利用流行病学和基因组数据重建小学严重急性呼吸系统综合征冠状病毒2型疫情。

IF 3 3区 医学 Q2 INFECTIOUS DISEASES
Cécile Kremer , Andrea Torneri , Pieter J.K. Libin , Cécile Meex , Marie-Pierre Hayette , Sébastien Bontems , Keith Durkin , Maria Artesi , Vincent Bours , Philippe Lemey , Gilles Darcis , Niel Hens , Christelle Meuris
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引用次数: 0

摘要

数学模型研究表明,重复筛查可以用来缓解小学中严重急性呼吸系统综合征冠状病毒2型的传播,同时保持学校开放。然而,关于学校内传播的进展以及是否存在输入家庭的风险,目前还知之甚少。2020-2021学年,在列日(比利时)的一所小学和相关家庭中进行了一项使用重复筛查的前瞻性监测研究。严重急性呼吸系统综合征冠状病毒2型筛查是通过每周清洗一到两次喉咙进行的。我们使用基因组和流行病学数据,使用两个不同的模型重建了观察到的学校疫情。爆发者2模型将生成时间和接触模式的信息与序列进化模型相结合。为了进行比较,我们还使用了SCOTTI,这是一种基于结构化聚结物的系统发育模型。此外,我们进行了一项模拟研究,以调查学校中估计阳性率的准确性如何取决于在重复筛查策略中抽样的学校比例。我们发现儿童和成人之间的严重急性呼吸系统综合征冠状病毒2型阳性率没有差异,与成人相比,儿童往往没有症状。两个疫情重建模型都显示,传播主要发生在学校环境中。当包括基因组和流行病学数据时,疫情重建的不确定性最低。我们发现,即使只有25%的学校人口被抽样,观察到的每周阳性率也很好地接近真实的周阳性率,尤其是在儿童中。这些结果表明,除了如模型研究所示减少感染外,在学校环境中进行重复筛查还可以更好地了解疫情期间学校的传播程度和社区层面的输入风险。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Reconstruction of SARS-CoV-2 outbreaks in a primary school using epidemiological and genomic data

Reconstruction of SARS-CoV-2 outbreaks in a primary school using epidemiological and genomic data

Reconstruction of SARS-CoV-2 outbreaks in a primary school using epidemiological and genomic data

Reconstruction of SARS-CoV-2 outbreaks in a primary school using epidemiological and genomic data

Mathematical modelling studies have shown that repetitive screening can be used to mitigate SARS-CoV-2 transmission in primary schools while keeping schools open. However, not much is known about how transmission progresses within schools and whether there is a risk of importation to households. During the academic year 2020–2021, a prospective surveillance study using repetitive screening was conducted in a primary school and associated households in Liège (Belgium). SARS-CoV-2 screening was performed via throat washing either once or twice a week. We used genomic and epidemiological data to reconstruct the observed school outbreaks using two different models. The outbreaker2 model combines information on the generation time and contact patterns with a model of sequence evolution. For comparison we also used SCOTTI, a phylogenetic model based on the structured coalescent. In addition, we performed a simulation study to investigate how the accuracy of estimated positivity rates in a school depends on the proportion of a school that is sampled in a repetitive screening strategy. We found no difference in SARS-CoV-2 positivity between children and adults and children were not more often asymptomatic compared to adults. Both models for outbreak reconstruction revealed that transmission occurred mainly within the school environment. Uncertainty in outbreak reconstruction was lowest when including genomic as well as epidemiological data. We found that observed weekly positivity rates are a good approximation to the true weekly positivity rate, especially in children, even when only 25% of the school population is sampled. These results indicate that, in addition to reducing infections as shown in modelling studies, repetitive screening in school settings can lead to a better understanding of the extent of transmission in schools during a pandemic and importation risk at the community level.

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来源期刊
Epidemics
Epidemics INFECTIOUS DISEASES-
CiteScore
6.00
自引率
7.90%
发文量
92
审稿时长
140 days
期刊介绍: Epidemics publishes papers on infectious disease dynamics in the broadest sense. Its scope covers both within-host dynamics of infectious agents and dynamics at the population level, particularly the interaction between the two. Areas of emphasis include: spread, transmission, persistence, implications and population dynamics of infectious diseases; population and public health as well as policy aspects of control and prevention; dynamics at the individual level; interaction with the environment, ecology and evolution of infectious diseases, as well as population genetics of infectious agents.
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