A quantitative understanding of local transmission dynamics is essential for designing effective prevention strategies. In this study, we developed a novel algorithm to identify 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 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 counties. Harris County sustained the local epidemic with fewer external introductions and 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.

This dataset includes genomic data and associated demographic metadata used to trace SARS-CoV-2 clusters in Greater Houston from January to October 2021. It provides GISAID accession IDs and demographic metadata, which are available in XML files formatted for BEAST analyses.