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

Author

Listed:
  • Steven A. Kemp

    (University of Cambridge
    University of Oxford)

  • 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
    University College London)

  • Thumbi Ndung’u

    (KwaZulu-Natal
    University College London)

  • 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
    Massachusetts General Hospital
    University of KwaZulu-Natal
    Harvard University)

  • Ravindra K. Gupta

    (University of Cambridge
    KwaZulu-Natal)

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 (

Suggested Citation

  • 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, 2024. "HIV transmission dynamics and population-wide drug resistance in rural South Africa," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-47254-z
    DOI: 10.1038/s41467-024-47254-z
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    References listed on IDEAS

    as
    1. Mark J. Siedner & Michelle A. Moorhouse & Bryony Simmons & Tulio Oliveira & Richard Lessells & Jennifer Giandhari & Stephen A. Kemp & Benjamin Chimukangara & Godspower Akpomiemie & Celicia M. Serenata, 2020. "Reduced efficacy of HIV-1 integrase inhibitors in patients with drug resistance mutations in reverse transcriptase," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    2. Kathy Baisley & Natsayi Chimbindi & Nondumiso Mthiyane & Sian Floyd & Nuala McGrath & Deenan Pillay & Janet Seeley & Thembelihle Zuma & Jaco Dreyer & Dickman Gareta & Theresa Smit & Tinofa Mutevedzi &, 2018. "High HIV incidence and low uptake of HIV prevention services: The context of risk for young male adults prior to DREAMS in rural KwaZulu-Natal, South Africa," PLOS ONE, Public Library of Science, vol. 13(12), pages 1-17, December.
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