Local-Scale phylodynamics reveal differential community impact of SARS-CoV-2 in metropolitan US county.

Autor:	Paredes MI; Department of Epidemiology, University of Washington, Seattle, WA, USA.; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA., Perofsky AC; Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA USA.; Fogarty International Center, National Institutes of Health, Bethesda, MD, USA., Frisbie L; Washington State Department of Health, Shoreline, WA USA., Moncla LH; The University of Pennsylvania, Department of Pathobiology, Philadelphia, PA., Roychoudhury P; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA.; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA., Xie H; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA., Mohamed Bakhash SA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA., Kong K; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA., Arnould I; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA., Nguyen TV; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA., Wendm ST; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA., Hajian P; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA., Ellis S; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA., Mathias PC; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA., Greninger AL; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA.; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA., Starita LM; Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA USA.; Department of Genome Sciences, University of Washington, Seattle, WA, USA., Frazar CD; Department of Genome Sciences, University of Washington, Seattle, WA, USA., Ryke E; Department of Genome Sciences, University of Washington, Seattle, WA, USA., Zhong W; Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA USA., Gamboa L; Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA USA., Threlkeld M; Department of Genome Sciences, University of Washington, Seattle, WA, USA., Lee J; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA., Stone J; Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA USA., McDermot E; Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA USA., Truong M; Department of Genome Sciences, University of Washington, Seattle, WA, USA., Shendure J; Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA USA.; Department of Genome Sciences, University of Washington, Seattle, WA, USA.; Howard Hughes Medical Institute, Seattle, WA, USA., Oltean HN; Washington State Department of Health, Shoreline, WA USA., Viboud C; Fogarty International Center, National Institutes of Health, Bethesda, MD, USA., Chu H; Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA., Müller NF; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA., Bedford T; Department of Epidemiology, University of Washington, Seattle, WA, USA.; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA.; Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA USA.; Department of Genome Sciences, University of Washington, Seattle, WA, USA.; Howard Hughes Medical Institute, Seattle, WA, USA.
Jazyk:	angličtina
Zdroj:	MedRxiv : the preprint server for health sciences [medRxiv] 2022 Dec 16. Date of Electronic Publication: 2022 Dec 16.
DOI:	10.1101/2022.12.15.22283536
Abstrakt:	SARS-CoV-2 transmission is largely driven by heterogeneous dynamics at a local scale, leaving local health departments to design interventions with limited information. We analyzed SARS-CoV-2 genomes sampled between February 2020 and March 2022 jointly with epidemiological and cell phone mobility data to investigate fine scale spatiotemporal SARS-CoV-2 transmission dynamics in King County, Washington, a diverse, metropolitan US county. We applied an approximate structured coalescent approach to model transmission within and between North King County and South King County alongside the rate of outside introductions into the county. Our phylodynamic analyses reveal that following stay-at-home orders, the epidemic trajectories of North and South King County began to diverge. We find that South King County consistently had more reported and estimated cases, COVID-19 hospitalizations, and longer persistence of local viral transmission when compared to North King County, where viral importations from outside drove a larger proportion of new cases. Using mobility and demographic data, we also find that South King County experienced a more modest and less sustained reduction in mobility following stay-at-home orders than North King County, while also bearing more socioeconomic inequities that might contribute to a disproportionate burden of SARS-CoV-2 transmission. Overall, our findings suggest a role for local-scale phylodynamics in understanding the heterogeneous transmission landscape. Competing Interests: Declaration of interests ALG reports contract testing from Abbott, Cepheid, Novavax, Pfizer, Janssen and Hologic and research support from Gilead and Merck, outside of the described work. All other authors declare no competing interests.
Databáze:	MEDLINE
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