Tracing SARS-CoV-2 Clusters Across Local-scales Using Genomic Data
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Understanding local-scale transmission dynamics of SARS-CoV-2 is crucial for planning effective prevention strategies. This study analyzed over 26,000 genomes and their associated metadata collected between January and October 2021 to explore the introduction and dispersal patterns of SARS-CoV-2 in Greater Houston, a major metropolitan area noted for its demographic diversity. We identified more than a thousand independent introduction events, resulting in clusters of varying sizes, with earlier clusters presenting larger sizes and posing greater control challenges. Characterization of the sources of these introductions showed that domestic origins were more significant than international ones. Further examination of locally circulating clusters across different subregions of Greater Houston revealed varied transmission dynamics. Notably, subregions that served as primary viral sources sustained the local epidemic effectively, evidenced by: (1) a smaller proportion of new cases driven by external viral importations, and (2) longer persistence times of circulating lineages. Overall, our high-resolution spatiotemporal reconstruction of the epidemic in Greater Houston enhances understanding of the heterogeneous transmission landscape, providing key insights into regional response strategies and public health planning.
Significance Statement
The growing recognition of genome sequencing as critical for outbreak response has led to a rapid increase in the availability of sequence data. In this context, we put forward an analytical workflow within the Bayesian phylodynamic framework to identify and trace imported SARS-CoV-2 clusters using large-scale genome datasets. By utilizing metrics such as the Source-Sink Score, Local Import Score, and Persistent Time, our approach characterizes transmission patterns in each subregion and elucidates transmission heterogeneity. As new variants continue to emerge, the insights provided by our analysis are crucial for addressing the challenges of current and future pandemics effectively.
