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Rapid intra-host diversification and evolution of SARS-CoV-2 in advanced HIV infection

Author

Listed:
  • Sung Hee Ko

    (National Institutes of Health)

  • Pierce Radecki

    (National Institutes of Health)

  • Frida Belinky

    (National Institutes of Health)

  • Jinal N. Bhiman

    (a division of the National Health Laboratory Service
    University of the Witwatersrand)

  • Susan Meiring

    (a division of the National Health Laboratory Service)

  • Jackie Kleynhans

    (a division of the National Health Laboratory Service
    University of the Witwatersrand)

  • Daniel Amoako

    (a division of the National Health Laboratory Service
    University of Guelph)

  • Vanessa Guerra Canedo

    (National Institutes of Health)

  • Margaret Lucas

    (National Institutes of Health)

  • Dikeledi Kekana

    (a division of the National Health Laboratory Service)

  • Neil Martinson

    (University of the Witwatersrand
    Center for TB Research)

  • Limakatso Lebina

    (University of the Witwatersrand)

  • Josie Everatt

    (a division of the National Health Laboratory Service)

  • Stefano Tempia

    (a division of the National Health Laboratory Service
    University of the Witwatersrand)

  • Tatsiana Bylund

    (National Institutes of Health)

  • Reda Rawi

    (National Institutes of Health)

  • Peter D. Kwong

    (National Institutes of Health)

  • Nicole Wolter

    (a division of the National Health Laboratory Service
    University of the Witwatersrand)

  • Anne Gottberg

    (a division of the National Health Laboratory Service
    University of the Witwatersrand)

  • Cheryl Cohen

    (a division of the National Health Laboratory Service
    University of the Witwatersrand)

  • Eli A. Boritz

    (National Institutes of Health)

Abstract

Previous studies have linked the evolution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic variants to persistent infections in people with immunocompromising conditions, but the processes responsible for these observations are incompletely understood. Here we use high-throughput, single-genome amplification and sequencing (HT-SGS) to sequence SARS-CoV-2 spike genes from people with HIV (PWH, n = 22) and people without HIV (PWOH, n = 25). In PWOH and PWH with CD4 T cell counts (i.e., CD4 counts) ≥ 200 cells/μL, we find that most SARS-CoV-2 genomes sampled in each person share one spike sequence. By contrast, in people with advanced HIV infection (i.e., CD4 counts

Suggested Citation

  • Sung Hee Ko & Pierce Radecki & Frida Belinky & Jinal N. Bhiman & Susan Meiring & Jackie Kleynhans & Daniel Amoako & Vanessa Guerra Canedo & Margaret Lucas & Dikeledi Kekana & Neil Martinson & Limakats, 2024. "Rapid intra-host diversification and evolution of SARS-CoV-2 in advanced HIV infection," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-51539-8
    DOI: 10.1038/s41467-024-51539-8
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