Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil.

Brazil COVID-19 Genomics Humans SARS-CoV-2

Journal

Nature microbiology
ISSN: 2058-5276
Titre abrégé: Nat Microbiol
Pays: England
ID NLM: 101674869

Informations de publication

Date de publication:
09 2022
Historique:
received: 07 10 2021
accepted: 28 06 2022
pubmed: 19 8 2022
medline: 31 8 2022
entrez: 18 8 2022
Statut: ppublish

Résumé

The high numbers of COVID-19 cases and deaths in Brazil have made Latin America an epicentre of the pandemic. SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, but important gaps remain in our understanding of virus transmission dynamics at a national scale. We use 17,135 near-complete genomes sampled from 27 Brazilian states and bordering country Paraguay. From March to November 2020, we detected co-circulation of multiple viral lineages that were linked to multiple importations (predominantly from Europe). After November 2020, we detected large, local transmission clusters within the country. In the absence of effective restriction measures, the epidemic progressed, and in January 2021 there was emergence and onward spread, both within and abroad, of variants of concern and variants under monitoring, including Gamma (P.1) and Zeta (P.2). We also characterized a genomic overview of the epidemic in Paraguay and detected evidence of importation of SARS-CoV-2 ancestor lineages and variants of concern from Brazil. Our findings show that genomic surveillance in Brazil enabled assessment of the real-time spread of emerging SARS-CoV-2 variants.

Identifiants

DOI: 10.1038/s41564-022-01191-z PMID: 35982313 PMC: PMC9417986
pubmed: 35982313
doi: 10.1038/s41564-022-01191-z
pii: 10.1038/s41564-022-01191-z
pmc: PMC9417986
doi:

Types de publication

Journal Article Research Support, Non-U.S. Gov't Research Support, N.I.H., Extramural

Langues

eng

Sous-ensembles de citation

IM

Pagination

1490-1500

Subventions

Organisme : World Health Organization
ID : 001
Pays : International
Organisme : NIAID NIH HHS
ID : U01 AI151698
Pays : United States

Commentaires et corrections

Type : UpdateOf

Informations de copyright

© 2022. The Author(s).

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Auteurs

Marta Giovanetti (M)

Laboratório de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil.
Laboratório de Genética Celular e Molecular, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy.

Svetoslav Nanev Slavov (SN)

Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
Butantan Institute, São Paulo, Brazil.

Vagner Fonseca (V)

Laboratório de Genética Celular e Molecular, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
Pan American Health Organization (PAHO)/World Health Organization (WHO), Brasilia, Distrito Federal, Brazil.
Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
ORCID: 0000-0001-5521-6448

Eduan Wilkinson (E)

Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
ORCID: 0000-0002-2503-9441

Houriiyah Tegally (H)

Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.

José Salvatore Leister Patané (JSL)

Butantan Institute, São Paulo, Brazil.

Vincent Louis Viala (VL)

Butantan Institute, São Paulo, Brazil.
ORCID: 0000-0003-2267-9985

Emmanuel James San (EJ)

Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
ORCID: 0000-0002-5736-664X

Evandra Strazza Rodrigues (ES)

Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.

Elaine Vieira Santos (EV)

Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.

Flavia Aburjaile (F)

Laboratório de Genética Celular e Molecular, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
ORCID: 0000-0002-1067-1882

Joilson Xavier (J)

Laboratório de Genética Celular e Molecular, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
Laboratório Central de Saúde Pública do Estado de Minas Gerais (LACEN-MG), Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil.
ORCID: 0000-0003-3916-2018

Hegger Fritsch (H)

Laboratório de Genética Celular e Molecular, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
Laboratório Central de Saúde Pública do Estado de Minas Gerais (LACEN-MG), Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil.

Talita Emile Ribeiro Adelino (TER)

Laboratório de Genética Celular e Molecular, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
Laboratório Central de Saúde Pública do Estado de Minas Gerais (LACEN-MG), Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil.
ORCID: 0000-0002-1471-0084

Felicidade Pereira (F)

Laboratório Central de Saúde Pública do Estado da Bahia (LACEN-BA), Salvador, Bahia, Brazil.

Arabela Leal (A)

Laboratório Central de Saúde Pública do Estado da Bahia (LACEN-BA), Salvador, Bahia, Brazil.

Felipe Campos de Melo Iani (FCM)

Laboratório Central de Saúde Pública do Estado de Minas Gerais (LACEN-MG), Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil.
ORCID: 0000-0002-3629-8529

Glauco de Carvalho Pereira (G)

Laboratório Central de Saúde Pública do Estado de Minas Gerais (LACEN-MG), Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil.

