HIV drug resistance among key populations in Nigeria: Insights from the 2020 integrated biological and behavioural surveillance survey

Objectives: HIV drug resistance mutations (DRMs) undermine the effectiveness of antiretroviral therapy (ART) and can lead to treatment failure. This study aimed to characterize HIV drug resistance among key populations in Nigeria. Design: A cross-sectional integrated biological and behavioural surveillance survey was conducted across six Nigerian geopolitical zones among female sex workers, men who have sex with men, people who inject drugs (PWID), and transgender individuals (August to December 2020). Methods: Dried blood spot specimens were collected from 2,309 participants, of whom 719 (31.1%) were HIV viremic (>1,000 copies/mL). Partial HIV pol genes were sequenced using an in-house genotyping assay. DRMs were identified from MiSeq reads using HyDRA Web and interpreted with Stanford HIVdb. Pearson chi-square tests assessed associations between sociodemographic factors and DRMs. Results: Among 414 HIV genotyped specimens, 16.7% contained at least one DRM. Common DRMs included K103N, M41L, and M184V, with 9.2% showing high-level resistance to efavirenz and nevirapine. DRM prevalence was highest among PWID (21.6%) and residents of the North Central zone (25.8%). Age was significantly associated with DRMs ( p <0.001). Notably, 58.7% of participants were unaware of their HIV-positive status and had never received ART. Conclusion: The presence of DRMs among ART-naïve participants suggests transmitted drug resistance. The association between older age and DRMs may reflect sub-optimal adherence, prior regimen exposure, or longer treatment. High-level resistance to efavirenz supports transitioning to dolutegravir-based first-line regimens and highlights the importance of supporting key populations in accessing and adhering to ART to prevent the spread of drug-resistant HIV.