Fine-scale patterns of SARS-CoV-2 spread from identical pathogen sequences

Cécile Tran-Kiem (), Miguel I. Paredes, Amanda C. Perofsky, Lauren A. Frisbie, Hong Xie, Kevin Kong, Amelia Weixler, Alexander L. Greninger, Pavitra Roychoudhury, JohnAric M. Peterson, Andrew Delgado, Holly Halstead, Drew MacKellar, Philip Dykema, Luis Gamboa, Chris D. Frazar, Erica Ryke, Jeremy Stone, David Reinhart, Lea Starita, Allison Thibodeau, Cory Yun, Frank Aragona, Allison Black, Cécile Viboud and Trevor Bedford
Additional contact information
Cécile Tran-Kiem: Fred Hutchinson Cancer Center
Miguel I. Paredes: Fred Hutchinson Cancer Center
Amanda C. Perofsky: University of Washington
Lauren A. Frisbie: Washington State Department of Health
Hong Xie: University of Washington
Kevin Kong: University of Washington
Amelia Weixler: University of Washington
Alexander L. Greninger: Fred Hutchinson Cancer Center
Pavitra Roychoudhury: Fred Hutchinson Cancer Center
JohnAric M. Peterson: Washington State Department of Health
Andrew Delgado: Washington State Department of Health
Holly Halstead: Washington State Department of Health
Drew MacKellar: Washington State Department of Health
Philip Dykema: Washington State Department of Health
Luis Gamboa: University of Washington
Chris D. Frazar: University of Washington
Erica Ryke: University of Washington
Jeremy Stone: University of Washington
David Reinhart: University of Washington
Lea Starita: University of Washington
Allison Thibodeau: Washington State Department of Health
Cory Yun: Washington State Department of Health
Frank Aragona: Washington State Department of Health
Allison Black: Washington State Department of Health
Cécile Viboud: National Institutes of Health
Trevor Bedford: Fred Hutchinson Cancer Center

Nature, 2025, vol. 640, issue 8057, 176-185

Abstract: Abstract Pathogen genomics can provide insights into underlying infectious disease transmission patterns1,2, but new methods are needed to handle modern large-scale pathogen genome datasets and realize this full potential3–5. In particular, genetically proximal viruses should be highly informative about transmission events as genetic proximity indicates epidemiological linkage. Here we use pairs of identical sequences to characterize fine-scale transmission patterns using 114,298 SARS-CoV-2 genomes collected through Washington State (USA) genomic sentinel surveillance with associated age and residence location information between March 2021 and December 2022. This corresponds to 59,660 sequences with another identical sequence in the dataset. We find that 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 postcodes with male prisons, consistent with transmission between prison facilities. We find that transmission patterns between age groups vary across spatial scales. Finally, we use the timing of sequence collection to understand the age groups driving transmission. Overall, this study improves our ability to use large pathogen genome datasets to understand the determinants of infectious disease spread.

Date: 2025
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DOI: 10.1038/s41586-025-08637-4

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