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

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

doi:10.1016/j.epidem.2023.100701

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

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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Abstract

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.

Original language	English
Article number	100701
Number of pages	10
Journal	Epidemics
Volume	44
DOIs	https://doi.org/10.1016/j.epidem.2023.100701
Publication status	Published - Sept 2023

Bibliographical note

Funding Information:
The study was funded by Fondation Léon Fredericq and by the Liège University Hospital Research funds . P.J.K.L. gratefully acknowledges support from the Research Foundation Flanders (FWO), Belgium via postdoctoral fellowship 1242021N (P.J.K.L.). P.J.K.L. also acknowledges support from the Research council of the Vrije Universiteit Brussel (OZR-VUB), Belgium via grant number OZR3863BOF , and from the Flemish Government through the AI Research Program . G.D. is an FNRS postdoctoral clinical master specialist. P.L. acknowledges support by the European Research Council under the European Union’s Horizon 2020 research and innovation programme (grant agreement number 725422 - ReservoirDOCS) and the Research Foundation – Flanders (‘Fonds voor Wetenschappelijk Onderzoek – Vlaanderen’ , G066215N , G0D5117N and G0B9317N ). N.H. and A.T. acknowledge funding from the European Union’s Horizon 2020 research and innovation programme - project EpiPose (Grant agreement number 101003688 ). This project was supported by the VERDI project ( 101045989 ), funded by the European Union . Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the Health and Digital Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.

Funding Information:
The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center), funded by the Research Foundation Flanders (FWO) and the Flemish Government department EWI .

Funding Information:
The study was funded by Fondation Léon Fredericq and by the Liège University Hospital Research funds. P.J.K.L. gratefully acknowledges support from the Research Foundation Flanders (FWO), Belgium via postdoctoral fellowship 1242021N (P.J.K.L.). P.J.K.L. also acknowledges support from the Research council of the Vrije Universiteit Brussel (OZR-VUB), Belgium via grant number OZR3863BOF, and from the Flemish Government through the AI Research Program. G.D. is an FNRS postdoctoral clinical master specialist. P.L. acknowledges support by the European Research Council under the European Union's Horizon 2020 research and innovation programme (grant agreement number 725422 - ReservoirDOCS) and the Research Foundation – Flanders (‘Fonds voor Wetenschappelijk Onderzoek – Vlaanderen’, G066215N, G0D5117N and G0B9317N). N.H. and A.T. acknowledge funding from the European Union's Horizon 2020 research and innovation programme - project EpiPose (Grant agreement number 101003688). This project was supported by the VERDI project (101045989), funded by the European Union. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the Health and Digital Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center), funded by the Research Foundation Flanders (FWO) and the Flemish Government department EWI.

Publisher Copyright:
© 2023

Keywords

Outbreak reconstruction
Primary school
SARS-coV-2 transmission
Screening protocol
Whole genome sequences

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10.1016/j.epidem.2023.100701Licence: CC BY

105789140Final published version, 1.73 MBLicence: CC BY

Cite this

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

abstract = "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 Li{\`e}ge (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.",

keywords = "Outbreak reconstruction, Primary school, SARS-coV-2 transmission, Screening protocol, Whole genome sequences",

author = "C{\'e}cile Kremer and Andrea Torneri and Libin, {Pieter J.K.} and C{\'e}cile Meex and Hayette, {Marie Pierre} and S{\'e}bastien Bontems and Keith Durkin and Maria Artesi and Vincent Bours and Philippe Lemey and Gilles Darcis and Niel Hens and Christelle Meuris",

note = "Funding Information: The study was funded by Fondation L{\'e}on Fredericq and by the Li{\`e}ge University Hospital Research funds . P.J.K.L. gratefully acknowledges support from the Research Foundation Flanders (FWO), Belgium via postdoctoral fellowship 1242021N (P.J.K.L.). P.J.K.L. also acknowledges support from the Research council of the Vrije Universiteit Brussel (OZR-VUB), Belgium via grant number OZR3863BOF , and from the Flemish Government through the AI Research Program . G.D. is an FNRS postdoctoral clinical master specialist. P.L. acknowledges support by the European Research Council under the European Union{\textquoteright}s Horizon 2020 research and innovation programme (grant agreement number 725422 - ReservoirDOCS) and the Research Foundation – Flanders ({\textquoteleft}Fonds voor Wetenschappelijk Onderzoek – Vlaanderen{\textquoteright} , G066215N , G0D5117N and G0B9317N ). N.H. and A.T. acknowledge funding from the European Union{\textquoteright}s Horizon 2020 research and innovation programme - project EpiPose (Grant agreement number 101003688 ). This project was supported by the VERDI project ( 101045989 ), funded by the European Union . Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the Health and Digital Executive Agency. Neither the European Union nor the granting authority can be held responsible for them. Funding Information: The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center), funded by the Research Foundation Flanders (FWO) and the Flemish Government department EWI . Funding Information: The study was funded by Fondation L{\'e}on Fredericq and by the Li{\`e}ge University Hospital Research funds. P.J.K.L. gratefully acknowledges support from the Research Foundation Flanders (FWO), Belgium via postdoctoral fellowship 1242021N (P.J.K.L.). P.J.K.L. also acknowledges support from the Research council of the Vrije Universiteit Brussel (OZR-VUB), Belgium via grant number OZR3863BOF, and from the Flemish Government through the AI Research Program. G.D. is an FNRS postdoctoral clinical master specialist. P.L. acknowledges support by the European Research Council under the European Union's Horizon 2020 research and innovation programme (grant agreement number 725422 - ReservoirDOCS) and the Research Foundation – Flanders ({\textquoteleft}Fonds voor Wetenschappelijk Onderzoek – Vlaanderen{\textquoteright}, G066215N, G0D5117N and G0B9317N). N.H. and A.T. acknowledge funding from the European Union's Horizon 2020 research and innovation programme - project EpiPose (Grant agreement number 101003688). This project was supported by the VERDI project (101045989), funded by the European Union. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the Health and Digital Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center), funded by the Research Foundation Flanders (FWO) and the Flemish Government department EWI. Publisher Copyright: {\textcopyright} 2023",