Cynthia Vazquez (C)

Laboratório Central de Salud Pública, Asunción, Paraguay.

Gladys Mercedes Estigarribia Sanabria (GME)

Laboratório Central de Salud Pública, Asunción, Paraguay.
Instituto Regional de Investigación em Salud, Universidad Nacional del Caaguazú, Caaguazú, Paraguay.
Laboratório de Biología Molecular, Hospital Regional de Coronel Oviedo, Ministerio de Salud Pública y Bienestar Social, Asunción, Paraguay.

Elaine Cristina de Oliveira (EC)

Laboratório Central de Saúde Pública do Estado de Mato Grosso (LACEN-MT), Cuiabá, Mato Grosso, Brazil.

Luiz Demarchi (L)

Laboratório Central de Saúde Pública do Estado de Mato Grosso do Sul (LACEN-MS), Campo Grande, Mato Grosso do Sul, Brazil.
ORCID: 0000-0001-8693-7897

Julio Croda (J)

Universidade Federal do Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil.
ORCID: 0000-0002-6665-6825

Rafael Dos Santos Bezerra (R)

Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.

Loyze Paola Oliveira de Lima (L)

Butantan Institute, São Paulo, Brazil.

Antonio Jorge Martins (AJ)

Butantan Institute, São Paulo, Brazil.

Claudia Renata Dos Santos Barros (C)

Butantan Institute, São Paulo, Brazil.

Elaine Cristina Marqueze (EC)

Butantan Institute, São Paulo, Brazil.
ORCID: 0000-0002-4987-7757

Jardelina de Souza Todao Bernardino (J)

Butantan Institute, São Paulo, Brazil.

Debora Botequio Moretti (DB)

Butantan Institute, São Paulo, Brazil.
ORCID: 0000-0003-0912-9989

Ricardo Augusto Brassaloti (RA)

Centro de Genômica Funcional da ESALQ, University of São Paulo, Piracicaba, São Paulo, Brazil.

Raquel de Lello Rocha Campos Cassano (R)

Centro de Genômica Funcional da ESALQ, University of São Paulo, Piracicaba, São Paulo, Brazil.

Pilar Drummond Sampaio Corrêa Mariani (PDSC)

NGS Soluções Genômicas, Piracicaba, São Paulo, Brazil.

João Paulo Kitajima (JP)

Mendelics Análise Genômica, São Paulo, Brazil.

Bibiana Santos (B)

Mendelics Análise Genômica, São Paulo, Brazil.

Rodrigo Proto-Siqueira (R)

Instituto de Biologia Molecular, Laboratório Antonello, Rio Grande do Sul, Brazil.

Vlademir Vicente Cantarelli (VV)

Universidade Federal de Ciencias da Saúde de Porto Alegre (UFCSPA), Universidade Feevale, Grupo Exame Laboratórios, Rio Grande do Sul, Brazil.

Stephane Tosta (S)

Laboratório de Genética Celular e Molecular, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
Laboratório Central de Saúde Pública do Estado da Bahia (LACEN-BA), Salvador, Bahia, Brazil.

Vanessa Brandão Nardy (VB)

Laboratório Central de Saúde Pública do Estado da Bahia (LACEN-BA), Salvador, Bahia, Brazil.

Luciana Reboredo de Oliveira da Silva (L)

Laboratório Central de Saúde Pública do Estado da Bahia (LACEN-BA), Salvador, Bahia, Brazil.

Marcela Kelly Astete Gómez (MKA)

Laboratório Central de Saúde Pública do Estado da Bahia (LACEN-BA), Salvador, Bahia, Brazil.

Jaqueline Gomes Lima (JG)

Laboratório Central de Saúde Pública do Estado da Bahia (LACEN-BA), Salvador, Bahia, Brazil.

Adriana Aparecida Ribeiro (AA)

Laboratório Central de Saúde Pública do Estado de Minas Gerais (LACEN-MG), Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil.

Natália Rocha Guimarães (NR)

Laboratório Central de Saúde Pública do Estado de Minas Gerais (LACEN-MG), Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil.

Luiz Takao Watanabe (LT)

Laboratório Central de Saúde Pública do Estado de Mato Grosso (LACEN-MT), Cuiabá, Mato Grosso, Brazil.

