Epidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil
Autor(a) principal: | |
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Data de Publicação: | 2021 |
Outros Autores: | , , , , , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | por |
Título da fonte: | Repositório Institucional da UFMG |
Texto Completo: | https://doi.org/10.1093/ve/veab087 http://hdl.handle.net/1843/56354 https://orcid.org/0000-0002-7162-5070 https://orcid.org/0000-0001-6587-3871 https://orcid.org/0000-0003-2970-7889 https://orcid.org/0000-0001-5255-5938 https://orcid.org/0000-0003-0348-8374 https://orcid.org/0000-0002-1970-8936 https://orcid.org/0009-0001-0494-2631 https://orcid.org/0000-0001-5182-4366 https://orcid.org/0000-0002-4746-6049 https://orcid.org/0000-0003-3644-0246 https://orcid.org/0000-0003-1382-9988 https://orcid.org/0000-0002-7660-7058 https://orcid.org/0000-0002-6177-163X https://orcid.org/0000-0001-6235-8807 https://orcid.org/0000-0001-7919-612X https://orcid.org/0000-0001-9372-6561 |
Resumo: | The emergence and widespread circulation of severe acute respiratory syndrome coronavirus 2 variants of concern (VOCs) or interest impose an enhanced threat to global public health. In Brazil, one of the countries most severely impacted throughout the pandemic, a complex dynamics involving variants co-circulation and turnover events has been recorded with the emergence and spread of VOC Gamma in Manaus in late 2020. In this context, we present a genomic epidemiology investigation based on samples collected between December 2020 and May 2021 in the second major Brazilian metropolis, Rio de Janeiro. By sequencing 244 novel genomes through all epidemiological weeks in this period, we were able to document the introduction and rapid dissemination of VOC Gamma in the city, driving the rise of the third local epidemic wave. Molecular clock analysis indicates that this variant has circulated locally since the first weeks of 2021 and only 7 weeks were necessary for it to achieve a frequency above 70per cent, consistent with rates of growth observedinManausandotherstates.Moreover,aBayesianphylogeographicreconstructionindicatesthatVOCGammaspreadthroughout Brazil between December 2020 and January 2021 and that it was introduced in Rio de Janeiro through at least 13 events coming from nearly all regions of the country. Comparative analysis of reverse transcription-quantitative polymerase chain reaction (RT-qPCR) cycle threshold (Ct) values provides further evidence that VOC Gamma induces higher viral loads (N1 target; mean reduction of Ct: 2.7, 95percentconfidenceinterval=±0.7).Thisanalysiscorroboratesthepreviouslyproposedmechanisticbasisforthisvariant-enhanced transmissibility and distinguished epidemiological behavior. Our results document the evolution of VOC Gamma and provide independent assessment of scenarios previously studied in Manaus, therefore contributing to the better understanding of the epidemiological dynamics currently being surveyed in other Brazilian regions. |
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2023-07-15T00:17:12Z2023-07-15T00:17:12Z202172111https://doi.org/10.1093/ve/veab0872057-1577http://hdl.handle.net/1843/56354https://orcid.org/0000-0002-7162-5070https://orcid.org/0000-0001-6587-3871https://orcid.org/0000-0003-2970-7889https://orcid.org/0000-0001-5255-5938https://orcid.org/0000-0003-0348-8374https://orcid.org/0000-0002-1970-8936https://orcid.org/0009-0001-0494-2631https://orcid.org/0000-0001-5182-4366https://orcid.org/0000-0002-4746-6049https://orcid.org/0000-0003-3644-0246https://orcid.org/0000-0003-1382-9988https://orcid.org/0000-0002-7660-7058https://orcid.org/0000-0002-6177-163Xhttps://orcid.org/0000-0001-6235-8807https://orcid.org/0000-0001-7919-612Xhttps://orcid.org/0000-0001-9372-6561The emergence and widespread circulation of severe acute respiratory syndrome coronavirus 2 variants of concern (VOCs) or interest impose an enhanced threat to global public health. In Brazil, one of the countries most severely impacted throughout the pandemic, a complex dynamics involving variants co-circulation and turnover events has been recorded with the emergence and spread of VOC Gamma in Manaus in late 2020. In this context, we present a genomic epidemiology investigation based on samples collected between December 2020 and May 2021 in the second major Brazilian metropolis, Rio de Janeiro. By sequencing 244 novel genomes through all epidemiological weeks in this period, we were able to document the introduction and rapid dissemination of VOC Gamma in the city, driving the rise of the third local epidemic wave. Molecular clock analysis indicates that this variant has circulated locally since the first weeks of 2021 and only 7 weeks were necessary for it to achieve a frequency above 70per cent, consistent with rates of growth observedinManausandotherstates.Moreover,aBayesianphylogeographicreconstructionindicatesthatVOCGammaspreadthroughout Brazil between December 2020 and January 2021 