Combined analyses of within-host SARS-CoV-2 viral kinetics and information on past exposures to the virus in a human cohort identifies intrinsic differences of Omicron and Delta variants

Timothy W. Russell; Hermaleigh Townsley; Sam Abbott; Joel Hellewell; Edward J. Carr; Lloyd A. C. Chapman; Rachael Pung; Billy J. Quilty; David Hodgson; Ashley S. Fowler; Lorin Adams; Chris Bailey; Harriet V. Mears; Ruth Harvey; Bobbi Clayton; Nicola O’Reilly; Yenting Ngai; Jerome Nicod; Steve Gamblin; Bryan Williams; Sonia Gandhi; Charles Swanton; Rupert Beale; David L. V. Bauer; Emma C. Wall; Adam J. Kucharski

doi:10.1371/journal.pbio.3002463

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Open Access

Peer-reviewed

Research Article

Combined analyses of within-host SARS-CoV-2 viral kinetics and information on past exposures to the virus in a human cohort identifies intrinsic differences of Omicron and Delta variants

Timothy W. Russell ,

Contributed equally to this work with: Timothy W. Russell, Hermaleigh Townsley, Sam Abbott

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

* E-mail: timothy.russell@lshtm.ac.uk

Affiliation Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom

https://orcid.org/0000-0001-5610-6080

⨯
Hermaleigh Townsley ,

Contributed equally to this work with: Timothy W. Russell, Hermaleigh Townsley, Sam Abbott

Roles Data curation, Methodology, Validation, Writing – original draft, Writing – review & editing

Affiliations The Francis Crick Institute, London, United Kingdom, National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
⨯
Sam Abbott ,

Contributed equally to this work with: Timothy W. Russell, Hermaleigh Townsley, Sam Abbott

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

Affiliation Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
⨯
Joel Hellewell ,

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

¶‡ JH and EJC also contributed equally to this work. ECW and AJK also contributed equally to this work.

Affiliation European Molecular Biology Laboratory-European Bioinformatics Institute, Cambridge, United Kingdom
⨯
Edward J. Carr ,

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

¶‡ JH and EJC also contributed equally to this work. ECW and AJK also contributed equally to this work.

Affiliations The Francis Crick Institute, London, United Kingdom, University College London, London, United Kingdom
⨯
Lloyd A. C. Chapman,

Roles Conceptualization, Formal analysis, Methodology, Writing – review & editing

Affiliations Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom, Lancaster University, Bailrigg, Lancaster, United Kingdom
⨯
Rachael Pung,

Roles Conceptualization, Visualization, Writing – review & editing

Affiliation Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
⨯
Billy J. Quilty,

Roles Conceptualization, Writing – review & editing

Affiliation Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
⨯
David Hodgson,

Roles Conceptualization, Writing – review & editing

Affiliation Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
⨯
Ashley S. Fowler,

Roles Data curation, Writing – review & editing

Affiliation The Francis Crick Institute, London, United Kingdom
⨯
Lorin Adams,

Roles Data curation, Writing – review & editing

Affiliation The Francis Crick Institute, London, United Kingdom
⨯
Chris Bailey,

Roles Data curation, Writing – review & editing

Affiliations The Francis Crick Institute, London, United Kingdom, University College London, London, United Kingdom
⨯
Harriet V. Mears,

Roles Data curation, Writing – review & editing

Affiliation The Francis Crick Institute, London, United Kingdom
⨯
Ruth Harvey,

Roles Data curation, Writing – review & editing

Affiliation The Francis Crick Institute, London, United Kingdom
⨯
Bobbi Clayton,

Roles Data curation, Writing – review & editing

Affiliation The Francis Crick Institute, London, United Kingdom
⨯
Nicola O’Reilly,

Roles Data curation, Writing – review & editing

Affiliation The Francis Crick Institute, London, United Kingdom
⨯
Yenting Ngai,

Roles Data curation, Writing – review & editing

Affiliations The Francis Crick Institute, London, United Kingdom, University College London, London, United Kingdom
⨯
Jerome Nicod,

Roles Data curation, Writing – review & editing

Affiliation The Francis Crick Institute, London, United Kingdom
⨯
Steve Gamblin,

Roles Data curation, Writing – review & editing

Affiliation The Francis Crick Institute, London, United Kingdom
⨯
Bryan Williams,

Roles Data curation, Writing – review & editing

Affiliations National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom, University College London, London, United Kingdom
⨯
Sonia Gandhi,

Roles Data curation, Writing – review & editing

Affiliations The Francis Crick Institute, London, United Kingdom, University College London, London, United Kingdom
⨯
Charles Swanton,

Roles Data curation, Funding acquisition, Investigation, Writing – review & editing

Affiliations The Francis Crick Institute, London, United Kingdom, University College London, London, United Kingdom
⨯
Rupert Beale,

Roles Conceptualization, Investigation, Methodology, Project administration, Writing – original draft, Writing – review & editing

Affiliations The Francis Crick Institute, London, United Kingdom, University College London, London, United Kingdom, Genotype-to-Phenotype UK National Virology Consortium (G2P-UK), London, United Kingdom
⨯
David L. V. Bauer,

Roles Conceptualization, Data curation, Investigation, Methodology, Project administration, Supervision, Visualization, Writing – original draft, Writing – review & editing

Affiliations The Francis Crick Institute, London, United Kingdom, Genotype-to-Phenotype UK National Virology Consortium (G2P-UK), London, United Kingdom
⨯
Emma C. Wall ,

Roles Conceptualization, Data curation, Funding acquisition, Investigation, Methodology, Project administration, Supervision, Visualization, Writing – original draft, Writing – review & editing

¶‡ JH and EJC also contributed equally to this work. ECW and AJK also contributed equally to this work.

Affiliations The Francis Crick Institute, London, United Kingdom, National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom, University College London, London, United Kingdom
⨯
[ ... ],
Adam J. Kucharski

Roles Conceptualization, Formal analysis, Investigation, Methodology, Project administration, Supervision, Visualization, Writing – original draft, Writing – review & editing

¶‡ JH and EJC also contributed equally to this work. ECW and AJK also contributed equally to this work.

Affiliation Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
⨯
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Combined analyses of within-host SARS-CoV-2 viral kinetics and information on past exposures to the virus in a human cohort identifies intrinsic differences of Omicron and Delta variants

Timothy W. Russell,
Hermaleigh Townsley,
Sam Abbott,
Joel Hellewell,
Edward J. Carr,
Lloyd A. C. Chapman,
Rachael Pung,
Billy J. Quilty,
David Hodgson,
Ashley S. Fowler

Published: January 30, 2024
https://doi.org/10.1371/journal.pbio.3002463

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