Genetic determination of regional connectivity in modelling the spread of COVID-19 outbreak for more efficient mitigation strategies.
Genetic determination of regional connectivity in modelling the spread of COVID-19 outbreak for more efficient mitigation strategies.
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DOI：
10.1038/s41598-023-34959-2
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发表时间：
2023-05-25
影响因子：
4.6
通讯作者：
中科院分区：
文献类型：
--
作者：
对于COVID-19大流行，病毒传播在许多历史和地理背景下都有记录。然而，很少有研究明确建模的时空流的基因序列的基础上，制定缓解策略。此外，已经对数千个SARS-CoV-2基因组进行了测序，并记录了相关记录，这可能为此类时空分析提供了丰富的来源，在一次爆发期间，这是前所未有的数量。在这里，在七个州的案例研究中，除了传统的流行病学和人口统计学参数外，我们还通过从系统发育序列信息（即“遗传连接性”）确定区域连接性来模拟疫情的第一波。我们的研究表明，几乎所有的初始爆发都可以追溯到几个谱系，而不是断开的爆发，这表明最初的病毒流基本上是连续的。虽然与热点的地理距离最初在建模中很重要，但遗传连接性在第一波中变得越来越重要。此外，我们的模型预测，孤立的局部策略（例如依赖群体免疫）可能会对邻近地区产生负面影响，这表明通过统一的跨境干预措施可以实现更有效的缓解。最后，我们的研究结果表明，基于连通性的一些有针对性的干预措施可以产生类似于全面封锁的效果。他们还表明，虽然成功的封锁在缓解疫情方面非常有效，但纪律不严的封锁很快就会降低有效性。我们的研究提供了一个框架，结合动力学和计算方法，以确定有针对性的干预措施。
For the COVID-19 pandemic, viral transmission has been documented in many historical and geographical contexts. Nevertheless, few studies have explicitly modeled the spatiotemporal flow based on genetic sequences, to develop mitigation strategies. Additionally, thousands of SARS-CoV-2 genomes have been sequenced with associated records, potentially providing a rich source for such spatiotemporal analysis, an unprecedented amount during a single outbreak. Here, in a case study of seven states, we model the first wave of the outbreak by determining regional connectivity from phylogenetic sequence information (i.e. “genetic connectivity”), in addition to traditional epidemiologic and demographic parameters. Our study shows nearly all of the initial outbreak can be traced to a few lineages, rather than disconnected outbreaks, indicative of a mostly continuous initial viral flow. While the geographic distance from hotspots is initially important in the modeling, genetic connectivity becomes increasingly significant later in the first wave. Moreover, our model predicts that isolated local strategies (e.g. relying on herd immunity) can negatively impact neighboring regions, suggesting more efficient mitigation is possible with unified, cross-border interventions. Finally, our results suggest that a few targeted interventions based on connectivity can have an effect similar to that of an overall lockdown. They also suggest that while successful lockdowns are very effective in mitigating an outbreak, less disciplined lockdowns quickly decrease in effectiveness. Our study provides a framework for combining phylodynamic and computational methods to identify targeted interventions.
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