4.7 Article

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

Journal

SCIENTIFIC REPORTS
Volume 10, Issue 1, Pages -

Publisher

NATURE PUBLISHING GROUP
DOI: 10.1038/s41598-020-63731-z

Keywords

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Funding

  1. International AIDS Vaccine Initiative (IAVI)
  2. Sub-Saharan African Network for TB/HIV Research Excellence (SANTHE), a DELTAS Africa Initiative [DEL-15-006]
  3. African Academy of Sciences (AAS)'s Alliance for Accelerating Excellence in Science in Africa (AESA)
  4. New Partnership for Africa's Development Planning and Coordinating Agency (NEPAD Agency)
  5. Wellcome Trust [107752/Z/15/Z]
  6. UK government
  7. Swedish Research Council [2016-01417]
  8. Swedish Society for Medical Research [SA-2016]
  9. Lund University

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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.

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