and that it was introduced in Rio de Janeiro through at least 13 events coming from nearly all regions of the country. Comparative analysis of reverse transcription-quantitative polymerase chain reaction (RT-qPCR) cycle threshold (Ct) values provides further evidence that VOC Gamma induces higher viral loads (N1 target; mean reduction of Ct: 2.7, 95percentconfidenceinterval=±0.7).Thisanalysiscorroboratesthepreviouslyproposedmechanisticbasisforthisvariant-enhanced transmissibility and distinguished epidemiological behavior. Our results document the evolution of VOC Gamma and provide independent assessment of scenarios previously studied in Manaus, therefore contributing to the better understanding of the epidemiological dynamics currently being surveyed in other Brazilian regions.porUniversidade Federal de Minas GeraisUFMGBrasilICB - INSTITUTO DE CIÊNCIAS BIOLOGICASVirus EvolutionCOVID-19BrasilSARS-CoV-2COVID-19Variant of concern GammaLineage P.1Rio de JaneiroBrazilPhylodynamicsPhylogeographyEpidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazilinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttps://academic.oup.com/ve/article/7/2/veab087/6378621?login=trueFilipe Romero Rebello MoreiraMarcelo Calado de Paula TôrresRaíssa Mirella dos Santos Cunha da CostaCássia Cristina Alves GonçalvesDébora Souza FaffeRafael Mello GalliezOrlando da Costa Ferreira JuniorRenato Santana de AguiarAndré Felipe Andrade dos SantosCarolina Moreira VolochTerezinha Marta Pereira Pinto CastiñeirasMirela D'arcAmilcar TanuriDiana MarianiAlice Laschuk HerlingerFrancine Bittencourt SchifflerÁtila Duque RossiIsabela de Carvalho LeitãoThamiris dos Santos MirandaMatheus Augusto Calvano Cosentinoinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da UFMGinstname:Universidade Federal de Minas Gerais (UFMG)instacron:UFMGLICENSELicense.txtLicense.txttext/plain; charset=utf-82042https://repositorio.ufmg.br/bitstream/1843/56354/1/License.txtfa505098d172de0bc8864fc1287ffe22MD51ORIGINALEpidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil.pdfEpidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil.pdfapplication/pdf959335https://repositorio.ufmg.br/bitstream/1843/56354/2/Epidemiological%20dynamics%20of%20SARS-CoV-2%20VOC%20Gamma%20in%20Rio%20de%20Janeiro%2c%20Brazil.pdf2ad1f57d0ec1cc73363882b5672fb2cfMD521843/563542023-07-14 21:17:12.976oai:repositorio.ufmg.br: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Repositório de PublicaçõesPUBhttps://repositorio.ufmg.br/oaiopendoar:2023-07-15T00:17:12Repositório Institucional da UFMG - Universidade Federal de Minas Gerais (UFMG)false |
dc.title.pt_BR.fl_str_mv |
Epidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil |
title |
Epidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil |
spellingShingle |
Epidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil Filipe Romero Rebello Moreira SARS-CoV-2 COVID-19 Variant of concern Gamma Lineage P.1 Rio de Janeiro Brazil Phylodynamics Phylogeography COVID-19 Brasil |
title_short |
Epidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil |
title_full |
Epidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil |
title_fullStr |
Epidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil |
title_full_unstemmed |
Epidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil |
title_sort |
Epidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil |
author |
Filipe Romero Rebello Moreira |
author_facet |
Filipe Romero Rebello Moreira Marcelo Calado de Paula Tôrres Raíssa Mirella dos Santos Cunha da Costa Cássia Cristina Alves Gonçalves Débora Souza Faffe Rafael Mello Galliez Orlando da Costa Ferreira Junior Renato Santana de Aguiar André Felipe Andrade dos Santos Carolina Moreira Voloch Terezinha Marta Pereira Pinto Castiñeiras Mirela D'arc Amilcar Tanuri Diana Mariani Alice Laschuk Herlinger Francine Bittencourt Schiffler Átila Duque Rossi Isabela de Carvalho Leitão Thamiris dos Santos Miranda Matheus Augusto Calvano Cosentino |
author_role |
author |
author2 |
Marcelo Calado de Paula Tôrres Raíssa Mirella dos Santos Cunha da Costa Cássia Cristina Alves Gonçalves Débora Souza Faffe Rafael Mello Galliez Orlando da Costa Ferreira Junior Renato Santana de Aguiar André Felipe Andrade dos Santos Carolina Moreira Voloch Terezinha Marta Pereira Pinto Castiñeiras Mirela D'arc Amilcar Tanuri Diana Mariani Alice Laschuk Herlinger Francine Bittencourt Schiffler Átila Duque Rossi Isabela de Carvalho Leitão Thamiris dos Santos Miranda Matheus Augusto Calvano Cosentino |
author2_role |
author author author author author author author author author author author author author author author author author author author |
dc.contributor.author.fl_str_mv |
Filipe Romero Rebello Moreira Marcelo Calado de Paula Tôrres Raíssa Mirella dos Santos Cunha da Costa Cássia Cristina Alves Gonçalves Débora Souza Faffe Rafael Mello Galliez Orlando da Costa Ferreira Junior Renato Santana de Aguiar André Felipe Andrade dos Santos Carolina Moreira Voloch Terezinha Marta Pereira Pinto Castiñeiras Mirela D'arc Amilcar Tanuri Diana Mariani Alice Laschuk Herlinger Francine Bittencourt Schiffler Átila Duque Rossi Isabela de Carvalho Leitão Thamiris dos Santos Miranda Matheus Augusto Calvano Cosentino |
