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

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, Limakatso Lebina, Josie Everatt, Stefano Tempia, Tatsiana Bylund, Reda Rawi, Peter D. Kwong, Nicole Wolter, Anne Gottberg, Cheryl Cohen and Eli A. Boritz ()
Additional contact information
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
Susan Meiring: a division of the National Health Laboratory Service
Jackie Kleynhans: a division of the National Health Laboratory Service
Daniel Amoako: a division of the National Health Laboratory Service
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
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
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
Anne Gottberg: a division of the National Health Laboratory Service
Cheryl Cohen: a division of the National Health Laboratory Service
Eli A. Boritz: National Institutes of Health

Nature Communications, 2024, vol. 15, issue 1, 1-14

Abstract: 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

Date: 2024
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DOI: 10.1038/s41467-024-51539-8

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