The Omicron Lineages BA.1 and BA.2 (Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal Hub
Autor(a) principal: | |
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Data de Publicação: | 2023 |
Outros Autores: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.3390/v15040888 http://hdl.handle.net/11449/247297 |
Resumo: | Brazil currently ranks second in absolute deaths by COVID-19, even though most of its population has completed the vaccination protocol. With the introduction of Omicron in late 2021, the number of COVID-19 cases soared once again in the country. We investigated in this work how lineages BA.1 and BA.2 entered and spread in the country by sequencing 2173 new SARS-CoV-2 genomes collected between October 2021 and April 2022 and analyzing them in addition to more than 18,000 publicly available sequences with phylodynamic methods. We registered that Omicron was present in Brazil as early as 16 November 2021 and by January 2022 was already more than 99% of samples. More importantly, we detected that Omicron has been mostly imported through the state of São Paulo, which in turn dispersed the lineages to other states and regions of Brazil. This knowledge can be used to implement more efficient non-pharmaceutical interventions against the introduction of new SARS-CoV variants focused on surveillance of airports and ground transportation. |
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The Omicron Lineages BA.1 and BA.2 (Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal HubCOVID-19dispersalgenomephylodynamicsvariant of concernviral evolutionBrazil currently ranks second in absolute deaths by COVID-19, even though most of its population has completed the vaccination protocol. With the introduction of Omicron in late 2021, the number of COVID-19 cases soared once again in the country. We investigated in this work how lineages BA.1 and BA.2 entered and spread in the country by sequencing 2173 new SARS-CoV-2 genomes collected between October 2021 and April 2022 and analyzing them in addition to more than 18,000 publicly available sequences with phylodynamic methods. We registered that Omicron was present in Brazil as early as 16 November 2021 and by January 2022 was already more than 99% of samples. More importantly, we detected that Omicron has been mostly imported through the state of São Paulo, which in turn dispersed the lineages to other states and regions of Brazil. This knowledge can be used to implement more efficient non-pharmaceutical interventions against the introduction of new SARS-CoV variants focused on surveillance of airports and ground transportation.Financiadora de Estudos e ProjetosFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ)Laboratório de Bioinformática Laboratório Nacional de Computação CientíficaLaboratório de Bioinformática e Biotecnologia Universidade Federal do Tocantins, Campus de GurupiLaboratório de Virologia Molecular Departamento de Genética Instituto de Biologia Universidade Federal do Rio de JaneiroCentro de Medicina Tropical da Tríplice FronteiraDepartamento de Pesquisa & Desenvolvimento Instituto Hermes PardiniLaboratório Central de Saúde Pública Noel NutelsDepartamento de Genética Ecologia e Evolução Instituto de Ciências Biológicas Universidade Federal de Minas GeraisLaboratório de Biologia Molecular Parque Científico e Tecnológico Regional Universidade de Santa Cruz do SulCentro de Ciências de Saúde e do Desporto Universidade Federal do AcreInstituto de Biotecnologia Universidade Estadual PaulistaLaboratório Central de Saúde Pública do Estado do TocantinsDepartmento de Ciências da Vida Universidade de Santa Cruz do SulCentro de Infectologia Charles Mérieux and Laboratório Rodolphe Mérieux Hospital das Clínicas do AcreLaboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica Universidade Federal de Santa MariaLaboratório de Virologia Departamento de Microbiologia Imunologia e Parasitologia Instituto de Ciências Básicas da Saúde Universidade Federal do Rio Grande do SulInstituto de Biotecnologia Universidade Estadual PaulistaFinanciadora de Estudos e Projetos: 0494/20 01.20.0026.00Financiadora de Estudos e Projetos: 1139/20FAPESP: 2019/18581-6FAPESP: 307145/2021-2FAPESP: 309626/2021-8FAPESP: 309948/2020-7FAPESP: 315192/2020-8FAPERJ: E-26/201.046/2022Laboratório Nacional de Computação CientíficaUniversidade Federal do TocantinsUniversidade Federal do Rio de Janeiro (UFRJ)Centro de Medicina Tropical da Tríplice FronteiraInstituto Hermes PardiniLaboratório Central de Saúde Pública Noel NutelsUniversidade Federal de Minas Gerais (UFMG)Universidade de Santa Cruz do