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

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Giovanetti, Marta ; Slavov, Svetoslav Nanev ; Fonseca, Vagner ; Wilkinson, Eduan ; Tegally, Houriiyah ; Leister Patane, Jose Salvatore ; Viala, Vincent Louis ; San, Emmanuel James ; Rodrigues, Evandra Strazza ; Santos, Elaine Vieira ; Aburjaile, Flavia ; Xavier, Joilson ; Fritsch, Hegger ; Ribeiro Adelino, Talita Emile ; Pereira, Felicidade ; Leal, Arabela ; De Melo Iani, Felipe Campos ; De Carvalho Pereira, Glauco ; Vazquez, Cynthia ; Estigarribia Sanabria, Gladys Mercedes ; De Oliveira, Elaine Cristina ; Demarchi, Luiz ; Croda, Julio ; Dos Santos Bezerra, Rafael ; Oliveira De Lima, Loyze Paola ; Martins, Antonio Jorge ; Dos Santos Barros, Claudia Renata ; Marqueze, Elaine Cristina ; Todao Bernardino, Jardelina De Souza ; Moretti, Debora Botequio ; Brassaloti, Ricardo Augusto ; Rocha Campos Cassano, Raquel De Lello ; Sampaio Correa Mariani, Pilar Drummond ; Kitajima, Joao Paulo ; Santos, Bibiana ; Proto-Siqueira, Rodrigo ; Cantarelli, Vlademir Vicente ; Tosta, Stephane ; Nardy, Vanessa Brandao ; De Oliveira Da Silva, Luciana Reboredo ; Astete Gomez, Marcela Kelly ; Lima, Jaqueline Gomes ; Ribeiro, Adriana Aparecida ; Guimaraes, Natalia Rocha ; Watanabe, Luiz Takao ; Da Silva, Luana Barbosa ; Ferreira, Raquel Da Silva ; Da Penha, Mara Patricia F. ; Ortega, Maria Jose ; De La Fuente, Andrea Gomez ; Villalba, Shirley ; Torales, Juan ; Gamarra, Maria Liz ; Aquino, Carolina ; Martinez Figueredo, Gloria Patricia ; Fava, Wellington Santos ; Motta-Castro, Ana Rita C. ; Venturini, James ; Do Vale Leone De Oliveira, Sandra Maria ; Maymone Goncalves, Crhistinne Cavalheiro ; Debur Rossa, Maria Do Carmo ; Becker, Guilherme Nardi ; Giacomini, Mayra Presibella ; Marques, Nelson Quallio ; Riediger, Irina Nastassja ; Raboni, Sonia ; Mattoso, Gabriela ; Cataneo, Allan D. ; Zanluca, Camila ; Duarte Dos Santos, Claudia N. ; Assato, Patricia Akemi ; Da Silva Da Costa, Felipe Allan ; Poleti, Mirele Daiana ; Chagas Lesbon, Jessika Cristina ; Mattos, Elisangela Chicaroni ; Banho, Cecilia Artico ; Sacchetto, Livia ; Moraes, Marilia Mazzi ; Tommasini Grotto, Rejane Maria ; Souza-Neto, Jayme A. ; Nogueira, Mauricio Lacerda ; Fukumasu, Heidge ; Coutinho, Luiz Lehmann ; Calado, Rodrigo Tocantins ; Neto, Raul Machado ; Bispo De Filippis, Ana Maria ; Da Cunha, Rivaldo Venancio ; Freitas, Carla ; Leonel Peterka, Cassio Roberto ; Rangel Fernandes, Cassia De Fatima ; Navegantes, Wildo ; Do Carmo Said, Rodrigo Fabiano ; Melo, Carlos F. Campelo De A. E. ; Almiron, Maria ; Lourenco, Jose ; De Oliveira, Tulio ; Holmes, Edward C. ; Haddad, Ricardo ; Sampaio, Sandra Coccuzzo ; Elias, Maria Carolina ; Kashima, Simone ; Junior De Alcantara, Luiz Carlos ; Covas, Dimas Tadeu

• Tipo de documento: Artigo Científico
• Fonte: NATURE MICROBIOLOGY; v. 7, n. 9, p. 14-pg., 2022-08-18.

Resumo

The COVID-19 pandemic in Brazil is assessed using phylogenetic and phylogeographic analysis. 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. (AU)

• Processo FAPESP: 13/08135-2 - CTC - Centro de Terapia Celular
• Beneficiário: Dimas Tadeu Covas
• Modalidade de apoio: Auxílio à Pesquisa - Centros de Pesquisa, Inovação e Difusão - CEPIDs
• Processo FAPESP: 20/10127-1 - Desenvolvimento de vacina contra a COVID-19
• Beneficiário: Dimas Tadeu Covas
• Modalidade de apoio: Auxílio à Pesquisa - Pesquisa em Políticas Públicas
• Processo FAPESP: 20/04836-0 - Estudo clínico e epidemiológico de SARS-CoV-2 em uma coorte prospectiva populacional e hospitalar em São José do Rio Preto, São Paulo, Brasil, durante pandemia de 2020
• Beneficiário: Maurício Lacerda Nogueira
• Modalidade de apoio: Auxílio à Pesquisa - Regular
• Processo FAPESP: 20/05367-3 - Uso de plasma de doador convalescente para tratar pacientes com infecção grave pelo SARS-CoV-2 (COVID-19)
• Beneficiário: Rodrigo do Tocantins Calado de Saloma Rodrigues
• Modalidade de apoio: Auxílio à Pesquisa - Regular