Unraveling the hurdles of a large Covid-19 epidemiological investigation by viral genomics
Autor(a) principal: | |
---|---|
Data de Publicação: | 2022 |
Outros Autores: | , , , , , , , |
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. |
id |
RCAP_c4fe488daff303d5945a18845a9df96a |
---|---|
oai_identifier_str |
oai:run.unl.pt:10362/140923 |
network_acronym_str |
RCAP |
network_name_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository_id_str |
7160 |
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 |
repository.mail.fl_str_mv |
|
_version_ |
1799138096478945280 |