, J., Heyndrickx, L., Takebe, Y., Ampofo, W., Sata, T., Yamazaki, S., Osei-Kwasi, M., Yamamoto, N., Koyanagi, Y., Van der Groen, G. & Kurata, T. ( 1996; ). Genetic and phylogenetic analysis of HIV type 1 env subtypes in Ghana, west Africa. AIDS Research and Human Retroviruses 12, 1575-1578.[CrossRef]
    [Google Scholar]
  9. Kalish, M. L., Robbins, K. E., Schaefer, A., Saekhou, A., Phillips, J., Nzilambi, N., Shyr, J., St Louis, M., Quinn, T., Pieniazek, D. & Folks, T. M. (2001). Evidence for the presence of all known HIV-1 group M subtypes and some unclassified strains in Kinshasa, Zaire in the early to mid-1980s. 8th Conference on Retroviruses and Opportunistic Infections, Chicago, USA. Abstract 268.
  10. Kimura, M. ( 1980; ). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequence. Journal of Molecular Evolution 16, 111-120.[CrossRef]
    [Google Scholar]
  11. Korber, B., Muldoon, M., Theiler, J., Gao, F., Gupta, R., Lapedes, A., Hahn, B. H., Wolinsky, S. & Bhattacharya, T. ( 2000; ). Timing the ancestor of the HIV-1 pandemic strains. Science 288, 1789-1796.[CrossRef]
    [Google Scholar]
  12. Kostrikis, L. G., Bagdades, E., Cao, Y., Zhang, L., Dimitriou, D. & Ho, D. D. ( 1995; ). Genetic analysis of human immunodeficiency virus type 1 strains from patients in Cyprus: identification of a new subtype designated subtype I. Journal of Virology 69, 6122-6130.
    [Google Scholar]
  13. Kuiken, C. L., Foley, B., Hahn, B., Korber, B., McCutchan, F., Marx, P. A., Mellors, J. W., Mullins, J. I., Sodroski, J. & Wolinksy, S. (1999). Human retroviruses and AIDS 1999: a compilation and analysis of nucleic acid and amino acid sequences. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA.
  14. Louwagie, J., Janssens, W., Mascola, J., Heyndrickx, L., Hegerich, P., Van Der Groen, G., McCutchan, F. E. & Burke, D. S. ( 1995; ). Genetic diversity of the envelope glycoprotein from human immunodeficiency virus type 1 isolates of African origin. Journal of Virology 69, 263-271.
    [Google Scholar]
  15. McCutchan, F. E., Carr, J. K., Bajani, M., Sanders-Buell, E., Harry, T. O., Stoeckli, T. C., Robbins, K. E., Gashau, W., Naisidi, A., Janssens, W. & Kalish, M. L. ( 1999; ). Subtype G and multiple forms of A/G intersubtype recombinant human immunodeficiency virus type 1 in Nigeria. Virology 254, 226-234.[CrossRef]
    [Google Scholar]
  16. Mboudjeka, I., Bikandou, B., Zekeng, L., Takehisa, J., Harada, Y., Yamaguchi-Kabata, Y., Taniguchi, Y., Ido, E., Kaptue, L., M’pelle, P., Parra, H. J., Ikeda, M., Hayami, M. & Miura, T. ( 1999; ). Genetic diversity of HIV-1 group M from Cameroon and Republic of Congo. Archives of Virology 144, 2291-2311.[CrossRef]
    [Google Scholar]
  17. Mokili, J. L. K., Christopher, M. W., Burns, S. M., Cutting, W. A., Bopopi, J. M., Green, S. D., Peutherer, J. F. & Simmonds, P. ( 1999; ). Genetic heterogeneity of HIV type 1 subtypes in Kimpese, rural Democratic Republic of Congo. AIDS Research and Human Retroviruses 15, 655-664.[CrossRef]
    [Google Scholar]
  18. Müller-Trutwin, M. C., Chaix, M. L., Letourneur, F., Bégaud, E., Beaumont, D., Deslandres, A., You, B., Morvan, J., Mathiot, C., Barré-Sinousi, F. & Saragosti, S. ( 1999; ). Increase of HIV-1 subtype A in Central African Republic. Journal of Acquired Immune Deficiency Syndromes and Human Retrovirology 21, 164-171.
