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Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal

2020-12Artigo científico Acesso aberto
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dc.contributor.authorBorges, Vítor
dc.contributor.authorIsidro, Joana
dc.contributor.authorCortes-Martins, Helena
dc.contributor.authorDuarte, Sílvia
dc.contributor.authorVieira, Luís
dc.contributor.authorLeite, Ricardo
dc.contributor.authorGordo, Isabel
dc.contributor.authorCaetano, Constantino P.
dc.contributor.authorNunes, Baltazar
dc.contributor.authorSá, Regina
dc.contributor.authorOliveira, Ana
dc.contributor.authorGuiomar, Raquel
dc.contributor.authorPortuguese network for SARS-CoV-2 genomics
dc.contributor.authorGomes, João Paulo
dc.date.accessioned2021-03-31T14:52:22Z
dc.date.available2021-03-31T14:52:22Z
dc.date.issued2020-12
dc.description.abstractGenomic surveillance of SARS-CoV-2 was rapidly implemented in Portugal by the National Institute of Health in collaboration with a nationwide consortium of >50 hospitals/laboratories. Here, we track the geotemporal spread of a SARS-CoV-2 variant with a mutation (D839Y) in a potential host-interacting region involving the Spike fusion peptide, which is a target motif of anti-viral drugs that plays a key role in SARS-CoV-2 infectivity. The Spike Y839 variant was most likely imported from Italy in mid-late February and massively disseminated in Portugal during the early epidemic, becoming prevalent in the Northern and Central regions of Portugal where it represented 22% and 59% of the sampled genomes, respectively, by 30 April. Based on our high sequencing sampling during the early epidemics [15.5% (1275/8251) and 6.0% (1500/24987) of all confirmed cases until the end of March and April, respectively], we estimate that, between 14 March and 9 April (covering the epidemic exponential phase) the relative frequency of the Spike Y839 variant increased at a rate of 12.1% (6.1%-18.2%, CI 95%) every three days, being potentially associated with 24.8% (20.8-29.7%, CI 95%; 3177-4542 cases, CI 95%) of all COVID-19 cases in Portugal during this period. Our data supports population/epidemiological (founder) effects contributing to the Y839 variant superspread. The potential existence of selective advantage is also discussed, although experimental validation is required. Despite huge differences in genome sampling worldwide, SARS-CoV-2 Spike D839Y has been detected in 13 countries in four continents, supporting the need for close surveillance and functional assays of Spike variants.pt_PT
dc.description.sponsorshipThis study is co-funded by Fundação para a Ciência e a Tecnologia and Agência de Investigação Clínica e Inovação Biomédica [grant number 234_596874175] on behalf of the Research 4 COVID-19 call. This work is also a result of the GenomePT project [grant number 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.citationEmerg Microbes Infect. 2020 Dec;9(1):2488-2496. doi: 10.1080/22221751.2020.1844552pt_PT
dc.identifier.doi10.1080/22221751.2020.1844552pt_PT
dc.identifier.issn2222-1751
dc.identifier.urihttp://hdl.handle.net/10400.18/7607
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherTaylor & Francis/ Shanghai Shangyixun Cultural Communicationpt_PT
dc.relation.publisherversionhttps://www.tandfonline.com/doi/full/10.1080/22221751.2020.1844552pt_PT
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.subjectCOVID-19pt_PT
dc.subjectEpidemiological Monitoringpt_PT
dc.subjectGenomicspt_PT
dc.subjectHigh-Throughput Nucleotide Sequencingpt_PT
dc.subjectHumanspt_PT
dc.subjectPhylogenypt_PT
dc.subjectPortugalpt_PT
dc.subjectSARS-CoV-2pt_PT
dc.subjectSeverity of Illness Indexpt_PT
dc.subjectSpike Glycoprotein, Coronaviruspt_PT
dc.subjectGenome, Viralpt_PT
dc.subjectMutationpt_PT
dc.subjectPandemicspt_PT
dc.subjectInfecções Respiratóriaspt_PT
dc.subjectEstados de Saúde e de Doençapt_PT
dc.titleMassive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugalpt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.citation.endPage2496pt_PT
oaire.citation.issue1pt_PT
oaire.citation.startPage2488pt_PT
oaire.citation.titleEmerging Microbes and Infectionspt_PT
oaire.citation.volume9pt_PT
rcaap.embargofctAcesso de acordo com página web do editor da revista.pt_PT
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT

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