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Nosocomial Outbreak of SARS-CoV-2 in a “Non-COVID-19” Hospital Ward: Virus Genome Sequencing as a Key Tool to Understand Cryptic Transmission

2021-04-01Journal article Open access
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dc.contributor.authorBorges, Vítor
dc.contributor.authorIsidro, Joana
dc.contributor.authorMacedo, Filipe
dc.contributor.authorNeves, José
dc.contributor.authorSilva, Luís
dc.contributor.authorPaiva, Mário
dc.contributor.authorBarata, José
dc.contributor.authorCatarino, Judite
dc.contributor.authorCiobanu, Liliana
dc.contributor.authorDuarte, Sílvia
dc.contributor.authorVieira, Luís
dc.contributor.authorGuiomar, Raquel
dc.contributor.authorGomes, João Paulo
dc.date.accessioned2022-07-03T16:28:45Z
dc.date.available2022-07-03T16:28:45Z
dc.date.issued2021-04-01
dc.description(This article belongs to the Collection SARS-CoV-2 and COVID-19)pt_PT
dc.description.abstractDissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in healthcare institutions affects both patients and health-care workers (HCW), as well as the institutional capacity to provide essential health services. Here, we investigated an outbreak of SARS-CoV-2 in a "non-COVID-19" hospital ward unveiled by massive testing, which challenged the reconstruction of transmission chains. The contacts network during the 15-day period before the screening was investigated, and positive SARS-CoV-2 RNA samples were subjected to virus genome sequencing. Of the 245 tested individuals, 48 (21 patients and 27 HCWs) tested positive for SARS-CoV-2. HCWs were mostly asymptomatic, but the mortality among patients reached 57.1% (12/21). Phylogenetic reconstruction revealed that all cases were part of the same transmission chain. By combining contact tracing and genomic data, including analysis of emerging minor variants, we unveiled a scenario of silent SARS-CoV-2 dissemination, mostly driven by the close contact within the HCWs group and between HCWs and patients. This investigation triggered enhanced prevention and control measures, leading to more timely detection and containment of novel outbreaks. This study shows the benefit of combining genomic and epidemiological data for disclosing complex nosocomial outbreaks, and provides valuable data to prevent transmission of COVID-19 in healthcare facilities.pt_PT
dc.description.sponsorshipThis 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. This work is also a result of 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). This work was also supported by Fundos FEDER through the Programa Operacional Factores de Competitividade–COMPETE and by Fundos Nacionais through the Fundação para a Ciência e a Tecnologia within the scope of the project UID/BIM/00009/2019 (Centre for Toxicogenomics and Human Health -ToxOmics).pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationViruses. 2021 Apr 1;13(4):604. doi: 10.3390/v13040604.pt_PT
dc.identifier.doi10.3390/v13040604pt_PT
dc.identifier.issn1999-4915
dc.identifier.urihttp://hdl.handle.net/10400.18/8054
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherMDPIpt_PT
dc.relationCentre for Toxicogenomics and Human Health
dc.relation.publisherversionhttps://www.mdpi.com/1999-4915/13/4/604pt_PT
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.subjectCOVID-19pt_PT
dc.subjectSARS-CoV-2pt_PT
dc.subjectContact Tracingpt_PT
dc.subjectGenome Sequencingpt_PT
dc.subjectHealthcare Institutionpt_PT
dc.subjectNosocomial Outbreakpt_PT
dc.subjectInfecções Respiratóriaspt_PT
dc.titleNosocomial Outbreak of SARS-CoV-2 in a “Non-COVID-19” Hospital Ward: Virus Genome Sequencing as a Key Tool to Understand Cryptic Transmissionpt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleCentre for Toxicogenomics and Human Health
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UID%2FBIM%2F00009%2F2019/PT
oaire.citation.issue4pt_PT
oaire.citation.startPage604pt_PT
oaire.citation.titleVirusespt_PT
oaire.citation.volume13pt_PT
oaire.fundingStream6817 - DCRRNI ID
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.embargofctAcesso de acordo com política editorial da revista.pt_PT
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
relation.isProjectOfPublicationda24f146-9eb6-459d-8a8d-8adef9929107
relation.isProjectOfPublication.latestForDiscoveryda24f146-9eb6-459d-8a8d-8adef9929107

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