Title: Complex subtype diversity of HIV-1 among drug users in major Kenyan cities
Authors: Gounder K, Oyaro M, Padayachi N, Zulu TM,de Oliveira T, Wylie J, Ndung'u T.
Journal: AIDS Res Hum Retroviruses,:10.1089/AID.2016.0321 (2017)


Drug users are increasingly recognized as a key population driving 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.

We sequenced gag and env from 55 drug users. Subtype analysis from 220 gag clonal sequences from 54/55 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 48/55 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 2 cases of dual infection. These data are indicative of extensive HIV-1 intersubtype recombination in Kenya and suggest decline in subtype D prevalence.