Tracing SARS-CoV-2 clusters across local scales using genomic data

Abstract

A quantitative understanding of local transmission dynamics is essential for designing effective prevention strategies. In this study, we developed a computational workflow to identify viral introductions and trace locally circulating clusters. We analyzed over 26,000 SARS-CoV-2 genomes and their associated metadata, collected between January and October 2021, to explore introduction and local dispersal patterns in Greater Houston, a major metropolitan area known for its demographic diversity. Our analysis identified more than 1,000 independent introduction events, resulting in clusters of varying sizes. The majority of introductions originated from domestic sources, while international introductions occurred earlier and were associated with larger cluster sizes. An analysis of locally circulating clusters revealed age-structured transmission dynamics. Geographic reconstruction of cluster spread identified Harris County as the primary viral source for surrounding areas. The outbreak in the source population was characterized by 1) a smaller proportion of new cases associated with external viral imports and 2) longer persistence times of circulating lineages. Overall, our high-resolution spatiotemporal reconstruction of the epidemic provides essential insights into the local-scale transmission landscape, supporting outbreak-specific, regional response strategies and public health planning.