Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections

Ke Li; Chrispin Chaguza; Julian Stamp; Yi Ting Chew; Nicholas F. G. Chen; David Ferguson; Sameer Pandya; Nick Kerantzas; Wade Schulz; Yale SARS-CoV-2 Genomic Surveillance Initiative; Anne M. Hahn; C. Brandon Ogbunugafor; Virginia E. Pitzer; Lorin Crawford; Daniel M. Weinberger; Nathan D. Grubaugh

doi:10.1371/journal.pcbi.1012469

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Open Access

Peer-reviewed

Research Article

Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections

Ke Li ,

Roles Conceptualization, Data curation, Formal analysis, Methodology, Visualization, Writing – original draft, Writing – review & editing

* E-mail: ke.li.kl662@yale.edu (KL); nathan.grubaugh@yale.edu (NDG)

Affiliations Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America, Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, United States of America

https://orcid.org/0000-0002-1252-670X

⨯
Chrispin Chaguza,

Roles Conceptualization, Methodology, Writing – review & editing

Affiliations Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America, Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, United States of America
⨯
Julian Stamp,

Roles Methodology, Software, Writing – review & editing

Affiliation Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America

https://orcid.org/0000-0003-3014-6249

⨯
Yi Ting Chew,

Roles Visualization, Writing – review & editing

Affiliations Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America, Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, United States of America
⨯
Nicholas F. G. Chen,

Roles Data curation, Writing – review & editing

Affiliation Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America

https://orcid.org/0000-0002-7715-0619

⨯
David Ferguson,

Roles Data curation, Investigation

Affiliations Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America, Yale School of Medicine Biorepository, Yale University, New Haven, Connecticut, United States of America
⨯
Sameer Pandya,

Roles Data curation, Investigation

Affiliations Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America, Yale School of Medicine Biorepository, Yale University, New Haven, Connecticut, United States of America
⨯
Nick Kerantzas,

Roles Data curation, Investigation

Affiliations Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America, Yale School of Medicine Biorepository, Yale University, New Haven, Connecticut, United States of America
⨯
Wade Schulz,

Roles Data curation, Investigation

Affiliations Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America, Yale School of Medicine Biorepository, Yale University, New Haven, Connecticut, United States of America
⨯
Yale SARS-CoV-2 Genomic Surveillance Initiative ,

¶Authors of Yale SARS-CoV-2 Genomic Surveillance Initiative are listed in the Acknowledgments.
⨯
Anne M. Hahn,

Roles Data curation, Writing – review & editing

Affiliation Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America

https://orcid.org/0000-0003-0710-6775

⨯
C. Brandon Ogbunugafor,

Roles Methodology, Writing – review & editing

Affiliations Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, United States of America, Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America, Santa Fe Institute, Santa Fe, New Mexico, United States of America
⨯
Virginia E. Pitzer,

Roles Supervision, Writing – review & editing

Affiliations Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America, Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, United States of America
⨯
Lorin Crawford,

Roles Methodology, Software, Writing – review & editing

Affiliations Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America, Department of Biostatistics, Brown University, Providence, Rhode Island, United States of America, Microsoft Research, Cambridge, Massachusetts, United States of America
⨯
Daniel M. Weinberger,

Roles Supervision, Writing – review & editing

Affiliations Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America, Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, United States of America
⨯
[ ... ],
Nathan D. Grubaugh

Roles Funding acquisition, Supervision, Writing – review & editing

* E-mail: ke.li.kl662@yale.edu (KL); nathan.grubaugh@yale.edu (NDG)

Affiliations Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America, Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, United States of America, Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
⨯
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Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections

Ke Li,
Chrispin Chaguza,
Julian Stamp,
Yi Ting Chew,
Nicholas F. G. Chen,
David Ferguson,
Sameer Pandya,
Nick Kerantzas,
Wade Schulz,
Yale SARS-CoV-2 Genomic Surveillance Initiative

Published: September 17, 2024
https://doi.org/10.1371/journal.pcbi.1012469

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