HIV phylogenetic clusters point to unmet hiv prevention, testing and treatment needs among men who have sex with men in kenya

François Cholette; Lisa Lazarus; Pascal Macharia; Jeffrey Walimbwa; Samuel Kuria; Parinita Bhattacharjee; Helgar Musyoki; Mary Mugambi; Martin K Ongaro; Kennedy Olango; Janet Musimbi; Faran Emmanuel; Shajy Isac; Michael Pickles; Marissa L Becker; Sharmistha Mishra; Lyle R McKinnon; James Blanchard; John Ho; Omari Henry; Rissa Fabia; Paul Sandstrom; Robert Lorway; Souradet Y Shaw

doi:10.1186/s12879-024-10052-5

HIV phylogenetic clusters point to unmet hiv prevention, testing and treatment needs among men who have sex with men in kenya

BMC Infect Dis. 2024 Nov 20;24(1):1323. doi: 10.1186/s12879-024-10052-5.

Authors

François Cholette^{1

2}, Lisa Lazarus³, Pascal Macharia⁴, Jeffrey Walimbwa⁵, Samuel Kuria⁶, Parinita Bhattacharjee^{3

7}, Helgar Musyoki⁸, Mary Mugambi⁸, Martin K Ongaro⁹, Kennedy Olango¹⁰, Janet Musimbi⁷, Faran Emmanuel³, Shajy Isac^{3

11}, Michael Pickles¹², Marissa L Becker³, Sharmistha Mishra^{13

14

15

16}, Lyle R McKinnon^{17

18

19}, James Blanchard³, John Ho²⁰, Omari Henry²⁰, Rissa Fabia²⁰, Paul Sandstrom^{20

17}, Robert Lorway³, Souradet Y Shaw³

Affiliations

¹ National Sexually Transmitted and Blood Borne Infection Laboratory, National Microbiology Laboratory at J.C. Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada. cholettf@myumanitoba.ca.
² Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada. cholettf@myumanitoba.ca.
³ Institute for Global Public Health, University of Manitoba, Winnipeg, Canada.
⁴ Health Options for Young Men On HIV/AIDS and STIs, Nairobi, Kenya.
⁵ G10 Research Advisory Committee, Nairobi, Kenya.
⁶ Mamboleo Peer Empowerment Group, Kiambu, Kenya.
⁷ Partners for Health and Development in Africa, Nairobi, Kenya.
⁸ National AIDS and STI Control Programme, Ministry of Health, Nairobi, Kenya.
⁹ HIV and AIDS People's Alliance of Kenya, Mombasa, Kenya.
¹⁰ Men Against AIDS Youth Group, Kisumu, Kenya.
¹¹ India Health Action Trust, New Delhi, India.
¹² Medical Research Council Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
¹³ MAP Centre for Urban Health Solutions, St. Michael's Hospital, Toronto, Canada.
¹⁴ Department of Medicine, University of Toronto, Toronto, Canada.
¹⁵ Institute of Medical Sciences, University of Toronto, Toronto, Canada.
¹⁶ Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Canada.
¹⁷ Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada.
¹⁸ Centre for the AIDS Programme of Research in South Africa, Durban, South Africa.
¹⁹ Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya.
²⁰ National Sexually Transmitted and Blood Borne Infection Laboratory, National Microbiology Laboratory at J.C. Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada.

Abstract

Background: The HIV epidemic in Kenya remains a significant public health concern, particularly among gay, bisexual, and other men who have sex with men (GBMSM), who continue to bear a disproportionate burden of the epidemic. This study's objective is to describe HIV phylogenetic clusters among different subgroups of Kenyan GBMSM, including those who use physical hotspots, virtual spaces, or a combination of both to find male sexual partners.

Methods: Dried blood spots (DBS) were collected from GBMSM in Kisumu, Mombasa, and Kiambu counties, Kenya, in 2019 (baseline) and 2020 (endline). HIV pol sequencing was attempted on all seropositive DBS. HIV phylogenetic clusters were inferred using a patristic distance cutoff of ≤ 0.02 nucleotide substitutions per site. We used descriptive statistics to analyze sociodemographic characteristics and risk behaviors stratified by clustering status.

Results: Of the 2,450 participants (baseline and endline), 453 (18.5%) were living with HIV. Only a small proportion of seropositive DBS specimens were successfully sequenced (n = 36/453; 7.9%), likely due to most study participants being virally suppressed (87.4%). Among these sequences, 13 (36.1%) formed eight distinct clusters comprised of seven dyads and one triad. The clusters mainly consisted of GBMSM seeking partners online (n = 10/13; 76.9%) and who tested less frequently than recommended by Kenyan guidelines (n = 11/13; 84.6%).

Conclusions: Our study identified HIV phylogenetic clusters among Kenyan GBMSM who predominantly seek sexual partners online and test infrequently. These findings highlight potential unmet HIV prevention, testing, and treatment needs within this population. Furthermore, these results underscore the importance of tailoring HIV programs to address the diverse needs of GBMSM in Kenya across different venues, including both physical hotspots and online platforms, to ensure comprehensive prevention and care strategies.

Keywords: HIV; Kenya; Molecular epidemiology; Phylogenetic clustering; Sequence analysis; Sexual and gender minorities.

MeSH terms

Adolescent
Adult
HIV Infections* / epidemiology
HIV Infections* / prevention & control
HIV Infections* / virology
Homosexuality, Male* / statistics & numerical data
Humans
Kenya / epidemiology
Male
Middle Aged
Phylogeny*
Risk-Taking
Sexual Partners
Sexual and Gender Minorities
Young Adult