Luana Barbosa Da Silva (L)

Laboratório Central de Saúde Pública do Estado de Mato Grosso (LACEN-MT), Cuiabá, Mato Grosso, Brazil.

Raquel da Silva Ferreira (R)

Laboratório Central de Saúde Pública do Estado de Mato Grosso (LACEN-MT), Cuiabá, Mato Grosso, Brazil.

Mara Patricia F da Penha (MPF)

Vigilancia em Saúde do Estado de Mato Grosso, Cuiabá, Mato Grosso, Brazil.

María José Ortega (MJ)

Laboratório Central de Salud Pública, Asunción, Paraguay.

Andrea Gómez de la Fuente (AG)

Laboratório Central de Salud Pública, Asunción, Paraguay.

Shirley Villalba (S)

Laboratório Central de Salud Pública, Asunción, Paraguay.

Juan Torales (J)

Laboratório Central de Salud Pública, Asunción, Paraguay.

María Liz Gamarra (ML)

Laboratório Central de Salud Pública, Asunción, Paraguay.

Carolina Aquino (C)

Laboratório Central de Salud Pública, Asunción, Paraguay.

Gloria Patricia Martínez Figueredo (GPM)

Laboratório Central de Salud Pública, Asunción, Paraguay.
Instituto Regional de Investigación em Salud, Universidad Nacional del Caaguazú, Caaguazú, Paraguay.
Laboratório de Biología Molecular, Hospital Regional de Coronel Oviedo, Ministerio de Salud Pública y Bienestar Social, Asunción, Paraguay.

Wellington Santos Fava (WS)

Universidade Federal do Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil.

Ana Rita C Motta-Castro (ARC)

Universidade Federal do Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil.

James Venturini (J)

Universidade Federal do Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil.

Sandra Maria do Vale Leone de Oliveira (SM)

Universidade Federal do Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil.

Crhistinne Cavalheiro Maymone Gonçalves (CCM)

Secretaria de Saude do Estado do Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil.

Maria do Carmo Debur Rossa (M)

Laboratório Central de Saúde Pública do Estado do Paraná (Lacen-PR), Curitiba, Paraná, Brazil.

Guilherme Nardi Becker (GN)

Laboratório Central de Saúde Pública do Estado do Paraná (Lacen-PR), Curitiba, Paraná, Brazil.

Mayra Presibella Giacomini (MP)

Laboratório Central de Saúde Pública do Estado do Paraná (Lacen-PR), Curitiba, Paraná, Brazil.

Nelson Quallio Marques (NQ)

Laboratório Central de Saúde Pública do Estado do Paraná (Lacen-PR), Curitiba, Paraná, Brazil.

Irina Nastassja Riediger (IN)

Laboratório Central de Saúde Pública do Estado do Paraná (Lacen-PR), Curitiba, Paraná, Brazil.

Sonia Raboni (S)

Hospital de Clínicas da Universidade Federal do Paraná, Curitiba, Paraná, Brazil.
ORCID: 0000-0001-7907-7585

Gabriela Mattoso (G)

Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil.

Allan D Cataneo (AD)

Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil.

Camila Zanluca (C)

Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil.
ORCID: 0000-0001-7350-9105

Claudia N Duarte Dos Santos (CN)

Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil.

Patricia Akemi Assato (PA)

Department of Bioprocesses and Biotechnology, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.

Felipe Allan da Silva da Costa (F)

Department of Bioprocesses and Biotechnology, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.

Mirele Daiana Poleti (MD)

Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil.

Jessika Cristina Chagas Lesbon (JCC)

Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil.

Elisangela Chicaroni Mattos (EC)

Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil.

Cecilia Artico Banho (CA)

Medicine School of São José do Rio Preto (FAMERP), São José do Rio Preto, São Paulo, Brazil.

Lívia Sacchetto (L)

Medicine School of São José do Rio Preto (FAMERP), São José do Rio Preto, São Paulo, Brazil.
ORCID: 0000-0001-9716-6899

Marília Mazzi Moraes (MM)

Medicine School of São José do Rio Preto (FAMERP), São José do Rio Preto, São Paulo, Brazil.
ORCID: 0000-0002-3545-8551

Rejane Maria Tommasini Grotto (RMT)

Department of Bioprocesses and Biotechnology, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.
Molecular Biology Laboratory, Applied Biotechnology Laboratory, Clinical Hospital of the Botucatu Medical School, São Paulo, Brazil.

Jayme A Souza-Neto (JA)

Department of Bioprocesses and Biotechnology, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.

