INTRODUCTION: There is evidence of increasing levels of pre-treatment HIV drug resistance (PDR) in Southern Africa. We used data from two large population-based HIV surveillance studies to estimate prevalence of PDR in KwaZulu-Natal, the province with the highest HIV prevalence in South Africa.METHODS: Sanger sequencing was performed on samples obtained from a longitudinal HIV surveillance programme (study A, 2013-2014) and the HIV Incidence Provincial Surveillance System (study B, 2014-2015). Sequences were included for adult HIV positive participants (age =15 years for study A, age 15-49 years for study B) with no documented prior exposure to ART. Overall and drug class-specific PDR was estimated using the World Health Organization 2009 surveillance drug resistance mutation (SDRM) list and phylogenetic analysis was performed to establish evidence of drug resistance transmission linkage.RESULTS: One thousand eight hundred and forty-five (1845) sequences were analysed (611 study A; 1234 study B). An overall PDR prevalence of 9.2% (95% confidence interval (CI): 7.0-11.7) was observed for study A and 11.0% (95% CI 8.9-13.2) for study B. In study B, the prevalence of non-nucleoside reverse-transcriptase inhibitor (NNRTI) PDR exceeded 10% for sequences collected in 2014 (10.2%, 95% CI 7.5-12.9). The most prevalent SDRMs were K103NS (7.5%), M184VI (2.4%) and V106AM (1.4%). There was no evidence of large transmission chains of drug-resistant virus.CONCLUSION: High level NNRTI-PDR (>10%) suggests a need to modify the standard first-line ART regimen and to focus attention on improving the quality of HIV prevention, treatment and care.
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