Fine-scale spatial and social patterns of SARS-CoV-2 transmission from identical pathogen sequences.

Autor:	Tran-Kiem C; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA., Paredes MI; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.; Department of Epidemiology, University of Washington, Seattle, WA, USA., Perofsky AC; Brotman Baty Institute, University of Washington, Seattle, WA, USA.; Fogarty International Center, National Institutes of Health, Bethesda, MD, USA., Frisbie LA; Washington State Department of Health, Shoreline, WA, USA., Xie H; 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., Weixler A; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA., Greninger AL; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA., Roychoudhury P; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA., Peterson JM; Washington State Department of Health, Shoreline, WA, USA., Delgado A; Washington State Department of Health, Shoreline, WA, USA., Halstead H; Washington State Department of Health, Shoreline, WA, USA., MacKellar D; Washington State Department of Health, Shoreline, WA, USA., Dykema P; Washington State Department of Health, Shoreline, WA, USA., Gamboa L; Brotman Baty Institute, 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., Stone J; Brotman Baty Institute, University of Washington, Seattle, WA, USA., Reinhart D; Brotman Baty Institute, University of Washington, Seattle, WA, USA., Starita L; Brotman Baty Institute, University of Washington, Seattle, WA, USA.; Department of Genome Sciences, University of Washington, Seattle, WA, USA., Thibodeau A; Washington State Department of Health, Shoreline, WA, USA., Yun C; Washington State Department of Health, Shoreline, WA, USA., Aragona F; Washington State Department of Health, Shoreline, WA, USA., Black A; Washington State Department of Health, Shoreline, WA, USA., Viboud C; Fogarty International Center, National Institutes of Health, Bethesda, MD, USA., Bedford T; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.; Howard Hughes Medical Institute, Seattle, WA, USA.
Jazyk:	angličtina
Zdroj:	MedRxiv : the preprint server for health sciences [medRxiv] 2024 May 25. Date of Electronic Publication: 2024 May 25.
DOI:	10.1101/2024.05.24.24307811
Abstrakt:	Pathogen genomics can provide insights into disease transmission patterns, but new methods are needed to handle modern large-scale pathogen genome datasets. Genetically proximal viruses indicate epidemiological linkage and are informative about transmission events. Here, we leverage pairs of identical sequences using 114,298 SARS-CoV-2 genomes collected via sentinel surveillance from March 2021 to December 2022 in Washington State, USA, with linked age and residence information to characterize fine-scale transmission. The location of pairs of identical sequences is highly consistent with expectations from mobility and social contact data. Outliers in the relationship between genetic and mobility data can be explained by SARS-CoV-2 transmission between postal codes with male prisons, consistent with transmission between prison facilities. Transmission patterns between age groups vary across spatial scales. Finally, we use the timing of sequence collection to understand the age groups driving transmission. This work improves our ability to characterize transmission from large pathogen genome datasets. Competing Interests: Competing interests ALG reports contract testing from Abbott, Cepheid, Novavax, Pfizer, Janssen and Hologic, research support from Gilead, and salary and stock grants for LabCorp an immediate family member, outside of the described work. All other authors declare no competing interests.
Databáze:	MEDLINE
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