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局部尺度系统发育动力学揭示了 SARS-CoV-2 在一个美国大都市区县对社区的差异化影响。

Local-scale phylodynamics reveal differential community impact of SARS-CoV-2 in a metropolitan US county.

机构信息

Department of Epidemiology, University of Washington, Seattle, Washington, United States of America.

Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America.

出版信息

PLoS Pathog. 2024 Mar 26;20(3):e1012117. doi: 10.1371/journal.ppat.1012117. eCollection 2024 Mar.

DOI:10.1371/journal.ppat.1012117
PMID:38530853
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10997136/
Abstract

SARS-CoV-2 transmission is largely driven by heterogeneous dynamics at a local scale, leaving local health departments to design interventions with limited information. We analyzed SARS-CoV-2 genomes sampled between February 2020 and March 2022 jointly with epidemiological and cell phone mobility data to investigate fine scale spatiotemporal SARS-CoV-2 transmission dynamics in King County, Washington, a diverse, metropolitan US county. We applied an approximate structured coalescent approach to model transmission within and between North King County and South King County alongside the rate of outside introductions into the county. Our phylodynamic analyses reveal that following stay-at-home orders, the epidemic trajectories of North and South King County began to diverge. We find that South King County consistently had more reported and estimated cases, COVID-19 hospitalizations, and longer persistence of local viral transmission when compared to North King County, where viral importations from outside drove a larger proportion of new cases. Using mobility and demographic data, we also find that South King County experienced a more modest and less sustained reduction in mobility following stay-at-home orders than North King County, while also bearing more socioeconomic inequities that might contribute to a disproportionate burden of SARS-CoV-2 transmission. Overall, our findings suggest a role for local-scale phylodynamics in understanding the heterogeneous transmission landscape.

摘要

SARS-CoV-2 的传播在很大程度上受到局部尺度上异质动态的驱动，这使得地方卫生部门只能在有限信息的情况下设计干预措施。我们分析了 2020 年 2 月至 2022 年 3 月间采集的 SARS-CoV-2 基因组，同时结合流行病学和手机移动性数据，以调查美国华盛顿州金县的 SARS-CoV-2 精细时空传播动态。金县是一个多样化的大都市区县。我们应用近似结构协变方法，在北金县和南金县内部以及外部引入该县的速度方面，对传播进行建模。我们的系统发育动力学分析表明，在居家令发布后，北金县和南金县的疫情轨迹开始出现分歧。我们发现，与北金县相比，南金县的报告病例和估计病例、COVID-19 住院病例更多，本地病毒传播的持续时间更长，而北金县的新病例则更多地来自外部输入。通过使用移动性和人口统计数据，我们还发现，与北金县相比，居家令发布后，南金县的移动性减少幅度较小，持续时间也较短，而南金县的社会经济不平等程度更高，这可能导致 SARS-CoV-2 传播的负担不成比例。总的来说，我们的研究结果表明，局部尺度的系统发育动力学在理解异质传播格局方面发挥了作用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fafa/10997136/e08b86f42e27/ppat.1012117.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fafa/10997136/c86c48687d54/ppat.1012117.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fafa/10997136/936b6f9d37b2/ppat.1012117.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fafa/10997136/c6fae315b882/ppat.1012117.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fafa/10997136/9fd1a38153c7/ppat.1012117.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fafa/10997136/4d7d76ddecd8/ppat.1012117.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fafa/10997136/e08b86f42e27/ppat.1012117.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fafa/10997136/c86c48687d54/ppat.1012117.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fafa/10997136/936b6f9d37b2/ppat.1012117.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fafa/10997136/c6fae315b882/ppat.1012117.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fafa/10997136/9fd1a38153c7/ppat.1012117.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fafa/10997136/4d7d76ddecd8/ppat.1012117.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fafa/10997136/e08b86f42e27/ppat.1012117.g006.jpg

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