The Genetic Diversity and Drug Resistance Patterns of HIV-1 Pol Gene in East Africa.

Abstract

Human immunodeficiency virus-1 (HIV-1) is among the most genetically diverse pathogens due to expeditious molecular evolution. The rapid change in HIV genomes intricates HIV transmission and progression and attributes HIV resistance to antiretroviral therapy (ART). In East Africa, as in other parts of the globe, HIV-1 occurs in various subtypes, circulating recombinant form (CRF) and unique recombinant forms, with subtype A1 being the most predominant. Surveillance of HIV-1 molecular diversity and drug resistance mutations (DRMs) is a linchpin for monitoring viral evolution and treatment efficiency. However, consolidated reports on the same are limited, and therefore, the pursuit of meta-analysis was sought to analyze genetic diversity and drug resistance patterns of HIV-1 pol gene and their geographical distributions in four East African countries (Kenya, Uganda, Tanzania, and Ethiopia). We retrieved 7614 HIV-1 pol gene sequences, deposited between 2015 and 2025 from the Los Alamos HIV databases. The predominant HIV-1 subtypes were A1 (40.2%), C (21.5%), and D (17.7%), with geographical variability. A notable frequency of inter-subtype recombinant was observed with recombinants A1D (9.5%) and A1C (2.94%) being prevalent. Few CRFs (> 0.1%) were identified. DRM were present in 42.8% of the sequences, with the majority associated with NNRTIs (36.5%) and NRTIs (25.5%). The most frequently associated mutations were K103N and M184V. Although resistance to INSTI (3.7%) remained minimal, its presence warrants continued monitoring. A significant association between HIV-1 subtypes and DRM prevalence was observed (χ ² = 102.43, p < 0.0001), with subtypes showing varied resistance burdens. These findings underscore the variability in HIV-1 genetic diversity across studied East African countries, highlighting the need for region-specific interventions, to optimize HIV-1 control in this region.