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doi = "10.1016/j.epidem.2023.100701",

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T1 - Reconstruction of SARS-CoV-2 outbreaks in a primary school using epidemiological and genomic data

AU - Kremer, Cécile

AU - Torneri, Andrea

AU - Libin, Pieter J.K.

AU - Meex, Cécile

AU - Hayette, Marie Pierre

AU - Bontems, Sébastien

AU - Durkin, Keith

AU - Artesi, Maria

AU - Bours, Vincent

AU - Lemey, Philippe

AU - Darcis, Gilles

AU - Hens, Niel

AU - Meuris, Christelle

N1 - Funding Information: The study was funded by Fondation Léon Fredericq and by the Liège University Hospital Research funds . P.J.K.L. gratefully acknowledges support from the Research Foundation Flanders (FWO), Belgium via postdoctoral fellowship 1242021N (P.J.K.L.). P.J.K.L. also acknowledges support from the Research council of the Vrije Universiteit Brussel (OZR-VUB), Belgium via grant number OZR3863BOF , and from the Flemish Government through the AI Research Program . G.D. is an FNRS postdoctoral clinical master specialist. P.L. acknowledges support by the European Research Council under the European Union’s Horizon 2020 research and innovation programme (grant agreement number 725422 - ReservoirDOCS) and the Research Foundation – Flanders (‘Fonds voor Wetenschappelijk Onderzoek – Vlaanderen’ , G066215N , G0D5117N and G0B9317N ). N.H. and A.T. acknowledge funding from the European Union’s Horizon 2020 research and innovation programme - project EpiPose (Grant agreement number 101003688 ). This project was supported by the VERDI project ( 101045989 ), funded by the European Union . Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the Health and Digital Executive Agency. Neither the European Union nor the granting authority can be held responsible for them. Funding Information: The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center), funded by the Research Foundation Flanders (FWO) and the Flemish Government department EWI . Funding Information: The study was funded by Fondation Léon Fredericq and by the Liège University Hospital Research funds. P.J.K.L. gratefully acknowledges support from the Research Foundation Flanders (FWO), Belgium via postdoctoral fellowship 1242021N (P.J.K.L.). P.J.K.L. also acknowledges support from the Research council of the Vrije Universiteit Brussel (OZR-VUB), Belgium via grant number OZR3863BOF, and from the Flemish Government through the AI Research Program. G.D. is an FNRS postdoctoral clinical master specialist. P.L. acknowledges support by the European Research Council under the European Union's Horizon 2020 research and innovation programme (grant agreement number 725422 - ReservoirDOCS) and the Research Foundation – Flanders (‘Fonds voor Wetenschappelijk Onderzoek – Vlaanderen’, G066215N, G0D5117N and G0B9317N). N.H. and A.T. acknowledge funding from the European Union's Horizon 2020 research and innovation programme - project EpiPose (Grant agreement number 101003688). This project was supported by the VERDI project (101045989), funded by the European Union. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the Health and Digital Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center), funded by the Research Foundation Flanders (FWO) and the Flemish Government department EWI. Publisher Copyright: © 2023

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N2 - 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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KW - SARS-coV-2 transmission

KW - Screening protocol

KW - Whole genome sequences

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VL - 44

JO - Epidemics

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

Abstract

Bibliographical note

Keywords

Access to Document

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VLAAI1: Flanders Artificial Intelligence Research program (FAIR) – second cycle

Cite this

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

Abstract

Bibliographical note

Keywords

Access to Document

Other files and links

Fingerprint

Projects

VLAAI1: Flanders Artificial Intelligence Research program (FAIR) – second cycle

Cite this