HIV-1 drug resistance and genetic diversity in people with HIV-1 in Cape Verde

Abstract

Objectives: To characterize the genetic diversity and drug resistance profiles of people with HIV-1 failing ART in Cape Verde (CV). Design: Cross- sectional study conducted between January 2019 and December 2021 in 24 health centres on the islands of Santiago and São Vicente. Methods: The HIV-1 pol gene was sequenced in individuals with a detectable viral load (VL). HIV-1 genetic diversity was determined by phylogenetic analysis. Drug resistance mutation patterns and resistance phenotypes were estimated using the Stanford algorithm. Result: VL was detected in 73 of 252 (29%) enrolled participants and sequencing data were produced for 58 (79%) participants. CRF02_AG strains predominated (46.5%), followed by subtype G (22.4%). Most patients (80%) had mutations conferring resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs) (67%), nucleoside reverse transcriptase inhibitors (55%), integrase inhibitors (10%) and/or protease inhibitors (7%) used in CV, a significant increase compared to a study conducted in 2010–2011. The most common mutations were M184 V/I (43%), K103N/S (36%) and G190A/S (19%). NNRTI resistance was associated with younger age and exposure to two or more drug regimens. Conclusions: The HIV-1 epidemic in Cape Verde is mainly driven by CRF02_AG and subtype G. Resistance to NNRTIs and/or NRTIs is highly prevalent and resistance to LPV/r and DTG is emerging. Our results support the use of DTG-based first-line ART and PI-based regimens for patients with virological failure, but emerging resistance to LPV/r and DTG is a concern. Continued monitoring of drug resistance is essential to ensure adequate health care for PLWH in Cape Verde.