Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 lineages Gamma and P.2 in Brazil
| Autor(a) principal: | |
|---|---|
| Data de Publicação: | 2022 |
| Outros Autores: | , , , , , , , , , , , , , , , , , |
| Tipo de documento: | Artigo |
| Idioma: | por |
| Título da fonte: | Repositório Institucional da FIOCRUZ (ARCA) |
| Texto Completo: | https://www.arca.fiocruz.br/handle/icict/52502 |
Resumo: | Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, Brasil. |
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Graf, TiagoBello, GonzaloNaveca, Felipe GomesGomes, MarceloCardoso, Vanessa Leiko OikawaSilva, Alexandre Freitas daDezordi, Filipe ZimmerSantos, Mirleide Cordeiro dosSantos, Katia Correa de OliveiraBatista, Érika Lopes RochaMagalhães, Alessandro Leonardo ÁlvaresVinhal, FernandoMiyajima, FábioFaoro, HelissonKhouri, RicardoWallau, Gabriel LuzDelatorre, EdsonSiqueira, Marilda MendonçaResende, Paola Cristina2022-05-02T16:17:12Z2022-05-02T16:17:12Z2022GRAF, Tiago et al. Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 lineages Gamma and P.2 in Brazil. iScience, v. 25 n. 104156 , p. 1–16, 2022.2589-0042https://www.arca.fiocruz.br/handle/icict/5250210.1016/ j.isci.2022.104156porCell PressSARS-CoV-2COVID-19Linhagem P.2Linhagem GammaLineage P.2Lineage GammaDisease Transmission, InfectiousPandemicsCommunicable PeriodTransmisión de Enfermedad InfecciosaPandemiasPeriodo de TransmisiónTransmission de maladie infectieusePandémiesPériode de TransmissionTransmissão de Doença InfecciosaPandemiasPeríodo de TransmissibilidadePhylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 lineages Gamma and P.2 in Brazilinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de AIDS e Imunologia Molecular. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Leônidas e Maria Deane. Laboratório de Ecologia de Doenças Transmissíveis na Amazônia. Manaus, AM, Brasil.Fundação Oswaldo Cruz. Presidência. Programa de Computação Científica. Grupo de Métodos Analíticos em Vigilância Epidemiológica. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, Brasil.Fundação Oswaldo Cruz. Instituto Aggeu Magalhães. Recife, PE, Brasil.Fundação Oswaldo Cruz. Instituto Aggeu Magalhães. Recife, PE, Brasil.Instituto Nacional de Infectologia Evandro Chagas. Belém, PA, Brasil.Instituto Adolfo Lutz. São Paulo, SP, Brasil.Secretaria Municipal de Saúde de Aparecida de Goiânia. Aparecida de Goiânia, GO, Brasil.Secretaria Municipal de Saúde de Aparecida de Goiânia. Aparecida de Goiânia, GO, Brasil.Lab HLAGYN. Goiânia. GO, Brasil.Fundação Oswaldo Cruz. Fiocruz Ceará. Eusébio, CE, Brasil.Fundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, Brasil.Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, Brasil.Fundação Oswaldo Cruz. Instituto Aggeu Magalhães. Recife, PE, Brasil.Universidade Federal do Espírito Santo. Centro de Ciencias Exatas, Naturais e da Saude. Departamento de Biologia. Alegre, ES, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Vírus Respiratórios e Sarampo. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Vírus Respiratórios e Sarampo. Rio de Janeiro, RJ, Brasil.The COVID-19 epidemic in Brazil experienced two major lineage replacements until mid-2021. The first was driven by lineage P.2, in late 2020, and the second by lineage Gamma, in early 2021. To understand how these SARS-CoV-2 lineages spread in Brazil, we analyzed 11,724 genomes collected throughout the country between September 2020 and April 2021. Our findings indicate that lineage P.2 probably emerged in July 2020 in the Rio de Janeiro state and Gamma in November 2020 in the Amazonas state. Both states were the main hubs of viral disseminations to other Brazilian locations. We estimate that Gamma was 1.56– 3.06 times more transmissible than P.2 in Rio de Janeiro and that the median effective reproductive number (Re) of Gamma varied according to the geographic context (Re = 1.59–3.55). In summary, our findings support that lineage Gamma was more transmissible and spread faster than P.2 in Brazil.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-83084https://www.arca.fiocruz.br/bitstream/icict/52502/1/license.txt783568c2893d2e25a99990b126be1772MD51ORIGINALmainOK.pdfmainOK.pdfapplication/pdf15681123https://www.arca.fiocruz.br/bitstream/icict/52502/2/mainOK.pdf1ecd440fbfc1ba57fdb483a31d976d44MD52icict/525022023-07-14 11:27:26.272oai:www.arca.fiocruz.br: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ório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352023-07-14T14:27:26Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false |
| dc.title.pt_BR.fl_str_mv |
Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 lineages Gamma and P.2 in Brazil |
| title |
Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 lineages Gamma and P.2 in Brazil |
