Unraveling the hurdles of a large Covid-19 epidemiological investigation by viral genomics

Detalhes bibliográficos
Autor(a) principal: Sá, Regina
Data de Publicação: 2022
Outros Autores: Isidro, Joana, Borges, Vítor, Duarte, Sílvia, Vieira, Luís, Gomes, João P, Tedim, Sofia, Matias, Judite, Leite, Andreia
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10362/140923
Resumo: Copyright © 2022 The British Infection Association. Published by Elsevier Ltd. All rights reserved.
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spelling Unraveling the hurdles of a large Covid-19 epidemiological investigation by viral genomicsCOVID-19/epidemiologyDisease OutbreaksGenome, ViralGenomicsHumansSARS-CoV-2/geneticsSDG 3 - Good Health and Well-beingCopyright © 2022 The British Infection Association. Published by Elsevier Ltd. All rights reserved.COVID-19 local outbreak response relies on subjective information to reconstruct transmission chains. We assessed the concordance between epidemiologically linked cases and viral genetic profiles, in the Baixo Vouga Region (Portugal), from March to June 2020. A total of 1925 COVID-19 cases were identified, with 1143 being assigned to 154 epiclusters. Viral genomic data was available for 128 cases. Public health authorities identified two large epiclusters (280 and 101 cases each) with a central role on the spread of the disease. Still, the genomic data revealed that each epicluster included two distinct SARS-CoV-2 genetic profiles and thus more than one transmission network. We were able to show that the initial transmission dynamics reconstruction was most likely accurate, but the increasing dimension of the epiclusters and its extension to densely populated settings (healthcare and nursing home settings) triggered the misidentification of links. Genomics was also key to resolve some sporadic cases and misidentified direction of transmission. The epidemiological investigation showed a sensitivity of 70%-86% to detect transmission chains. This study contributes to the understanding of the hurdles and caveats associated with the epidemiological investigation of hundreds of community cases in the context of a massive outbreak caused by a highly transmissible and new respiratory virus.Escola Nacional de Saúde Pública (ENSP)Comprehensive Health Research Centre (CHRC) - Pólo ENSPCentro de Investigação em Saúde Pública (CISP/PHRC)RUNSá, ReginaIsidro, JoanaBorges, VítorDuarte, SílviaVieira, LuísGomes, João PTedim, SofiaMatias, JuditeLeite, Andreia2022-06-27T22:24:45Z2022-072022-07-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article11application/pdfhttp://hdl.handle.net/10362/140923eng0163-4453PURE: 44983355https://doi.org/10.1016/j.jinf.2022.05.013info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-03-11T05:18:07Zoai:run.unl.pt:10362/140923Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:49:51.495248Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv Unraveling the hurdles of a large Covid-19 epidemiological investigation by viral genomics
title Unraveling the hurdles of a large Covid-19 epidemiological investigation by viral genomics
spellingShingle Unraveling the hurdles of a large Covid-19 epidemiological investigation by viral genomics
Sá, Regina
COVID-19/epidemiology
Disease Outbreaks
Genome, Viral
Genomics
Humans
SARS-CoV-2/genetics
SDG 3 - Good Health and Well-being
title_short Unraveling the hurdles of a large Covid-19 epidemiological investigation by viral genomics
title_full Unraveling the hurdles of a large Covid-19 epidemiological investigation by viral genomics
title_fullStr Unraveling the hurdles of a large Covid-19 epidemiological investigation by viral genomics
title_full_unstemmed Unraveling the hurdles of a large Covid-19 epidemiological investigation by viral genomics
title_sort Unraveling the hurdles of a large Covid-19 epidemiological investigation by viral genomics
author Sá, Regina
author_facet Sá, Regina
Isidro, Joana
Borges, Vítor
Duarte, Sílvia
Vieira, Luís
Gomes, João P
Tedim, Sofia
Matias, Judite
Leite, Andreia
author_role author
author2 Isidro, Joana
Borges, Vítor
Duarte, Sílvia
Vieira, Luís
Gomes, João P
Tedim, Sofia
Matias, Judite
Leite, Andreia
author2_role author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Escola Nacional de Saúde Pública (ENSP)
Comprehensive Health Research Centre (CHRC) - Pólo ENSP
Centro de Investigação em Saúde Pública (CISP/PHRC)
RUN
dc.contributor.author.fl_str_mv Sá, Regina
Isidro, Joana
Borges, Vítor
Duarte, Sílvia
Vieira, Luís
Gomes, João P
Tedim, Sofia
Matias, Judite
Leite, Andreia
dc.subject.por.fl_str_mv COVID-19/epidemiology
Disease Outbreaks
Genome, Viral
Genomics
Humans
SARS-CoV-2/genetics
SDG 3 - Good Health and Well-being
topic COVID-19/epidemiology
Disease Outbreaks
Genome, Viral
Genomics
Humans
SARS-CoV-2/genetics
SDG 3 - Good Health and Well-being
description Copyright © 2022 The British Infection Association. Published by Elsevier Ltd. All rights reserved.
publishDate 2022
dc.date.none.fl_str_mv 2022-06-27T22:24:45Z
2022-07
2022-07-01T00:00:00Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10362/140923
url http://hdl.handle.net/10362/140923
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv 0163-4453
PURE: 44983355
https://doi.org/10.1016/j.jinf.2022.05.013
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 11
application/pdf
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
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