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

2020Journal article Open access
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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 (Consortium)
dc.contributor.authorPinto, M. Alice
dc.contributor.authorRodrigues, Carina
dc.date.accessioned2023-03-02T12:22:23Z
dc.date.available2023-03-02T12:22:23Z
dc.date.issued2020
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 geo-temporal 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 support population/epidemiological (founder) effects contributing to the Y839 variant super spread. 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.citationBorges, Vítor; Isidro, Joana; Cortes-Martins, Helena; Duarte, Sílvia; Vieira, Luís; Leite, Ricardo; Gordo, Isabel; Caetano, Constantino P.; Nunes, Baltazar; Sá, Regina; Oliveira, Ana; Guiomar, Raquel; Portuguese network for SARS-CoV-2 genomics (Consortium); Pinto, M. Alice; Rodrigues, Carina (2020). Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. Emerging Microbes & Infections. ISSN 2222-1751. 9:1, p. 2488-2496pt_PT
dc.identifier.doi10.1080/22221751.2020.1844552pt_PT
dc.identifier.eissn2222-1751
dc.identifier.urihttp://hdl.handle.net/10198/27403
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherTaylor & Francispt_PT
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.subjectSARS-CoV-2pt_PT
dc.subjectCOVID-19pt_PT
dc.subjectGenomic epidemiologypt_PT
dc.subjectMutationpt_PT
dc.subjectGenetic variantpt_PT
dc.subjectSpikept_PT
dc.subjectFusion peptidept_PT
dc.subjectD839Ypt_PT
dc.subjectResearch Subject Categories::MEDICINE::Microbiology, immunology, infectious diseasespt_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 & Infectionspt_PT
oaire.citation.volume9pt_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

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