EPIDEMIOLOGY Molecular Characterization of HIV Type 1 Among HIV-Infected Respondents in a Cohort Being Prepared for HIV Phase III Vaccine Clinical Trials, Western Kenya Micah Oyaro, 1,2 John Mbithi, 1 Fred Oyugi, 2 Annette Laten, 3 Omu Anzala, 2 and Susan Engelbrecht 3 Abstract Kenya is one of the sub-Saharan African countries affected by HIV-1 infection and AIDS. We investigated HIV-1 genetic diversity in 130 individuals from Busia, Bungoma, and Kakamega in western Kenya as part of an HIV-1 vaccine feasibility study in preparation for Phase III efficacy clinical trials. After RNA extraction the partial gag (484 bp) and env (1297 bp) regions were amplified and directly sequenced. Phylogenetic analysis was done using MEGA version 4 and recombinants were identified using the jpHMM tool and phylogenetic analysis. HIV-1 sequences were amplified from 122 of the 130 samples, 118 (90.8%) from the gag region and 78 (60 %) from the env region and 74 samples (56.9%) from both the gag and env regions. Of these sequenced on both regions, 51.4% were subtype A, 9.4% subtype D, 1.4% subtype C, 4.1% subtype G, and 33.7% were discordant and thus possible recombinants, including A1/C, A1/D, A1/A2, and A2/C. The jpHMM tool indicated a further two samples with CD and BD breakpoints within the env gene and one within the gag gene (A1C). An additional sample had an A1D breakpoint in the gag gene, but the envelope was not amplified. HIV-1 subtype diversity in western Kenya should be considered in vaccines designed for clinical trials in this region and this genetic diversity should be continuously monitored. Introduction S ub-Saharan Africa remains the region most affected by the HIV/AIDS pandemic, but in several regions, includ- ing Kenya, the HIV-1 prevalence rate is stable or declining. 1 In spite of this decline, the adult HIV-1 prevalence rate in Kenya is 7.8% with 1.4 million people living with the virus. 2 One of the major features of HIV-1 is the extreme genetic variability that may be reflected in differences in biological characteris- tics that determine transmissibility, pathogenesis, and im- munogenicity. Therefore the genetic variation of HIV-1 and its evolution in time have important implications for the control of the pandemic. Analysis of the HIV-1 env genes of virus strains from dif- ferent geographic regions reveals that HIV-1 can be divided into three main groups: M (major), O (outlier), and N (non-M, non-O). HIV-1 group M has been further subdivided into genetically equidistant clusters of HIV-1 env genes, compris- ing subtypes A–D, F–H, J, K, and at least 45 circulating re- combinant forms (CRFs) and numerous unique recombinant forms (URFs), http://www.hiv.lanl.gov/content/sequence/ HIV/CRFs/CRFs.html. Recently a new human immunode- ficiency virus, closely related to gorilla simian immunodefi- ciency virus (SIVgor), has been described and a fourth group, designated P, was proposed. 3 Previous molecular epidemiological studies done in Kenya mostly used samples from Nairobi. 4–9 A few other studies also investigated southern, 10 northern, 11 and western Kenya, 12 as well as the coastal region. 13,14 All of these studies indicated that HIV-1 subtype A is the most common subtype in Kenya, but that subtypes C, D, G, and recombinant forms were also detected. 4–14 The complexity of HIV-1 diversity creates major challenges for vaccine design and development strategies. More than one HIV-1 vaccine candidate based on HIV-1 subtype A has been evaluated in Kenya during Phase I and II clinical trials. 15 The western Kenya region, which is targeted for HIV-1 vaccine clinical trials, is close to Uganda, a neighboring country that is dominated by HIV-1 subtypes A and D in almost equal pro- portions. 16 Our aim was thus to investigate HIV-1 genetic diversity by amplification and sequencing of partial gag and env genes from 130 HIV-1-positive individuals from different 1 Kenyatta University, Department of Biological Sciences, Nairobi, Kenya. 2 Kenya Aids Vaccine Initiative (KAVI), Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya. 3 Division of Medical Virology, National Health Laboratory Services (NHLS) and University of Stellenbosch, Tygerberg, South Africa. AIDS RESEARCH AND HUMAN RETROVIRUSES Volume 27, Number 3, 2011 ª Mary Ann Liebert, Inc. DOI: 10.1089/aid.2010.0061 257 Downloaded by Kenyatta University Kenya from www.liebertpub.com at 07/25/18. For personal use only.