Genomic profiling and spatial SEIR modeling of COVID-19 transmission in Western New York

作者：Jonathan Bard, Na Jiang, Jamaal Emerson, Madeleine Bartz, Natalie A. Lamb, Brandon Marzullo, Alyssa Pohlman, Amanda Boccolucci, Norma J. Nowak, Donald Yergeau, Andrew Crooks, Jennifer A. Surtees · 发表于：Frontiers in Microbiology · 年份：2024 · DOI：10.3389/fmicb.2024.1416580 · 被引用次数：2 · 研究领域：COVID-19 epidemiological studies、SARS-CoV-2 and COVID-19 Research、Virology and Viral Diseases

The COVID-19 pandemic has prompted an unprecedented global effort to understand and mitigate the spread of the SARS-CoV-2 virus. In this study, we present a comprehensive analysis of COVID-19 in Western New York (WNY), integrating individual patient-level genomic sequencing data with a spatially informed agent-based disease Susceptible-Exposed-Infectious-Recovered (SEIR) computational model. The integration of genomic and spatial data enables a multi-faceted exploration of the factors influencing the transmission patterns of COVID-19, including genetic variations in the viral genomes, population density, and movement dynamics in New York State (NYS). Our genomic analyses provide insights into the genetic heterogeneity of SARS-CoV-2 within a single lineage, at region-specific resolutions, while our population analyses provide models for SARS-CoV-2 lineage transmission. Together, our findings shed light on localized dynamics of the pandemic, revealing potential cross-county transmission networks. This interdisciplinary approach, bridging genomics and spatial modeling, contributes to a more comprehensive understanding of COVID-19 dynamics. The results of this study have implications for future public health strategies, including guiding targeted interventions and resource allocations to control the spread of similar viruses.