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AIDS Res Hum Retroviruses. 2019 Feb;35(2):129-138. doi: 10.1089/AID.2018.0202. Epub 2019 Jan 7.

Moderate-to-High Levels of Pretreatment HIV Drug Resistance in KwaZulu-Natal Province, South Africa.

Author information

1 KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
2 Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
3 Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa.
4 Department of Medicine, Stanford University, Stanford, California.
5 Department of Medicine, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe.
6 Epicentre AIDS Risk Management (Pty) Limited, Paarl, Cape Town, South Africa.
7 Centers for Disease Control and Prevention (CDC), Pretoria, South Africa.
8 Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), Johannesburg, South Africa.
9 Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
10 Africa Health Research Institute, KwaZulu-Natal, South Africa.
11 Division of Infection and Immunity, University College London, London, United Kingdom.


There is evidence of increasing levels of pretreatment 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. Sanger sequencing was performed on samples obtained from a longitudinal HIV surveillance program (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 antiretroviral therapy (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. A total of 1,845 sequences were analyzed (611 study A; 1,234 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. 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.


HIV; South Africa; antiretroviral therapy; molecular epidemiology; pretreatment drug resistance; surveillance

[Available on 2020-02-01]

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