Maurício Lacerda Nogueira (ML)

Medicine School of São José do Rio Preto (FAMERP), São José do Rio Preto, São Paulo, Brazil.
ORCID: 0000-0003-1102-2419

Heidge Fukumasu (H)

Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil.

Luiz Lehmann Coutinho (LL)

Centro de Genômica Funcional da ESALQ, University of São Paulo, Piracicaba, São Paulo, Brazil.
ORCID: 0000-0002-7266-8881

Rodrigo Tocantins Calado (RT)

Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.

Raul Machado Neto (RM)

Butantan Institute, São Paulo, Brazil.

Ana Maria Bispo de Filippis (AM)

Laboratório de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil.

Rivaldo Venancio da Cunha (R)

Fundação Oswaldo Cruz, Bio-Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil.

Carla Freitas (C)

Coordenação Geral dos Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde, (CGLAB/SVS-MS), Brasília, Distrito Federal, Brazil.

Cassio Roberto Leonel Peterka (CRL)

Coordenação Geral das Arboviroses, Secretaria de Vigilância em Saúde/Ministério da Saúde (CGARB/SVS-MS), Brasília, Distrito Federal, Brazil.

Cássia de Fátima Rangel Fernandes (C)

Departamento de Imunização e Doenças Transmissíveisa/Secretaria de Vigilancia em Saude, Ministerio da Saude, Brasılia, Distrito Federal, Brazil.

Wildo Navegantes (W)

Pan American Health Organization (PAHO)/World Health Organization (WHO), Brasilia, Distrito Federal, Brazil.
ORCID: 0000-0002-6856-4094

Rodrigo Fabiano do Carmo Said (RF)

Pan American Health Organization (PAHO)/World Health Organization (WHO), Brasilia, Distrito Federal, Brazil.

Carlos F Campelo de A E Melo (CF)

Pan American Health Organization (PAHO)/World Health Organization (WHO), Brasilia, Distrito Federal, Brazil.
ORCID: 0000-0003-0581-5535

Maria Almiron (M)

Pan American Health Organization (PAHO)/World Health Organization (WHO), Brasilia, Distrito Federal, Brazil.

José Lourenço (J)

Department of Zoology, University of Oxford, Oxford, UK.
Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Lisboa, Portugal.
ORCID: 0000-0002-9318-2581

Tulio de Oliveira (T)

KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
Laboratório Central de Saúde Pública do Estado de Minas Gerais (LACEN-MG), Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil.
Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.
Department of Global Health, University of Washington, Seattle, WA, USA.

Edward C Holmes (EC)

Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia.
ORCID: 0000-0001-9596-3552

Ricardo Haddad (R)

Butantan Institute, São Paulo, Brazil.

Sandra Coccuzzo Sampaio (SC)

Butantan Institute, São Paulo, Brazil. aroli.coccuzzo@butantan.gov.br.

Maria Carolina Elias (MC)

Butantan Institute, São Paulo, Brazil. arolina.eliassabbaga@butantan.gov.br.
ORCID: 0000-0002-0501-8280

Simone Kashima (S)

Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil. skashima@hemocentro.fmrp.usp.br.

Luiz Carlos Junior de Alcantara (LC)

Laboratório de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil. luiz.alcantara@ioc.fiocruz.br.
Laboratório de Genética Celular e Molecular, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil. luiz.alcantara@ioc.fiocruz.br.
ORCID: 0000-0002-6769-9931

Dimas Tadeu Covas (DT)

Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil. dimas.covas@butantan.gov.br.
Butantan Institute, São Paulo, Brazil. dimas.covas@butantan.gov.br.

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Classifications MeSH

questionsmedicales.fr › Régions géographiques › Amériques › Amérique du Sud › Brésil › Genomic epidemiology of the SARS-CoV-2...
questionsmedicales.fr › Maladies de l'appareil respiratoire › Infections de l'appareil respiratoire › Pneumopathie infectieuse › Pneumopathie virale › COVID-19 › Genomic epidemiology of the SARS-CoV-2...
questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Génétique › Génomique › Genomic epidemiology of the SARS-CoV-2...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Genomic epidemiology of the SARS-CoV-2...
questionsmedicales.fr › Virus › Virus à ARN › Virus à ARN à brin positif › Nidovirales › Coronaviridae › Coronavirus › Betacoronavirus › Virus du SRAS › SARS-CoV-2 › Genomic epidemiology of the SARS-CoV-2...