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Open Access
Peer-reviewed
Research Article
Local-scale phylodynamics reveal differential community impact of SARS-CoV-2 in a metropolitan US county
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Miguel I. Paredes ,
Roles Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Validation, Visualization, Writing – original draft, Writing – review & editing
* E-mail: paredesm@uw.edu
Affiliations Department of Epidemiology, University of Washington, Seattle, Washington, United States of America, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
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Amanda C. Perofsky,
Roles Data curation, Formal analysis, Investigation, Methodology, Visualization, Writing – original draft, Writing – review & editing
Affiliations Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, United States of America, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
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Lauren Frisbie,
Roles Data curation, Writing – review & editing
Affiliation Washington State Department of Health, Shoreline, Washington, United States of America
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Louise H. Moncla,
Roles Conceptualization, Resources, Supervision, Writing – review & editing
Affiliation The University of Pennsylvania, Department of Pathobiology, Philadelphia, Pennsylvania, United States of America
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Pavitra Roychoudhury,
Roles Data curation, Funding acquisition, Writing – review & editing
Affiliations Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
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Hong Xie,
Roles Data curation, Writing – review & editing
Affiliation Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
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Shah A. Mohamed Bakhash,
Roles Data curation, Writing – review & editing
Affiliation Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
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Kevin Kong,
Roles Data curation, Writing – review & editing
Affiliation Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
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Isabel Arnould,
Roles Data curation, Writing – review & editing
Affiliation Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
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Tien V. Nguyen,
Roles Data curation, Writing – review & editing
Affiliation Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
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Seffir T. Wendm,
Roles Data curation, Writing – review & editing
Affiliation Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
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Pooneh Hajian,
Roles Data curation, Writing – review & editing
Affiliation Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
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Sean Ellis,
Roles Data curation, Writing – review & editing
Affiliation Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
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Patrick C. Mathias,
Roles Data curation, Funding acquisition, Writing – review & editing
Affiliation Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
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Alexander L. Greninger,
Roles Data curation, Funding acquisition, Writing – review & editing
Affiliations Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
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Lea M. Starita,
Roles Data curation, Funding acquisition, Supervision, Writing – review & editing
Affiliations Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, United States of America, Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
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Chris D. Frazar,
Roles Data curation, Funding acquisition, Writing – review & editing
Affiliation Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
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Erica Ryke,
Roles Data curation, Writing – review & editing
Affiliation Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
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Weizhi Zhong,
Roles Data curation, Writing – review & editing
Affiliation Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, United States of America
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Luis Gamboa,
Roles Data curation, Writing – review & editing
Affiliation Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, United States of America
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Machiko Threlkeld,
Roles Data curation, Writing – review & editing
Affiliation Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
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Jover Lee,
Roles Data curation, Software, Writing – review & editing
Affiliation Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
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Jeremy Stone,
Roles Data curation, Writing – review & editing
Affiliation Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, United States of America
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Evan McDermot,
Roles Data curation, Writing – review & editing
Affiliation Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, United States of America
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Melissa Truong,
Roles Data curation, Writing – review & editing
Affiliation Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
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Jay Shendure,
Roles Data curation, Funding acquisition, Writing – review & editing
Affiliations Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, United States of America, Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America, Howard Hughes Medical Institute, Seattle, Washington, United States of America
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Hanna N. Oltean,
Roles Data curation, Supervision, Writing – review & editing
Affiliation Washington State Department of Health, Shoreline, Washington, United States of America
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Cécile Viboud,
Roles Data curation, Funding acquisition, Supervision, Writing – review & editing
Affiliation Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
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Helen Chu,
Roles Data curation, Funding acquisition, Supervision, Writing – review & editing
Affiliation Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
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Nicola F. Müller ,
Roles Conceptualization, Formal analysis, Investigation, Methodology, Software, Supervision, Visualization, Writing – original draft, Writing – review & editing
¶‡ These authors are jointly supervised on this work.
Affiliation Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
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Trevor Bedford
Roles Conceptualization, Funding acquisition, Investigation, Methodology, Resources, Supervision, Writing – original draft, Writing – review & editing
¶‡ These authors are jointly supervised on this work.
Affiliations Department of Epidemiology, University of Washington, Seattle, Washington, United States of America, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America, Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, United States of America, Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America, Howard Hughes Medical Institute, Seattle, Washington, United States of America
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Local-scale phylodynamics reveal differential community impact of SARS-CoV-2 in a metropolitan US county
- Miguel I. Paredes,
- Amanda C. Perofsky,
- Lauren Frisbie,
- Louise H. Moncla,
- Pavitra Roychoudhury,
- Hong Xie,
- Shah A. Mohamed Bakhash,
- Kevin Kong,
- Isabel Arnould,
- Tien V. Nguyen
![PLOS](/resource/img/logo-plos.png)
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- Published: March 26, 2024
- https://doi.org/10.1371/journal.ppat.1012117