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Kremer C, Torneri A, Libin PJK, Meex C, Hayette MP, Bontems S, Durkin K, Artesi M, Bours V, Lemey P, Darcis G, Hens N, Meuris C. Reconstruction of SARS-CoV-2 outbreaks in a primary school using epidemiological and genomic data. Epidemics 2023; 44:100701. [PMID: 37379776 PMCID: PMC10273772 DOI: 10.1016/j.epidem.2023.100701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 06/02/2023] [Accepted: 06/12/2023] [Indexed: 06/30/2023] Open
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.
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Affiliation(s)
- Cécile Kremer
- Interuniversity Institute for Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Hasselt, Belgium.
| | - Andrea Torneri
- Interuniversity Institute for Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Hasselt, Belgium
| | - Pieter J K Libin
- 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
| | - Cécile Meex
- Department of Clinical Microbiology, University of Liège, Liège, Belgium
| | | | - Sébastien Bontems
- Department of Clinical Microbiology, University of Liège, Liège, Belgium
| | - Keith Durkin
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, Liège, Belgium
| | - Maria Artesi
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, Liège, Belgium
| | - Vincent Bours
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, Liège, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
| | - Gilles Darcis
- Department of Infectious Diseases, Liège University Hospital, Liège, Belgium
| | - Niel Hens
- 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
| | - Christelle Meuris
- Department of Infectious Diseases, Liège University Hospital, Liège, Belgium
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Hjorleifsson KE, Rognvaldsson S, Jonsson H, Agustsdottir AB, Andresdottir M, Birgisdottir K, Eiriksson O, Eythorsson ES, Fridriksdottir R, Georgsson G, Gudmundsson KR, Gylfason A, Haraldsdottir G, Jensson BO, Jonasdotti A, Jonasdottir A, Josefsdottir KS, Kristinsdottir N, Kristjansdottir B, Kristjansson T, Magnusdottir DN, Palsson R, le Roux L, Sigurbergsdottir GM, Sigurdsson A, Sigurdsson MI, Sveinbjornsson G, Thorarensen EA, Thorbjornsson B, Thordardottir M, Helgason A, Holm H, Jonsdottir I, Jonsson F, Magnusson OT, Masson G, Norddahl GL, Saemundsdottir J, Sulem P, Thorsteinsdottir U, Gudbjartsson DF, Melsted P, Stefansson K. Reconstruction of a large-scale outbreak of SARS-CoV-2 infection in Iceland informs vaccination strategies. Clin Microbiol Infect 2022; 28:852-858. [PMID: 35182757 PMCID: PMC8849849 DOI: 10.1016/j.cmi.2022.02.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 01/19/2022] [Accepted: 02/05/2022] [Indexed: 12/11/2022]
Abstract
OBJECTIVES The spread of SARS-CoV-2 is dependent on several factors, both biological and behavioural. The effectiveness of nonpharmaceutical interventions can be attributed largely to changes in human behaviour, but quantifying this effect remains challenging. Reconstructing the transmission tree of the third wave of SARS-CoV-2 infections in Iceland using contact tracing and viral sequence data from 2522 cases enables us to directly compare the infectiousness of distinct groups of persons. METHODS The transmission tree enables us to model the effect that a given population prevalence of vaccination would have had on the third wave had one of three different vaccination strategies been implemented before that time. This allows us to compare the effectiveness of the strategies in terms of minimizing the number of cases, deaths, critical cases, and severe cases. RESULTS We found that people diagnosed outside of quarantine (Rˆ=1.31) were 89% more infectious than those diagnosed while in quarantine (Rˆ=0.70) and that infectiousness decreased as a function of time spent in quarantine before diagnosis, with people diagnosed outside of quarantine being 144% more infectious than those diagnosed after ≥3 days in quarantine (Rˆ=0.54). People of working age, 16 to 66 years (Rˆ=1.08), were 46% more infectious than those outside of that age range (Rˆ=0.74). DISCUSSION We found that vaccinating the population in order of ascending age or uniformly at random would have prevented more infections per vaccination than vaccinating in order of descending age, without significantly affecting the expected number of deaths, critical cases, or severe cases.
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Affiliation(s)
- Kristjan E Hjorleifsson
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA
| | | | | | | | | | | | | | - Elias S Eythorsson
- Internal Medicine Services, Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Runolfur Palsson
- Internal Medicine Services, Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Martin I Sigurdsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Operative Services, Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland
| | | | | | | | | | - Agnar Helgason
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Hilma Holm
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland
| | - Ingileif Jonsdottir
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | | | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Pall Melsted
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland.
| | - Kari Stefansson
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
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Perini M, Batisti Biffignandi G, Di Carlo D, Pasala AR, Piazza A, Panelli S, Zuccotti GV, Comandatore F. MeltingPlot, a user-friendly online tool for epidemiological investigation using High Resolution Melting data. BMC Bioinformatics 2021; 22:76. [PMID: 33602119 PMCID: PMC7891011 DOI: 10.1186/s12859-021-04020-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/11/2021] [Indexed: 11/18/2022] Open
Abstract
Background The rapid identification of pathogen clones is pivotal for effective epidemiological control strategies in hospital settings. High Resolution Melting (HRM) is a molecular biology technique suitable for fast and inexpensive pathogen typing protocols. Unfortunately, the mathematical/informatics skills required to analyse HRM data for pathogen typing likely limit the application of this promising technique in hospital settings. Results MeltingPlot is the first tool specifically designed for epidemiological investigations using HRM data, easing the application of HRM typing to large real-time surveillance and rapid outbreak reconstructions. MeltingPlot implements a graph-based algorithm designed to discriminate pathogen clones on the basis of HRM data, producing portable typing results. The tool also merges typing information with isolates and patients metadata to create graphical and tabular outputs useful in epidemiological investigations and it runs in a few seconds even with hundreds of isolates. Availability: https://skynet.unimi.it/index.php/tools/meltingplot/. Conclusions The analysis and result interpretation of HRM typing protocols can be not trivial and this likely limited its application in hospital settings. MeltingPlot is a web tool designed to help the user to reconstruct epidemiological events by combining HRM-based clustering methods and the isolate/patient metadata. The tool can be used for the implementation of HRM based real time large scale surveillance programs in hospital settings.
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Affiliation(s)
- Matteo Perini
- Department of Biomedical and Clinical Sciences "L. Sacco", Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Gherard Batisti Biffignandi
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, 27100, Italia
| | - Domenico Di Carlo
- Department of Biomedical and Clinical Sciences "L. Sacco", Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Ajay Ratan Pasala
- Department of Biomedical and Clinical Sciences "L. Sacco", Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Aurora Piazza
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, 27100, Italia
| | - Simona Panelli
- Department of Biomedical and Clinical Sciences "L. Sacco", Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Gian Vincenzo Zuccotti
- Department of Biomedical and Clinical Sciences "L. Sacco", Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy.,Department of Pediatrics, Children's Hospital Vittore Buzzi, Università Di Milano, Milan, Italy
| | - Francesco Comandatore
- Department of Biomedical and Clinical Sciences "L. Sacco", Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy.
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