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25 Support of HIV-1 Vaccine Development in East Africa: Sequencing of 96 Full-Genome Sequences from Uganda, Kenya, and Tanzania
M. L. Robb*1, F. E. McCutchan2, J. K. Carr2, M. Harris1, W. Dowling1, M. Hoelscher3, N. Sewankambo4, J. Phillips2, L. Elson2, M. Wassunna5, M. L. Maboko6, T. Nkulila6, and D. L. Birx1
1Walter Reed Army Inst. of Res., Washington, DC, USA; 2Henry M, Jackson Fndn., Rockville, MD, USA; 3Univ. of Munich, Germany; 4Makerere Univ., Kampala, Uganda; 5KEMRI, Nairobi, Kenya; and 6Mbeya Referral Hosp., Mbeya, Tanzania
Background: HIV-1 vaccine trials in East Africa are planned in the near future, but populations in which trials may take place have not been fully characterized for the proportions of HIV-1 subtypes and recombinants. We conducted full sequencing of HIV-1 genomes from 96 individuals from Uganda, Kenya, or Tanzania.
Methods: HIV-1-positive samples were from the general population in Rakai district, Uganda (n = 46), from blood banks across Kenya (n = 41), and from a low-risk, young adult population in Tanzania (n = 9). DNA extracted from PBMC was the template for virtually full-genome amplification by nested PCR. PCR products were directly sequenced. Sequences were aligned with reference sequences and analyzed by Neighbor-joining, bootscanning, and distance scanning. Recombinants were confirmed with subregion trees.
Results: The proportions of subtypes varied by country, with a predominance of subtype A in Kenya, subtype D in Uganda, and subtype C in Tanzania, the latter result obtained using combined data from full genomes (n = 9) and from subtype-specific probe hybridization (n = 55). Intersubtype recombinant HIV-1 comprised 31, 39, and 52% of strains in Uganda, Kenya, and Tanzania, respectively. Almost all of the recombinants were unique. The majority of strains in Uganda were either subtype D or AD recombinant. In Kenya, subtype A and AD recombinants predominated. In Tanzania, subtype C and AC recombinants were the majority.
Conclusions: Evaluation of candidate vaccines in parallel in different countries in East Africa would be a highly effective strategy to determine their relative effectiveness against subtypes A, C, and D and their recombinants. Plans for such evaluations, including careful analysis of breakthrough infections, are underway.
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