HIV transmission dynamics and population-wide drug resistance in rural South Africa

Steven A. Kemp, Kimia Kamelian, Diego F. Cuadros, Mark T. K. Cheng, Elphas Okango, Willem Hanekom, Thumbi Ndung’u, Deenan Pillay, David Bonsall, Emily B. Wong, Frank Tanser, Mark J. Siedner and Ravindra K. Gupta ()
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Steven A. Kemp: University of Cambridge
Kimia Kamelian: University of Cambridge
Diego F. Cuadros: University of Cincinnati
Mark T. K. Cheng: University of Cambridge
Elphas Okango: KwaZulu-Natal
Willem Hanekom: KwaZulu-Natal
Thumbi Ndung’u: KwaZulu-Natal
Deenan Pillay: University College London
David Bonsall: University of Oxford
Emily B. Wong: KwaZulu-Natal
Frank Tanser: University of Stellenbosch
Mark J. Siedner: KwaZulu-Natal
Ravindra K. Gupta: University of Cambridge

Nature Communications, 2024, vol. 15, issue 1, 1-13

Abstract: Abstract Despite expanded antiretroviral therapy (ART) in South Africa, HIV-1 transmission persists. Integrase strand transfer inhibitors (INSTI) and long-acting injectables offer potential for superior viral suppression, but pre-existing drug resistance could threaten their effectiveness. In a community-based study in rural KwaZulu-Natal, prior to widespread INSTI usage, we enroled 18,025 individuals to characterise HIV-1 drug resistance and transmission networks to inform public health strategies. HIV testing and reflex viral load quantification were performed, with deep sequencing (20% variant threshold) used to detect resistance mutations. Phylogenetic and geospatial analyses characterised transmission clusters. One-third of participants were HIV-positive, with 21.7% having detectable viral loads; 62.1% of those with detectable viral loads were ART-naïve. Resistance to older reverse transcriptase (RT)-targeting drugs was found, but INSTI resistance remained low (

Date: 2024
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DOI: 10.1038/s41467-024-47254-z

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