Introduction: Men who have sex with men (MSM) and transgender women (TGW) are at increased risk for acquiring HIV, but there are limited HIV incidence data for these key populations in Africa. Understanding HIV prevalence and incidence provides important context for designing HIV prevention strategies, including pre-exposure prophylaxis (PrEP) programmes. We describe HIV prevalence, awareness of HIV infection, HIV incidence and associated factors for a cohort of MSM and TGW in Cape Town and Port Elizabeth, South Africa.

Methods: From 2015 to 2016, MSM and TGW in Cape Town and Port Elizabeth were enrolled and prospectively followed for 12 months, receiving a comprehensive package of HIV prevention services. HIV testing was conducted at baseline and at follow-up visits (targeted for three, six and twelve months). All HIV-negative PrEP-eligible participants were offered PrEP enrolment during the first four months of study participation. We determined HIV prevalence among participants at baseline, and incidence by repeat screening of initially HIV-negative participants with HIV tests at three, six and twelve months.

Results: Among 292 participants enrolled, HIV prevalence was high (43%; 95% CI: 38 to 49) and awareness of HIV status was low (50%). The 167 HIV-negative participants who were followed prospectively for 144.7 person-years; nine incident HIV infections were documented. Overall annual incidence was 6.2% (CI: 2.8 to 11.8) and did not differ by city. Annual HIV incidence was significantly higher for younger (18 to 19 years) MSM and TGW (MSM: 21.8% (CI: 1.2 to 100); TGW: 31.0 (CI: 3.7, 111.2)). About half of participants started PrEP during the study; the annual incidence of HIV among 82 (49%) PrEP starters was 3.6% (CI: 0.4, 13.1) and among those who did not start PrEP was 7.8% (CI: 3.1, 16.1).

Conclusions: HIV incidence was high among MSM and TGW in the context of receiving a comprehensive package of prevention interventions and offering of PrEP. PrEP uptake was high; the observed incidence of HIV in those who started PrEP was about half the incidence of HIV in those who did not. Future implementation-oriented studies should focus on decisions to start and continue PrEP for those at highest risk, including young MSM.