HIV-1 subtype diversity, transmission networks and transmitted drug resistance amongst acute and early infected MSM populations from Coastal Kenya

• Published in: PloS one Vol. 13; no. 12; p. e0206177
• Main Authors: Hassan, Amin S, Esbjörnsson, Joakim, Wahome, Elizabeth, Thiong'o, Alexander, Makau, George N, Price, Mathew A, Sanders, Eduard J
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 18.12.2018; Public Library of Science (PLoS)
• Subjects: Acquired immune deficiency syndrome; Adolescent; Adult; AIDS; Anti-Retroviral Agents - administration & dosage; Biology and Life Sciences; Clinical Medicine; Clusters; Coastal environments; Computer and Information Sciences; Disease transmission; Drug resistance; Drug Resistance, Viral - genetics; Epidemics; Epidemiology; Folkhälsovetenskap, global hälsa, socialmedicin och epidemiologi; Gays & lesbians; Health aspects; Health Sciences; HIV; HIV infections; HIV Infections - genetics; HIV Infections - prevention & control; HIV Infections - transmission; HIV-1 - genetics; HIV-1 - pathogenicity; Human immunodeficiency virus; Humans; Hälsovetenskap; Infectious Medicine; Infektionsmedicin; Kenya; Klinisk medicin; Medical and Health Sciences; Medicin och hälsovetenskap; Medicine and Health Sciences; Men; Mens health; MSM (Men who have sex with men); Mutation; Nucleosides; People and Places; Phylogenetics; Phylogeny; Prevention; Public Health, Global Health, Social Medicine and Epidemiology; Research and Analysis Methods; RNA-directed DNA polymerase; Sex; Sexual and Gender Minorities; Sexually transmitted diseases; STD; Kenya; New York; San Francisco California; Sweden; United Kingdom > UK; United States > US; Africa; England; California
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0206177

HIV-1 molecular epidemiology amongst men who have sex with men (MSM) in sub-Saharan Africa remains not well characterized. We aimed to determine HIV-1 subtype distribution, transmission clusters and transmitted drug resistance (TDR) in acute and early infected MSM from Coastal Kenya. Analysis of HIV-1 partial pol sequences from MSM recruited 2005-2017 and sampled within six months of the estimated date of infection. Volunteers were classified as men who have sex with men exclusively (MSME) or with both men and women (MSMW). HIV-1 subtype and transmission clusters were determined by maximum-likelihood phylogenetics. TDR mutations were determined using the Stanford HIV drug resistance database. Of the 97 volunteers, majority (69%) were MSMW; 74%, 16%, 9% and 1% had HIV-1 subtypes A1, D, C or G, respectively. Overall, 65% formed transmission clusters, with substantial mixing between MSME and MSMW. Majority of volunteer sequences were either not linked to any reference sequence (56%) or clustered exclusively with sequences of Kenyan origin (19%). Eight (8% [95% CI: 4-16]) had at least one TDR mutation against nucleoside (n = 2 [2%]) and/or non-nucleoside (n = 7 [7%]) reverse transcriptase inhibitors. The most prevalent TDR mutation was K103N (n = 5), with sequences forming transmission clusters of two and three taxa each. There were no significant differences in HIV-1 subtype distribution and TDR between MSME and MSMW. This HIV-1 MSM epidemic was predominantly sub-subtype A1, of Kenyan origin, with many transmission clusters and having intermediate level of TDR. Targeted HIV-1 prevention, early identification and care interventions are warranted to break the transmission cycle amongst MSM from Coastal Kenya.