Nationwide patterns of HIV drug resistance and high viral load in Sub-Saharan African countries

Objectives To (1) assess the prevalence and patterns of HIV drug resistance (HIVDR) mutations, (2) identify correlations between different HIVDR mutations within drug classes, and (3) examine the association between resistance mutations and high HIV viral load. Methods We conducted a secondary analysis of retrospective data collected through the Population-based HIV Impact Assessment (PHIA) surveys conducted between 2015 and 2019 in 13 African countries. We included participants aged ≥15 years with available HIVDR genotyping. The primary outcomes were (1) prevalence of HIVDR mutations, categorized by drug class into non-nucleoside reverse transcriptase inhibitors (NNRTIs), Nucleoside Reverse Transcriptase Inhibitors (NRTIs), and Protease inhibitors (PIs); (2) high HIV viral load (VL), (HIV RNA ≥1000 copies/mL). Results The analysis included 2292 participants, with a median age range between 31 and 41 years. More than one-third of participants were not receiving ART. Of all participants, 1949 (85%) had high VL. Resistance to NNRTIs and NRTIs was the most prevalent in most countries, ranging from 43% to 60%, and 37% to 53%, respectively. Resistance to PI ranges from 0.2% to 5%. Multiple drug resistance mutations across all ART classes were strongly associated with high VL. Among NNRTIs, 16/39 mutations (e.g. K103N, Y181C) and 18/34 NRTI mutations (e.g. M184V, K65R) showed strong associations with high VL in ≥10 countries. For PIs, Q58E and L33F emerged as key mutations strongly associated with high VL across multiple nations. Conclusions Strengthening resistance surveillance, optimising ART regimens, and improving adherence are crucial to curb resistance and sustain HIV epidemic control.