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Journal of Virology, November 2004, p. 12438-12445, Vol. 78, No. 22
0022-538X/04/$08.00+0     DOI: 10.1128/JVI.78.22.12438-12445.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Distinct Human Immunodeficiency Virus Type 1 Subtype A Virus Circulating in West Africa: Sub-Subtype A3

Seema Thakore Meloni,1 Bohye Kim,2 Jean-Louis Sankalé,1 Donald J. Hamel,1 Sodsai Tovanabutra,2 Souleymane Mboup,3 Francine E. McCutchan,2 and Phyllis J. Kanki1*

Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts,1 Henry M. Jackson Foundation, Rockville, Maryland,2 Laboratoire de Bactériologie-Virologie, Université Cheikh Anta Diop, Dakar, Senegal3

Received 16 February 2004/ Accepted 22 June 2004

Phylogenetic analyses demonstrate significant diversity in worldwide circulating strains of human immunodeficiency virus type 1 (HIV-1). Detailed studies have revealed a complex pattern of intersubtype recombinations, as well as evidence of sub-subtypes circulating in various populations. In this study, we characterized an HIV-1 strain that had previously been identified as a distinct subcluster within the subtype A radiation based on partial sequence data. These viruses were of particular interest given that we recently found that their prevalence was significantly higher in dually infected individuals compared to women who were singly infected with HIV-1. Five viruses isolated from commercial sex workers in Dakar, Senegal, were full-length PCR amplified and sequenced. Phylogenetic analyses indicated that, whereas three of these viruses were closely related and clustered overall within the HIV-1 subtype A radiation, they were distinct from previously characterized sub-subtype A1 and A2 viruses. The clustering pattern was maintained in the individual gag, pol, and env regions of the genome. Distance calculations between these viruses, which we termed A3, and other reference sub-subtype A1 and A2 viruses fell in the range of distances between previously characterized sub-subtype groups. In addition, we found evidence of two A3-containing recombinants in our cohort. These recombinants are mosaics composed of sequence from both sub-subtype A3 and CRF02_AG, the major circulating recombinant form in this West African population. Based on phylogenetic analyses, we propose that the group of viruses found in the Dakar sex worker cohort, previously referred to as HIV-1 A subcluster 2, be referred to as HIV-1 sub-subtype A3.

* Corresponding author. Mailing address: Department of Immunology and Infectious Diseases, Harvard School of Public Health, 651 Huntington Ave., Boston, MA 02115. Phone: (617) 432-1267. Fax: (617) 432-3575. E-mail: pkanki{at}hsph.harvard.edu.

Journal of Virology, November 2004, p. 12438-12445, Vol. 78, No. 22
0022-538X/04/$08.00+0     DOI: 10.1128/JVI.78.22.12438-12445.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Gifford, R. J., de Oliveira, T., Rambaut, A., Pybus, O. G., Dunn, D., Vandamme, A.-M., Kellam, P., Pillay, D., on Behalf of the UK Collaborative Group on HIV Dru, (2007). Phylogenetic Surveillance of Viral Genetic Diversity and the Evolving Molecular Epidemiology of Human Immunodeficiency Virus Type 1. J. Virol. 81: 13050-13056 [Abstract] [Full Text]  
  • Meloni, S. T., Sankale, J.-L., Hamel, D. J., Eisen, G., Gueye-Ndiaye, A., Mboup, S., Kanki, P. J. (2004). Molecular Epidemiology of Human Immunodeficiency Virus Type 1 Sub-Subtype A3 in Senegal from 1988 to 2001. J. Virol. 78: 12455-12461 [Abstract] [Full Text]  


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