SulUniversidade Federal do AcreUniversidade Estadual Paulista (UNESP)Laboratório Central de Saúde Pública do Estado do TocantinsHospital das Clínicas do AcreUniversidade Federal de Santa MariaUniversidade Federal do Rio Grande do SulLamarca, Alessandra P.Souza, Ueric José Borges deMoreira, Filipe Romero RebelloAlmeida, Luiz G. P. deMenezes, Mariane Talon deSouza, Adrieli Barboza deFerreira, Alessandro Clayton de SouzaGerber, Alexandra L.Lima, Aline B. deGuimarães, Ana Paula de C.Cavalcanti, Andréa ConySilva, Aryel B. Paz eLima, Bruna IsraelLobato, CirleySilva, Cristiane Gomes DaMendonça, Cristiane P. T. B.Queiroz, Daniel CostaZauli, Danielle Alves GomesMenezes, DiegoPossebon, Fábio Sossai [UNESP]Cardoso, Franciano Dias PereiraMalta, Frederico Scott VarellaBraga-Paz, IsabelaSilva, Joice do PradoFerreira, Jorge Gomes GoulartGalvão, Jucimária DantasSouza, Leandro Magalhães deFerreira, LeonardoPossuelo, Lia GonçalvesCavalcante, Liliane Tavares de FariaAlvim, Luige B.Souza, Luiz Fellype Alves deSantos, Luiza C. G. de Araújo EDias, Rillery CalixtoSouza, Rutilene BarbosaCastro, Thaís Regina yValim, Andréia Rosane de MouraCampos, Fabrício SouzaAraujo, João Pessoa [UNESP]Trindade, Priscila de ArrudaAguiar, Renato S.Michael Delai, RobsonVasconcelos, Ana Tereza R de2023-07-29T13:12:13Z2023-07-29T13:12:13Z2023-04-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.3390/v15040888Viruses, v. 15, n. 4, 2023.1999-4915http://hdl.handle.net/11449/24729710.3390/v150408882-s2.0-85156246637Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengVirusesinfo:eu-repo/semantics/openAccess2023-07-29T13:12:13Zoai:repositorio.unesp.br:11449/247297Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T17:06:39.778756Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
The Omicron Lineages BA.1 and BA.2 (Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal Hub |
title |
The Omicron Lineages BA.1 and BA.2 (Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal Hub |
spellingShingle |
The Omicron Lineages BA.1 and BA.2 (Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal Hub Lamarca, Alessandra P. COVID-19 dispersal genome phylodynamics variant of concern viral evolution |
title_short |
The Omicron Lineages BA.1 and BA.2 (Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal Hub |
title_full |
The Omicron Lineages BA.1 and BA.2 (Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal Hub |
title_fullStr |
The Omicron Lineages BA.1 and BA.2 (Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal Hub |
title_full_unstemmed |
The Omicron Lineages BA.1 and BA.2 (Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal Hub |
title_sort |
The Omicron Lineages BA.1 and BA.2 (Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal Hub |
author |
Lamarca, Alessandra P. |
author_facet |
Lamarca, Alessandra P. Souza, Ueric José Borges de Moreira, Filipe Romero Rebello Almeida, Luiz G. P. de Menezes, Mariane Talon de Souza, Adrieli Barboza de Ferreira, Alessandro Clayton de Souza Gerber, Alexandra L. Lima, Aline B. de Guimarães, Ana Paula de C. Cavalcanti, Andréa Cony Silva, Aryel B. Paz e Lima, Bruna Israel Lobato, Cirley Silva, Cristiane Gomes Da Mendonça, Cristiane P. T. B. Queiroz, Daniel Costa Zauli, Danielle Alves Gomes Menezes, Diego Possebon, Fábio Sossai [UNESP] Cardoso, Franciano Dias Pereira Malta, Frederico Scott Varella Braga-Paz, Isabela Silva, Joice do Prado Ferreira, Jorge Gomes Goulart Galvão, Jucimária Dantas Souza, Leandro Magalhães de Ferreira, Leonardo Possuelo, Lia Gonçalves Cavalcante, Liliane Tavares de Faria Alvim, Luige B. Souza, Luiz Fellype Alves de Santos, Luiza C. G. de Araújo E Dias, Rillery Calixto Souza, Rutilene Barbosa Castro, Thaís Regina y Valim, Andréia Rosane de Moura Campos, Fabrício Souza Araujo, João Pessoa [UNESP] Trindade, Priscila de Arruda Aguiar, Renato S. Michael Delai, Robson Vasconcelos, Ana Tereza R de |
author_role |
author |
author2 |
Souza, Ueric José Borges de Moreira, Filipe Romero Rebello Almeida, Luiz G. P. de Menezes, Mariane Talon de Souza, Adrieli Barboza de Ferreira, Alessandro Clayton de Souza Gerber, Alexandra L. Lima, Aline B. de Guimarães, Ana Paula de C. Cavalcanti, Andréa Cony Silva, Aryel B. Paz e Lima, Bruna Israel Lobato, Cirley Silva, Cristiane Gomes Da Mendonça, Cristiane P. T. B. Queiroz, Daniel Costa Zauli, Danielle Alves Gomes Menezes, Diego Possebon, Fábio Sossai [UNESP] Cardoso, Franciano Dias Pereira Malta, Frederico Scott Varella Braga-Paz, Isabela Silva, Joice do Prado Ferreira, Jorge Gomes Goulart Galvão, Jucimária Dantas Souza, Leandro Magalhães de Ferreira, Leonardo Possuelo, Lia Gonçalves Cavalcante, Liliane Tavares de Faria Alvim, Luige B. Souza, Luiz Fellype Alves de Santos, Luiza C. G. de Araújo E Dias, Rillery Calixto Souza, Rutilene Barbosa Castro, Thaís Regina y Valim, Andréia Rosane de Moura Campos, Fabrício Souza Araujo, João Pessoa [UNESP] Trindade, Priscila de Arruda Aguiar, Renato S. Michael Delai, Robson Vasconcelos, Ana Tereza R de |
