Article (Scientific journals)
Reconstruction of SARS-CoV-2 outbreaks in a primary school using epidemiological and genomic data.
Kremer, Cécile; Torneri, Andrea; Libin, Pieter J K et al.
2023In Epidemics, 44, p. 100701
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Keywords :
Outbreak reconstruction; Primary school; SARS-coV-2 transmission; Screening protocol; Whole genome sequences; Virology; Infectious Diseases; Public Health, Environmental and Occupational Health; Microbiology; Parasitology; Epidemiology
Abstract :
[en] 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.
Disciplines :
Immunology & infectious disease
Author, co-author :
Kremer, Cécile ;  Interuniversity Institute for Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Hasselt, Belgium. Electronic address: cecile.kremer@uhasselt.be
Torneri, Andrea;  Interuniversity Institute for Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Hasselt, Belgium
Libin, Pieter J K;  Interuniversity Institute for Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Hasselt, Belgium, Artificial Intelligence Lab, Department of Computer Science, Vrije Universiteit Brussel, Brussels, Belgium, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
Meex, Cécile ;  Centre Hospitalier Universitaire de Liège - CHU > > Service de microbiologie clinique
Hayette, Marie-Pierre ;  Centre Hospitalier Universitaire de Liège - CHU > > Service de microbiologie clinique
Bontems, Sébastien ;  Centre Hospitalier Universitaire de Liège - CHU > > Service de microbiologie clinique
Durkin, Keith William  ;  Centre Hospitalier Universitaire de Liège - CHU > > Service de génétique
Artesi, Maria ;  Centre Hospitalier Universitaire de Liège - CHU > > Service de génétique
Bours, Vincent ;  Centre Hospitalier Universitaire de Liège - CHU > > Service de génétique
Lemey, Philippe;  Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
Darcis, Gilles ;  Centre Hospitalier Universitaire de Liège - CHU > > Service des maladies infectieuses - médecine interne
Hens, Niel;  Interuniversity Institute for Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Hasselt, Belgium, Centre for Health Economics Research and Modelling Infectious Diseases, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
Meuris, Christelle ;  Centre Hospitalier Universitaire de Liège - CHU > > Service des maladies infectieuses - médecine interne
More authors (3 more) Less
Language :
English
Title :
Reconstruction of SARS-CoV-2 outbreaks in a primary school using epidemiological and genomic data.
Publication date :
16 June 2023
Journal title :
Epidemics
ISSN :
1755-4365
eISSN :
1878-0067
Publisher :
Elsevier BV, Netherlands
Volume :
44
Pages :
100701
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBi :
since 24 August 2023

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