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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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    as
    1. Sydney R. Stein & Sabrina C. Ramelli & Alison Grazioli & Joon-Yong Chung & Manmeet Singh & Claude Kwe Yinda & Clayton W. Winkler & Junfeng Sun & James M. Dickey & Kris Ylaya & Sung Hee Ko & Andrew P. , 2022. "SARS-CoV-2 infection and persistence in the human body and brain at autopsy," Nature, Nature, vol. 612(7941), pages 758-763, December.
    2. Ana S. Gonzalez-Reiche & Hala Alshammary & Sarah Schaefer & Gopi Patel & Jose Polanco & Juan Manuel Carreño & Angela A. Amoako & Aria Rooker & Christian Cognigni & Daniel Floda & Adriana Guchte & Zain, 2023. "Sequential intrahost evolution and onward transmission of SARS-CoV-2 variants," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    3. Mitchell D. Ramuta & Christina M. Newman & Savannah F. Brakefield & Miranda R. Stauss & Roger W. Wiseman & Amanda Kita-Yarbro & Eli J. O’Connor & Neeti Dahal & Ailam Lim & Keith P. Poulsen & Nasia Saf, 2022. "SARS-CoV-2 and other respiratory pathogens are detected in continuous air samples from congregate settings," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    4. Elham Khatamzas & Markus H. Antwerpen & Alexandra Rehn & Alexander Graf & Johannes Christian Hellmuth & Alexandra Hollaus & Anne-Wiebe Mohr & Erik Gaitzsch & Tobias Weiglein & Enrico Georgi & Clemens , 2022. "Accumulation of mutations in antibody and CD8 T cell epitopes in a B cell depleted lymphoma patient with chronic SARS-CoV-2 infection," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    5. Steven A. Kemp & Dami A. Collier & Rawlings P. Datir & Isabella A. T. M. Ferreira & Salma Gayed & Aminu Jahun & Myra Hosmillo & Chloe Rees-Spear & Petra Mlcochova & Ines Ushiro Lumb & David J. Roberts, 2021. "SARS-CoV-2 evolution during treatment of chronic infection," Nature, Nature, vol. 592(7853), pages 277-282, April.
    6. Smruthi Karthikeyan & Joshua I. Levy & Peter Hoff & Greg Humphrey & Amanda Birmingham & Kristen Jepsen & Sawyer Farmer & Helena M. Tubb & Tommy Valles & Caitlin E. Tribelhorn & Rebecca Tsai & Stefan A, 2022. "Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission," Nature, Nature, vol. 609(7925), pages 101-108, September.
    7. Farina Karim & Catherine Riou & Mallory Bernstein & Zesuliwe Jule & Gila Lustig & Strauss Graan & Roanne S. Keeton & Janine-Lee Upton & Yashica Ganga & Khadija Khan & Kajal Reedoy & Matilda Mazibuko &, 2024. "Clearance of persistent SARS-CoV-2 associates with increased neutralizing antibodies in advanced HIV disease post-ART initiation," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    8. Xiaobo Lei & Xiaojing Dong & Ruiyi Ma & Wenjing Wang & Xia Xiao & Zhongqin Tian & Conghui Wang & Ying Wang & Li Li & Lili Ren & Fei Guo & Zhendong Zhao & Zhuo Zhou & Zichun Xiang & Jianwei Wang, 2020. "Activation and evasion of type I interferon responses by SARS-CoV-2," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    9. Sebastian Weigang & Jonas Fuchs & Gert Zimmer & Daniel Schnepf & Lisa Kern & Julius Beer & Hendrik Luxenburger & Jakob Ankerhold & Valeria Falcone & Janine Kemming & Maike Hofmann & Robert Thimme & Ch, 2021. "Within-host evolution of SARS-CoV-2 in an immunosuppressed COVID-19 patient as a source of immune escape variants," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    10. Metin Balaban & Niema Moshiri & Uyen Mai & Xingfan Jia & Siavash Mirarab, 2019. "TreeCluster: Clustering biological sequences using phylogenetic trees," PLOS ONE, Public Library of Science, vol. 14(8), pages 1-20, August.
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