Fine-scale patterns of SARS-CoV-2 spread from identical pathogen sequences DOI Creative Commons
Cécile Tran Kiem, Miguel I. Paredes, Amanda C. Perofsky

et al.

Nature, Journal Year: 2025, Volume and Issue: unknown

Published: March 5, 2025

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 events as genetic proximity indicates epidemiological linkage. Here we use pairs of identical sequences characterize fine-scale patterns using 114,298 SARS-CoV-2 genomes collected through Washington State (USA) genomic sentinel surveillance with associated age residence location information between March 2021 December 2022. This corresponds 59,660 another sequence in the dataset. We find that is consistent expectations from mobility social contact data. Outliers relationship data explained by postcodes male prisons, prison facilities. groups vary across spatial scales. Finally, timing collection understand driving transmission. Overall, study improves our ability large determinants spread.

Language: Английский

Fine-scale patterns of SARS-CoV-2 spread from identical pathogen sequences DOI Creative Commons
Cécile Tran Kiem, Miguel I. Paredes, Amanda C. Perofsky

et al.

Nature, Journal Year: 2025, Volume and Issue: unknown

Published: March 5, 2025

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 events as genetic proximity indicates epidemiological linkage. Here we use pairs of identical sequences characterize fine-scale patterns using 114,298 SARS-CoV-2 genomes collected through Washington State (USA) genomic sentinel surveillance with associated age residence location information between March 2021 December 2022. This corresponds 59,660 another sequence in the dataset. We find that is consistent expectations from mobility social contact data. Outliers relationship data explained by postcodes male prisons, prison facilities. groups vary across spatial scales. Finally, timing collection understand driving transmission. Overall, study improves our ability large determinants spread.

Language: Английский

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