Repository logo
 
Publication

SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal

2022Journal article Open access
Simple item page
dc.contributor.authorBorges, Vítor
dc.contributor.authorIsidro, Joana
dc.contributor.authorTrovão, Nídia Sequeira
dc.contributor.authorDuarte, Sílvia
dc.contributor.authorCortes-Martins, Helena
dc.contributor.authorMartiniano, Hugo
dc.contributor.authorGordo, Isabel
dc.contributor.authorLeite, Ricardo
dc.contributor.authorVieira, Luís
dc.contributor.authorPortuguese network for SARS-CoV-2 genomics (Consortium)
dc.contributor.authorPinto, M. Alice
dc.contributor.authorRodrigues, Carina
dc.date.accessioned2022-03-23T15:11:43Z
dc.date.available2022-03-23T15:11:43Z
dc.date.issued2022
dc.description.abstractGenomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. Methods By applying recent phylodynamic models that allow integration of individual-based travel history, we reconstructed and characterized the spatio-temporal dynamics of SARSCoV-2 introductions and early dissemination in Portugal. Results We detected at least 277 independent SARS-CoV-2 introductions, mostly from European countries (namely the United Kingdom, Spain, France, Italy, and Switzerland), which were consistent with the countries with the highest connectivity with Portugal. Although most introductions were estimated to have occurred during early March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal throughout February, before the first cases were confirmed. Conclusions Here we conclude that the earlier implementation of measures could have minimized the number of introductions and subsequent virus expansion in Portugal. This study lays the foundation for genomic epidemiology of SARS-CoV-2 in Portugal, and highlights the need for systematic and geographically-representative genomic surveillance.pt_PT
dc.description.sponsorshipWe gratefully acknowledge to Sara Hill and Nuno Faria (University of Oxford) and Joshua Quick and Nick Loman (University of Birmingham) for kindly providing us with the initial sets of Artic Network primers for NGS; Rafael Mamede (MRamirez team, IMM, Lisbon) for developing and sharing a bioinformatics script for sequence curation (https://github.com/rfm-targa/BioinfUtils); Philippe Lemey (KU Leuven) for providing guidance on the implementation of the phylodynamic models; Joshua L. Cherry (National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health) for providing guidance with the subsampling strategies; and all authors, originating and submitting laboratories who have contributed genome data on GISAID (https://www.gisaid.org/) on which part of this research is based. The opinions expressed in this article are those of the authors and do not reflect the view of the National Institutes of Health, the Department of Health and Human Services, or the United States government. This study is co-funded by Fundação para a Ciência e Tecnologia and Agência de Investigação Clínica e Inovação Biomédica (234_596874175) on behalf of the Research 4 COVID-19 call. Some infrastructural resources used in this study come from the GenomePT project (POCI-01-0145-FEDER-022184), supported by COMPETE 2020 - Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by Fundação para a Ciência e a Tecnologia (FCT).pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationBorges, Vítor; Isidro, Joana; Trovão, Nídia Sequeira; Duarte, Sílvia; Cortes-Martins, Helena; Martiniano, Hugo; Gordo, Isabel; Leite, Ricardo; Vieira, Luís, Portuguese network for SARS-CoV-2 genomics (Consortium); Pinto, M. Alice; Rodrigues, Carina (2022). SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal. Communications Medicine. ISSN 2730-664X. 2:1, p. 1-11pt_PT
dc.identifier.doi10.1038/s43856-022-00072-0pt_PT
dc.identifier.issn2730-664X
dc.identifier.urihttp://hdl.handle.net/10198/25275
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.subjectSARS-CoV-2 infectionpt_PT
dc.subjectSurveillancept_PT
dc.subjectPortugalpt_PT
dc.titleSARS-CoV-2 introductions and early dynamics of the epidemic in Portugalpt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.citation.issue1pt_PT
oaire.citation.titleCommunications Medicinept_PT
oaire.citation.volume2pt_PT
person.familyNamePinto
person.familyNameRodrigues
person.givenNameM. Alice
person.givenNameCarina
person.identifier.ciencia-idF814-A1D0-8318
person.identifier.ciencia-idC415-C677-0253
person.identifier.orcid0000-0001-9663-8399
person.identifier.orcid0000-0001-9773-1413
person.identifier.scopus-author-id8085507800
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
relation.isAuthorOfPublication0667fe04-7078-483d-9198-56d167b19bc5
relation.isAuthorOfPublicationef666665-6593-48be-bc48-6a1bb58bedbd
relation.isAuthorOfPublication.latestForDiscovery0667fe04-7078-483d-9198-56d167b19bc5

Files

Original bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
SARS-CoV-2 introductions and early dynamics of.pdf
Size:
2.08 MB
Format:
Adobe Portable Document Format
Download

Collections

CIMO - Artigos em Revistas Não Indexados à WoS/Scopus