HIV-1 Transmission Patterns Within and Between Risk Groups in Coastal Kenya

George M. Nduva, Amin S. Hassan, Jamirah Nazziwa, Susan M. Graham, Joakim Esbjörnsson, Eduard J. Sanders

Research output: Contribution to journalArticlepeer-review


HIV-1 transmission patterns within and between populations at different risk of HIV-1 acquisition in Kenya are not well understood. We investigated HIV-1 transmission networks in men who have sex with men (MSM), injecting drug users (IDU), female sex workers (FSW) and heterosexuals (HET) in coastal Kenya. We used maximum-likelihood and Bayesian phylogenetics to analyse new (N = 163) and previously published (N = 495) HIV-1 polymerase sequences collected during 2005–2019. Of the 658 sequences, 131 (20%) were from MSM, 58 (9%) IDU, 109 (17%) FSW, and 360 (55%) HET. Overall, 206 (31%) sequences formed 61 clusters. Most clusters (85%) consisted of sequences from the same risk group, suggesting frequent within-group transmission. The remaining clusters were mixed between HET/MSM (7%), HET/FSW (5%), and MSM/FSW (3%) sequences. One large IDU-exclusive cluster was found, indicating an independent sub-epidemic among this group. Phylodynamic analysis of this cluster revealed a steady increase in HIV-1 infections among IDU since the estimated origin of the cluster in 1987. Our results suggest mixing between high-risk groups and heterosexual populations and could be relevant for the development of targeted HIV-1 prevention programmes in coastal Kenya.

Original languageEnglish
Article number6775
JournalScientific Reports
Issue number1
Publication statusPublished - 2020

Subject classification (UKÄ)

  • Infectious Medicine
  • Public Health, Global Health, Social Medicine and Epidemiology


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