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Characterizing spatial epidemiology in a heterogeneous transmission landscape using the spatial transmission count
Leke Lyu1,2,3,4, Gabriella Veytsel1,2,3,4, Guppy Stott1,2,3,4
1Institute of Bioinformatics, University of Georgia, Athens, GA, USA.
Communications Medicine
|May 9, 2025
Summary
Urban centers drove the SARS-CoV-2 epidemic in Texas, acting as sources connected globally. Rural areas experienced repeated introductions, highlighting the need for tailored public health interventions.
Area of Science:
- Genomics
- Epidemiology
- Computational Biology
Background:
- Viral genomes offer insights into geographic spread and transmission dynamics.
- Regional heterogeneity, especially between rural and urban areas, impacts viral spread but is understudied due to data limitations.
- Large-scale SARS-CoV-2 sequencing facilitates genomic approaches to reconstruct spatial transmission history.
Purpose of the Study:
- To develop and apply a novel statistical method for analyzing spatial transmission patterns of SARS-CoV-2.
- To investigate the role of urban and rural centers in the SARS-CoV-2 epidemic trajectory in Texas.
- To provide actionable epidemiological statistics for public health interventions.
Main Methods:
- Proposed a spatial transmission count statistic to summarize geographic patterns in viral phylogenies.
- Utilized time-scaled phylogenetic trees with ancestral trait states to identify spatial transmission linkages (imports, local, exports).
- Analyzed over 12,000 SARS-CoV-2 genomes linked with epidemiological data for outbreak analysis.
Main Results:
- Highly populated urban centers were identified as primary sources of the SARS-CoV-2 epidemic in Texas.
- Urban outbreaks showed connections to the global epidemic, indicating international importations.
- Urban outbreaks were locally sustained, whereas rural epidemics were characterized by recurrent introductions from external sources.
Conclusions:
- Introduced the Source Sink Score and Local Import Score to quantify outbreak roles and transmission dynamics.
- Demonstrated the utility of these scores for near real-time outbreak analysis.
- Highlighted the importance of understanding urban-rural transmission dynamics for targeted public health strategies.
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