author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Laboratório Nacional de Computação Científica Universidade Federal do Tocantins Universidade Federal do Rio de Janeiro (UFRJ) Centro de Medicina Tropical da Tríplice Fronteira Instituto Hermes Pardini Laboratório Central de Saúde Pública Noel Nutels Universidade Federal de Minas Gerais (UFMG) Universidade de Santa Cruz do Sul Universidade Federal do Acre Universidade Estadual Paulista (UNESP) Laboratório Central de Saúde Pública do Estado do Tocantins Hospital das Clínicas do Acre Universidade Federal de Santa Maria Universidade Federal do Rio Grande do Sul |
dc.contributor.author.fl_str_mv |
Lamarca, Alessandra P. Souza, Ueric José Borges de Moreira, Filipe Romero Rebello Almeida, Luiz G. P. de Menezes, Mariane Talon de Souza, Adrieli Barboza de Ferreira, Alessandro Clayton de Souza Gerber, Alexandra L. Lima, Aline B. de Guimarães, Ana Paula de C. Cavalcanti, Andréa Cony Silva, Aryel B. Paz e Lima, Bruna Israel Lobato, Cirley Silva, Cristiane Gomes Da Mendonça, Cristiane P. T. B. Queiroz, Daniel Costa Zauli, Danielle Alves Gomes Menezes, Diego Possebon, Fábio Sossai [UNESP] Cardoso, Franciano Dias Pereira Malta, Frederico Scott Varella Braga-Paz, Isabela Silva, Joice do Prado Ferreira, Jorge Gomes Goulart Galvão, Jucimária Dantas Souza, Leandro Magalhães de Ferreira, Leonardo Possuelo, Lia Gonçalves Cavalcante, Liliane Tavares de Faria Alvim, Luige B. Souza, Luiz Fellype Alves de Santos, Luiza C. G. de Araújo E Dias, Rillery Calixto Souza, Rutilene Barbosa Castro, Thaís Regina y Valim, Andréia Rosane de Moura Campos, Fabrício Souza Araujo, João Pessoa [UNESP] Trindade, Priscila de Arruda Aguiar, Renato S. Michael Delai, Robson Vasconcelos, Ana Tereza R de |
dc.subject.por.fl_str_mv |
COVID-19 dispersal genome phylodynamics variant of concern viral evolution |
topic |
COVID-19 dispersal genome phylodynamics variant of concern viral evolution |
description |
Brazil currently ranks second in absolute deaths by COVID-19, even though most of its population has completed the vaccination protocol. With the introduction of Omicron in late 2021, the number of COVID-19 cases soared once again in the country. We investigated in this work how lineages BA.1 and BA.2 entered and spread in the country by sequencing 2173 new SARS-CoV-2 genomes collected between October 2021 and April 2022 and analyzing them in addition to more than 18,000 publicly available sequences with phylodynamic methods. We registered that Omicron was present in Brazil as early as 16 November 2021 and by January 2022 was already more than 99% of samples. More importantly, we detected that Omicron has been mostly imported through the state of São Paulo, which in turn dispersed the lineages to other states and regions of Brazil. This knowledge can be used to implement more efficient non-pharmaceutical interventions against the introduction of new SARS-CoV variants focused on surveillance of airports and ground transportation. |
publishDate |
2023 |
dc.date.none.fl_str_mv |
2023-07-29T13:12:13Z 2023-07-29T13:12:13Z 2023-04-01 |
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://dx.doi.org/10.3390/v15040888 Viruses, v. 15, n. 4, 2023. 1999-4915 http://hdl.handle.net/11449/247297 10.3390/v15040888 2-s2.0-85156246637 |
url |
http://dx.doi.org/10.3390/v15040888 http://hdl.handle.net/11449/247297 |
identifier_str_mv |
Viruses, v. 15, n. 4, 2023. 1999-4915 10.3390/v15040888 2-s2.0-85156246637 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
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Viruses |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
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openAccess |
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Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
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UNESP |
institution |
UNESP |
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Repositório Institucional da UNESP |
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Repositório Institucional da UNESP |
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Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
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1808128757297315840 |