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This study was designed to provide information on the genetic diversity of HIV-1 and drug resistance mutations in Nigeria, as there is limited understanding of variants circulating in the country. We used an advanced next-generation sequencing platform, Primer ID, to investigate the presence of high and low abundance drug resistance mutations; characterize pre-existing INSTI mutations in ART-experienced but dolutegravir-naive individuals; detect recent HIV-1 infections and characterize subtype diversity from a cohort of people living wi