Molecular epidemiology of HIV in Ghana; Subtype diversity, drug resistance and coreceptor usage

HIV remains a global challenge, with the highest burden of infection occurring in Sub-Saharan Africa, and the highest HIV genetic diversity occurring in West/Central Africa due to the pandemic's origins in this region. This genetic diversity however remains understudied. Here, we combine traditional (Sanger) and next-generation (Illumina) sequencing to characterize HIV subtype diversity from full-genome viral sequence data, HIV drug resistance and coreceptor usage in a cohort of 103 predominantly HIV treatment-naive individuals living with HIV in Ghana. Our results reveal the circulating HIV recombinant form CRF02_AG as the dominant (>50%) subtype, with pure subtypes and unique recombinants present as well. We identify 16 persons as having low-high level resistance to one or more antiretroviral drugs, and CCR5 as the main HIV coreceptor in use. Our observations underscore the extensive HIV genetic diversity in Ghana, highlighting the dominance of CRF02_AG and the ongoing creation of new and complex recombinant forms. These findings improve our understanding of HIV molecular epidemiology and pre-treatment drug resistance mutation prevalence in Ghana.