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

Detalhes bibliográficos
Autor(a) principal: Portuguese network for SARS-CoV-2 genomics
Data de Publicação: 2020
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10362/108223
Resumo: Funding 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).
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spelling Massive dissemination of a SARS-CoV-2 Spike Y839 variant in PortugalCOVID-19D839Yfusion peptidegenetic variantgenomic epidemiologymutationSARS-CoV-2SpikeParasitologyEpidemiologyMicrobiologyImmunologyDrug DiscoveryVirologyInfectious DiseasesSDG 3 - Good Health and Well-beingFunding 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).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 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.Centre for Toxicogenomics and Human Health (ToxOmics)NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM)Centro de Investigação em Saúde Pública (CISP/PHRC)Escola Nacional de Saúde Pública (ENSP)Centro de Estudos de Doenças Crónicas (CEDOC)RUNPortuguese network for SARS-CoV-2 genomics2020-12-05T00:28:55Z2020-122020-12-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article9application/pdfhttp://hdl.handle.net/10362/108223engPURE: 26714185https://doi.org/10.1080/22221751.2020.1844552info: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:RCAAP2024-03-11T04:52:51Zoai:run.unl.pt:10362/108223Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:41:09.057510Repositório 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
Portuguese network for SARS-CoV-2 genomics
COVID-19
D839Y
fusion peptide
genetic variant
genomic epidemiology
mutation
SARS-CoV-2
Spike
Parasitology
Epidemiology
Microbiology
Immunology
Drug Discovery
Virology
Infectious Diseases
SDG 3 - Good Health and Well-being
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 Portuguese network for SARS-CoV-2 genomics
author_facet Portuguese network for SARS-CoV-2 genomics
author_role author
dc.contributor.none.fl_str_mv Centre for Toxicogenomics and Human Health (ToxOmics)
NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM)
Centro de Investigação em Saúde Pública (CISP/PHRC)
Escola Nacional de Saúde Pública (ENSP)
Centro de Estudos de Doenças Crónicas (CEDOC)
RUN
dc.contributor.author.fl_str_mv Portuguese network for SARS-CoV-2 genomics
dc.subject.por.fl_str_mv COVID-19
D839Y
fusion peptide
genetic variant
genomic epidemiology
mutation
SARS-CoV-2
Spike
Parasitology
Epidemiology
Microbiology
Immunology
Drug Discovery
Virology
Infectious Diseases
SDG 3 - Good Health and Well-being
topic COVID-19
D839Y
fusion peptide
genetic variant
genomic epidemiology
mutation
SARS-CoV-2
Spike
Parasitology
Epidemiology
Microbiology
Immunology
Drug Discovery
Virology
Infectious Diseases
SDG 3 - Good Health and Well-being
description Funding 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).
publishDate 2020
dc.date.none.fl_str_mv 2020-12-05T00:28:55Z
2020-12
2020-12-01T00:00:00Z
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/10362/108223
url http://hdl.handle.net/10362/108223
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv PURE: 26714185
https://doi.org/10.1080/22221751.2020.1844552
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 9
application/pdf
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
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
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