| spellingShingle |
Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 lineages Gamma and P.2 in Brazil Graf, Tiago SARS-CoV-2 COVID-19 Linhagem P.2 Linhagem Gamma Lineage P.2 Lineage Gamma Disease Transmission, Infectious Pandemics Communicable Period Transmisión de Enfermedad Infecciosa Pandemias Periodo de Transmisión Transmission de maladie infectieuse Pandémies Période de Transmission Transmissão de Doença Infecciosa Pandemias Período de Transmissibilidade |
| title_short |
Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 lineages Gamma and P.2 in Brazil |
| title_full |
Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 lineages Gamma and P.2 in Brazil |
| title_fullStr |
Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 lineages Gamma and P.2 in Brazil |
| title_full_unstemmed |
Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 lineages Gamma and P.2 in Brazil |
| title_sort |
Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 lineages Gamma and P.2 in Brazil |
| author |
Graf, Tiago |
| author_facet |
Graf, Tiago Bello, Gonzalo Naveca, Felipe Gomes Gomes, Marcelo Cardoso, Vanessa Leiko Oikawa Silva, Alexandre Freitas da Dezordi, Filipe Zimmer Santos, Mirleide Cordeiro dos Santos, Katia Correa de Oliveira Batista, Érika Lopes Rocha Magalhães, Alessandro Leonardo Álvares Vinhal, Fernando Miyajima, Fábio Faoro, Helisson Khouri, Ricardo Wallau, Gabriel Luz Delatorre, Edson Siqueira, Marilda Mendonça Resende, Paola Cristina |
| author_role |
author |
| author2 |
Bello, Gonzalo Naveca, Felipe Gomes Gomes, Marcelo Cardoso, Vanessa Leiko Oikawa Silva, Alexandre Freitas da Dezordi, Filipe Zimmer Santos, Mirleide Cordeiro dos Santos, Katia Correa de Oliveira Batista, Érika Lopes Rocha Magalhães, Alessandro Leonardo Álvares Vinhal, Fernando Miyajima, Fábio Faoro, Helisson Khouri, Ricardo Wallau, Gabriel Luz Delatorre, Edson Siqueira, Marilda Mendonça Resende, Paola Cristina |
| author2_role |
author author author author author author author author author author author author author author author author author author |
| dc.contributor.author.fl_str_mv |
Graf, Tiago Bello, Gonzalo Naveca, Felipe Gomes Gomes, Marcelo Cardoso, Vanessa Leiko Oikawa Silva, Alexandre Freitas da Dezordi, Filipe Zimmer Santos, Mirleide Cordeiro dos Santos, Katia Correa de Oliveira Batista, Érika Lopes Rocha Magalhães, Alessandro Leonardo Álvares Vinhal, Fernando Miyajima, Fábio Faoro, Helisson Khouri, Ricardo Wallau, Gabriel Luz Delatorre, Edson Siqueira, Marilda Mendonça Resende, Paola Cristina |
| dc.subject.other.pt_BR.fl_str_mv |
SARS-CoV-2 COVID-19 Linhagem P.2 Linhagem Gamma |
| topic |
SARS-CoV-2 COVID-19 Linhagem P.2 Linhagem Gamma Lineage P.2 Lineage Gamma Disease Transmission, Infectious Pandemics Communicable Period Transmisión de Enfermedad Infecciosa Pandemias Periodo de Transmisión Transmission de maladie infectieuse Pandémies Période de Transmission Transmissão de Doença Infecciosa Pandemias Período de Transmissibilidade |
| dc.subject.en.pt_BR.fl_str_mv |
Lineage P.2 Lineage Gamma Disease Transmission, Infectious Pandemics Communicable Period |
| dc.subject.es.pt_BR.fl_str_mv |
Transmisión de Enfermedad Infecciosa Pandemias Periodo de Transmisión |
| dc.subject.fr.pt_BR.fl_str_mv |
Transmission de maladie infectieuse Pandémies Période de Transmission |
| dc.subject.decs.pt_BR.fl_str_mv |
Transmissão de Doença Infecciosa Pandemias Período de Transmissibilidade |
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Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, Brasil. |
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2022 |
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2022-05-02T16:17:12Z |
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2022-05-02T16:17:12Z |
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2022 |
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GRAF, Tiago et al. Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 lineages Gamma and P.2 in Brazil. iScience, v. 25 n. 104156 , p. 1–16, 2022. |
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https://www.arca.fiocruz.br/handle/icict/52502 |
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2589-0042 |
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10.1016/ j.isci.2022.104156 |
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GRAF, Tiago et al. Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 lineages Gamma and P.2 in Brazil. iScience, v. 25 n. 104156 , p. 1–16, 2022. 2589-0042 10.1016/ j.isci.2022.104156 |
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Cell Press |
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Cell Press |
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