Journal
AIDS RESEARCH AND HUMAN RETROVIRUSES
Volume 33, Issue 5, Pages 500-510Publisher
MARY ANN LIEBERT, INC
DOI: 10.1089/aid.2016.0321
Keywords
drug users; HIV-1 subtypes; intersubtype recombinants; Kenya
Categories
Funding
- South African Research Chairs Initiative
- Victor Daitz Foundation
- International Early Career Scientist award from the Howard Hughes Medical Institute
- DELTAS Africa Initiative [107752/Z/15/Z]
- African Academy of Sciences (AAS)'s Alliance for Accelerating Excellence in Science in Africa (AESA)
- New Partnership for Africa's Development Planning and Coordinating Agency (NEPAD Agency)
- Wellcome Trust [107752/Z/15/Z]
- UK Government
- South African Medical Research Council (MRC)
- IAS/NIDA
- Wellcome Trust [107752/Z/15/Z] Funding Source: Wellcome Trust
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Drug users are increasingly recognized as a key population driving human immunodeficiency virus (HIV) spread in sub-Saharan Africa. To determine HIV-1 subtypes circulating in this population group and explore possible geographic differences, we analyzed HIV-1 sequences among drug users from Nairobi, Mombasa, and Kisumu in Kenya. Wesequenced gag and env from 55 drug users. Subtype analysis from 220 gag clonal sequences from 54 of 55 participants (median = 4/participant) showed that 44.4% were A, 16.7% were C, 3.7% were D, and 35.2% were intersubtype recombinants. Of 156 env clonal sequences from 48 of 55 subjects (median = 3/participant), 45.8% were subtype A, 14.6% were C, 6.3% were D, and 33.3% were recombinants. Comparative analysis of both genes showed that 30 (63.8%) participants had concordant subtypes, while 17 (36.2%) were discordant. We identified one genetically linked transmission pair and two cases of dual infection. These data are indicative of extensive HIV-1 intersubtype recombination in Kenya and suggest decline in subtype D prevalence.
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