HIV drug resistance, phylogenetic analysis, and superinfection among men who have sex with men and transgender women in sub-Saharan Africa: HPTN 075

• Published in: Clinical infectious diseases 2020-08
• Main Authors: Sivay, Mariya V, Palumbo, Philip J, Zhang, Yinfeng, Cummings, Vanessa, Guo, Xu, Hamilton, Erica L, McKinstry, Laura, Ogendo, Arthur, Kayange, Noel, Panchia, Ravindre, Dominguez, Karen, Chen, Ying Q, Sandfort, Theodorus G M, Eshleman, Susan H
• Format: Article
• Language: English
• ISSN: 1537-6591

The HIV Prevention Trials Network (HPTN) 075 study evaluated the feasibility of enrolling and retaining men who have sex with men (MSM) and transgender women (TWG) from Kenya, Malawi, and South Africa. Twenty-one participants acquired HIV during study follow-up (seroconverters). We analyzed HIV subtype diversity, drug resistance, transmission dynamics, and HIV superinfection among MSM and TGW enrolled in HPTN 075. HIV genotyping and drug resistance testing was performed for HIV-positive participants who had viral loads >400 copies/mL at screening (prevalent cases, N=124) and seroconverters (N=21). HIV pol clusters were identified using Cluster Picker. Superinfection was assessed by longitudinal analysis of env and pol sequences generated by next-generation sequencing. HIV genotyping was successful for 123/124 prevalent cases and all 21 seroconverters. The major HIV subtypes were A1 (Kenya) and C (Malawi and South Africa). Major drug resistance mutations were detected in samples from 21 (14.6%) of 144 participants; the most frequent mutations were K103N and M184V/I. Phylogenetic analysis identified 11 clusters (2-6 individuals). Clusters included seroconverters only (n=1), prevalent cases and seroconverters (n=4), and prevalent cases only (n=6). Superinfection was identified in one prevalent case and two seroconverters. The annual incidence of superinfection was higher among seroconverters than prevalent cases and was higher than the rate of primary HIV infection in the cohort. This report provides important insights into HIV genetic diversity, drug resistance, and superinfection among MSM and TWG in sub-Saharan Africa. These findings may help to inform future HIV prevention interventions in these high-risk groups.