    [Google Scholar]
  19. Nasioulas, G., Paraskevis, D., Magiorkinis, E., Theodoridou, M. & Hatzakis, A. ( 1999; ). Molecular analysis of the full-length genome of the HIV-1 subtype I: evidence of A/G/I recombination. AIDS Research and Human Retroviruses 15, 745-758.[CrossRef]
    [Google Scholar]
  20. Paraskevis, D. & Hatzakis, A. ( 1999; ). Molecular epidemiology of HIV-1 infection. AIDS Reviews 1, 238-249.
    [Google Scholar]
  21. Paraskevis, D., Magiorkinis, M., Paparizos, V., Pavlakis, G. N. & Hatzakis, A. ( 2000; ). Molecular characterization of a recombinant HIV type 1 isolate (A/G/E/?): unidentified regions may be derived from parental subtype E sequences. AIDS Research and Human Retroviruses 16, 845-855.[CrossRef]
    [Google Scholar]
  22. Paraskevis, D., Magiorkinis, M., Vandamme, A. M., Kostrikis, L. G. & Hatzakis, A. ( 2001; ). Re-analysis of human immunodeficiency virus type 1 isolates from Cyprus and Greece, initially designated as ‘subtype I’, reveals a unique complex A/G/H/K/? mosaic pattern. Journal of General Virology 82, 575-580.
    [Google Scholar]
  23. Peeters, M., Esu-Williams, E., Vergne, L., Montavon, C., Mulanga-Kabeya, C., Harry, T., Ibironke, A., Lesage, D., Patrel, D. & Delaporte, E. ( 2000; ). Predominance of subtype A and G HIV type 1 in Nigeria, with geographical differences in their distribution. AIDS Research and Human Retroviruses 16, 315-325.[CrossRef]
    [Google Scholar]
  24. Quiñones-Mateu, M. L. & Arts, E. J. ( 1999; ). Recombination in HIV-1: update and implications. AIDS Reviews 1, 89-100.
    [Google Scholar]
  25. Ray, S. C. (1998). SimPlot. Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA. http://www.med.jhu.edu/deptmed/sray/download/.
  26. Robertson, D. L., Hahn, B. H. & Sharp, P. M. ( 1995a; ). Recombination in AIDS viruses. Journal of Molecular Evolution 40, 249-259.[CrossRef]
    [Google Scholar]
  27. Robertson, D. L., Sharp, P. M., McCutchan, F. E. & Hahn, B. H. ( 1995b; ). Recombination in HIV-1. Nature 374, 124-126.
    [Google Scholar]
  28. Salemi, M., Strimmer, K., Hall, W. W., Duffy, M., Delaporte, E., Mboup, S., Peeters, M. & Vandamme, A. M. ( 2001; ). Dating the common ancestor of SIVcpz and HIV-1 group M and the origin of HIV-1 subtypes using a new method to uncover clock-like molecular evolution. FASEB Journal 15, 276-278.
    [Google Scholar]
  29. Takehisa, J., Osei-Kwasi, M., Ayisi, N. K., Hishida, O., Miura, T., Igarashi, T., Brandful, J., Ampofo, W., Netty, V. B., Mensah, M., Yamashita, M., Ido, E. & Hayami, M. ( 1997; ). Phylogenetic analysis of human immunodeficiency virus 1 in Ghana. Acta Virologica 41, 51-54.
    [Google Scholar]
  30. Takehisa, J., Zekeng, L., Ido, E., Mboudjeka, I., Moriyama, H., Miura, T., Yamashita, M., Gürtler, L. G., Hayami, M. & Kaptué, L. ( 1998; ). Various types of HIV mixed infections in Cameroon. Virology 245, 1-10.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/0022-1317-82-10-2509
Loading
/content/journal/jgv/10.1099/0022-1317-82-10-2509
Loading

Data & Media loading...

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error