Evaluation of HIV type 1 strains in men having sex with men and in female sex workers in Mombasa, Kenya

Sodsai Tovanabutra*, Eduard J. Sanders, Susan M. Graham, Mary Mwangome, Norbert Peshu, R. Scott McClelland, Allan Muhaari, Jacqueline Crossler, Matt A. Price, Jill Gilmour, Nelson L. Michael, Francine M. McCutchan

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

28 Scopus citations


We compared HIV-1 strains in incident and prevalent infections in a cohort of men having sex with men (MSM) and female sex workers (FSW) near Mombasa, Kenya and conducted a cross-sectional study of viral isolates from a sample of HIV-1-infected MSM and FSW in Kilifi, Coast Province, Kenya. RNA extracted from plasma of 13 MSM, 9 FSW, and one heterosexual male was amplified by nested RT-PCR and the products were directly sequenced. HIV-1 strains from 21 individuals were characterized with one or more complete genome sequences, and two were sequenced in the Nef gene. The envelope quasispecies was also studied in one individual. Among MSM, eight strains were subtype A and five were recombinant. There were two epidemiologically linked pairs of sequences; one pair was subtype A and the other pair was a complex AA2CD recombinant of identical structure. Another MSM was dually infected with DG recombinant strains of related, but nonidentical, structure. MSM also harbored AC and AD recombinant strains. The FSW harbored seven subtype A strains, an AD recombinant, and an AA2D strain related to CRF16-A2D. The one heterosexual male studied had a subtype A infection. This MSM epidemic in Kenya appears to be of local origin, harboring many strains typical of the broader Kenyan epidemic. Characteristics of a close social network were identified, with extended chains of transmission, novel recombinant strains possibly generated within the network, and a relatively high proportion of recombinant and dual infections.

Original languageEnglish
Pages (from-to)123-131
Number of pages9
JournalAIDS Research and Human Retroviruses
Issue number2
StatePublished - 1 Feb 2010
Externally publishedYes


Dive into the research topics of 'Evaluation of HIV type 1 strains in men having sex with men and in female sex workers in Mombasa, Kenya'. Together they form a unique fingerprint.

Cite this