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274 Forty-One Virtually Full-Length HIV-1 Sequences from Kenya Reveal an Epidemic of Subtype A and Various A-Containing Recombinants
W. Dowling*1, C. Mason2, U. Alam2, K. M. Wasunna2, L. Elson2, B. Kim3, D. Birx1, M. Robb1, F. McCutchan3, and J. K. Carr3
1Walter Reed Army Inst. of Res., Washington, DC, USA; 2US Army Res. Unit, Nairobi, Kenya; and 3Henry M. Jackson Fndn., Rockville, MD, USA
Background: Previous studies of HIV-1 genetic diversity in Kenya reported that at least 70% of strains were subtype A, 15(30% were subtype D and a small percentage were subtypes C, G, or recombinant. These data were, however, usually based on analysis of small regions of the genome. In this study, HIV-1 subtypes and recombinants were evaluated using full genome sequencing and analysis.
Methods: HIV-1-positive blood units were collected between 1999 and 2000 from 6 hospitals across Kenya. PBMC were isolated and DNA extracted. Near full-length genomes were amplified by nested PCR and sequenced. The new sequences were aligned with reference strains and phylogenetic trees were generated to determine subtype. Recombinants were identified and confirmed by distance scanning and bootscanning.
Results: Forty-one nearly full-length genomes were amplified, sequenced, and analyzed. Twenty-four were pure subtypes (58.5%) and 17 were recombinants (41.5%). Of the pure subtypes, 22 were subtype A, 1 was subtype C, and 1 was subtype D. Most recombinants consisted of subtype A and at least 1 other subtype, including A2, a recently identified sub-subtype of A. Two A2/D recombinants had virtually identical breakpoints and may represent a circulating recombinant form (CRF).
Conclusions: About half of the HIV-1 strains analyzed were subtype A and close to half were A-containing recombinants, unlike previous studies in which higher percentages of subtypes A and D and few recombinants were reported. Those studies, however, only analyzed fragments of the genome and therefore many recombinants were likely not identified. Importantly, the 15(30% subtype D strains previously reported may have been D-containing recombinants. Vaccine candidates tested in Kenya should be based on subtype A strains, but evaluation should be capable of distinguishing pure A strains from recombinants.
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