dc.subject.por.fl_str_mv |
SARS-CoV-2 COVID-19 Variant of concern Gamma Lineage P.1 Rio de Janeiro Brazil Phylodynamics Phylogeography |
topic |
SARS-CoV-2 COVID-19 Variant of concern Gamma Lineage P.1 Rio de Janeiro Brazil Phylodynamics Phylogeography COVID-19 Brasil |
dc.subject.other.pt_BR.fl_str_mv |
COVID-19 Brasil |
description |
The emergence and widespread circulation of severe acute respiratory syndrome coronavirus 2 variants of concern (VOCs) or interest impose an enhanced threat to global public health. In Brazil, one of the countries most severely impacted throughout the pandemic, a complex dynamics involving variants co-circulation and turnover events has been recorded with the emergence and spread of VOC Gamma in Manaus in late 2020. In this context, we present a genomic epidemiology investigation based on samples collected between December 2020 and May 2021 in the second major Brazilian metropolis, Rio de Janeiro. By sequencing 244 novel genomes through all epidemiological weeks in this period, we were able to document the introduction and rapid dissemination of VOC Gamma in the city, driving the rise of the third local epidemic wave. Molecular clock analysis indicates that this variant has circulated locally since the first weeks of 2021 and only 7 weeks were necessary for it to achieve a frequency above 70per cent, consistent with rates of growth observedinManausandotherstates.Moreover,aBayesianphylogeographicreconstructionindicatesthatVOCGammaspreadthroughout Brazil between December 2020 and January 2021 and that it was introduced in Rio de Janeiro through at least 13 events coming from nearly all regions of the country. Comparative analysis of reverse transcription-quantitative polymerase chain reaction (RT-qPCR) cycle threshold (Ct) values provides further evidence that VOC Gamma induces higher viral loads (N1 target; mean reduction of Ct: 2.7, 95percentconfidenceinterval=±0.7).Thisanalysiscorroboratesthepreviouslyproposedmechanisticbasisforthisvariant-enhanced transmissibility and distinguished epidemiological behavior. Our results document the evolution of VOC Gamma and provide independent assessment of scenarios previously studied in Manaus, therefore contributing to the better understanding of the epidemiological dynamics currently being surveyed in other Brazilian regions. |
publishDate |
2021 |
dc.date.issued.fl_str_mv |
2021 |
dc.date.accessioned.fl_str_mv |
2023-07-15T00:17:12Z |
dc.date.available.fl_str_mv |
2023-07-15T00:17:12Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
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info:eu-repo/semantics/article |
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article |
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publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/1843/56354 |
dc.identifier.doi.pt_BR.fl_str_mv |
https://doi.org/10.1093/ve/veab087 |
dc.identifier.issn.pt_BR.fl_str_mv |
2057-1577 |
dc.identifier.orcid.pt_BR.fl_str_mv |
https://orcid.org/0000-0002-7162-5070 https://orcid.org/0000-0001-6587-3871 https://orcid.org/0000-0003-2970-7889 https://orcid.org/0000-0001-5255-5938 https://orcid.org/0000-0003-0348-8374 https://orcid.org/0000-0002-1970-8936 https://orcid.org/0009-0001-0494-2631 https://orcid.org/0000-0001-5182-4366 https://orcid.org/0000-0002-4746-6049 https://orcid.org/0000-0003-3644-0246 https://orcid.org/0000-0003-1382-9988 https://orcid.org/0000-0002-7660-7058 https://orcid.org/0000-0002-6177-163X https://orcid.org/0000-0001-6235-8807 https://orcid.org/0000-0001-7919-612X https://orcid.org/0000-0001-9372-6561 |
url |
https://doi.org/10.1093/ve/veab087 http://hdl.handle.net/1843/56354 https://orcid.org/0000-0002-7162-5070 https://orcid.org/0000-0001-6587-3871 https://orcid.org/0000-0003-2970-7889 https://orcid.org/0000-0001-5255-5938 https://orcid.org/0000-0003-0348-8374 https://orcid.org/0000-0002-1970-8936 https://orcid.org/0009-0001-0494-2631 https://orcid.org/0000-0001-5182-4366 https://orcid.org/0000-0002-4746-6049 https://orcid.org/0000-0003-3644-0246 https://orcid.org/0000-0003-1382-9988 https://orcid.org/0000-0002-7660-7058 https://orcid.org/0000-0002-6177-163X https://orcid.org/0000-0001-6235-8807 https://orcid.org/0000-0001-7919-612X https://orcid.org/0000-0001-9372-6561 |
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2057-1577 |
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Virus Evolution |
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Universidade Federal de Minas Gerais |
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ICB - INSTITUTO DE CIÊNCIAS BIOLOGICAS |
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Universidade Federal de Minas Gerais |
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