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

ABSTRACT: Pathogen genomics can provide insights into underlying infectious disease transmission patterns^1,2, but new methods are needed to handle modern large-scale pathogen genome datasets and realize this full potential^3-5. 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

SUBMITTER: Tran-Kiem C 

PROVIDER: S-EPMC11964829 | biostudies-literature | 2025 Apr

REPOSITORIES: biostudies-literature