Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal
Autor(a) principal: | |
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Data de Publicação: | 2020 |
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/10198/27403 |
Resumo: | Genomic 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. |
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Massive dissemination of a SARS-CoV-2 Spike Y839 variant in PortugalSARS-CoV-2COVID-19Genomic epidemiologyMutationGenetic variantSpikeFusion peptideD839YResearch Subject Categories::MEDICINE::Microbiology, immunology, infectious diseasesGenomic 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.This 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).Taylor & FrancisBiblioteca Digital do IPBBorges, VítorIsidro, JoanaCortes-Martins, HelenaDuarte, SílviaVieira, LuísLeite, RicardoGordo, IsabelCaetano, Constantino P.Nunes, BaltazarSá, ReginaOliveira, AnaGuiomar, RaquelPortuguese network for SARS-CoV-2 genomics (Consortium)Pinto, M. AliceRodrigues, Carina2023-03-02T12:22:23Z20202020-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10198/27403engBorges, 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. 2488-249610.1080/22221751.2020.18445522222-1751info: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:RCAAP2023-11-21T11:00:22Zoai:bibliotecadigital.ipb.pt:10198/27403Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T23:17:32.531715Repositório 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 |
Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal |
title |
Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal |
spellingShingle |
Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal Borges, Vítor SARS-CoV-2 COVID-19 Genomic epidemiology Mutation Genetic variant Spike Fusion peptide D839Y Research Subject Categories::MEDICINE::Microbiology, immunology, infectious diseases |
title_short |
Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal |
title_full |
Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal |
title_fullStr |
Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal |
title_full_unstemmed |
Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal |
title_sort |
Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal |
author |
Borges, Vítor |
author_facet |
Borges, 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 |
author_role |
author |
author2 |
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 |
author2_role |
author author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Biblioteca Digital do IPB |
dc.contributor.author.fl_str_mv |
Borges, 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 |
dc.subject.por.fl_str_mv |
SARS-CoV-2 COVID-19 Genomic epidemiology Mutation Genetic variant Spike Fusion peptide D839Y Research Subject Categories::MEDICINE::Microbiology, immunology, infectious diseases |
topic |
SARS-CoV-2 COVID-19 Genomic epidemiology Mutation Genetic variant Spike Fusion peptide D839Y Research Subject Categories::MEDICINE::Microbiology, immunology, infectious diseases |
description |
Genomic 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. |
publishDate |
2020 |
dc.date.none.fl_str_mv |
2020 2020-01-01T00:00:00Z 2023-03-02T12:22:23Z |
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/10198/27403 |
url |
http://hdl.handle.net/10198/27403 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Borges, 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. 2488-2496 10.1080/22221751.2020.1844552 2222-1751 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Taylor & Francis |
publisher.none.fl_str_mv |
Taylor & Francis |
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 |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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1817554182030229504 |