The Omicron Lineages BA.1 and BA.2 (Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal Hub

Detalhes bibliográficos
Autor(a) principal: Lamarca, Alessandra P.
Data de Publicação: 2023
Outros Autores: 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
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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spelling 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
dc.relation.none.fl_str_mv Viruses
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.source.none.fl_str_mv Scopus
reponame:Repositório Institucional da UNESP
instname:Universidade Estadual Paulista (UNESP)
instacron:UNESP
instname_str Universidade Estadual Paulista (UNESP)
instacron_str UNESP
institution UNESP
reponame_str Repositório Institucional da UNESP
collection Repositório Institucional da UNESP
repository.name.fl_str_mv Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)
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