Background The prevalence and impact of baseline archived HIV-1 drug resistance mutations (HDRMs) in people with HIV (PWH) switching to new regimen is not well understood. The aim of this study was to evaluate HDRMs among virologically suppressed individuals on NNRTI based ART in Botswana before they were switched to new dolutegravir (DTG) based ART.

Methods We included a total of 4524 virologically suppressed PWH (aged >18 years) on ART with viral loads <400 copies/ml who were recruited into an HIV cohort, the Botswana Combination Prevention Project, in Botswana between 2013 and 2018. The near full-length HIV-1 proviral DNA pol sequences were analysed for the presence of NRTI and NNRTI DRMs. The Stanford HIV drug resistance database was used for identification of HDRMs.

Results Among the 4524 virologically suppressed individuals, the majority (72%, 3267/4524) were female, with median age of 40 years [interquartile range (IQR): 34–48]. The overall prevalence of DRMs was 16.4% (742/4524, 95% CI: 15.3% - 17.5%). Females had a higher proportion of DRMs than males (12.1% vs. 4.3%, respectively). The prevalence of NRTI resistance was 2.9% (129/4524, 95% CI 2.4% - 3.3%), while the majority of DRMs were associated with NNRTI resistance at 15.1% (685/4524, 95% CI: 14.1% - 16.2%). The NNRTI mutation E138A which confers resistance to etravirine and rilpivirine was the most common (9.3%, 419/4524), followed by K103N (1.6%, 74/4524) which is associated with efavirenz and nevirapine resistance. The most common NRTI associated mutation was M184V (1.1%, 48/4524) followed by M184I (0.8%, 37/4524) which confer resistance to 3TC and emtricitabine.

Conclusion We report a prevalence of archived HDRMs in this cohort of 16.4%. Further research is warranted to understand the impact of the observed archived HDRMs on the efficacy of DTG based regimen.