학술논문
Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil
Document Type
Original Paper
Author
Giovanetti, Marta; Slavov, Svetoslav Nanev; Fonseca, Vagner; Wilkinson, Eduan; Tegally, Houriiyah; Patané, José Salvatore Leister; Viala, Vincent Louis; San, Emmanuel James; Rodrigues, Evandra Strazza; Santos, Elaine Vieira; Aburjaile, Flavia; Xavier, Joilson; Fritsch, Hegger; Adelino, Talita Emile Ribeiro; Pereira, Felicidade; Leal, Arabela; Iani, Felipe Campos de Melo; de Carvalho Pereira, Glauco; Vazquez, Cynthia; Sanabria, Gladys Mercedes Estigarribia; Oliveira, Elaine Cristina de; Demarchi, Luiz; Croda, Julio; dos Santos Bezerra, Rafael; Paola Oliveira de Lima, Loyze; Martins, Antonio Jorge; Renata dos Santos Barros, Claudia; Marqueze, Elaine Cristina; de Souza Todao Bernardino, Jardelina; Moretti, Debora Botequio; Brassaloti, Ricardo Augusto; de Lello Rocha Campos Cassano, Raquel; Mariani, Pilar Drummond Sampaio Corrêa; Kitajima, João Paulo; Santos, Bibiana; Proto-Siqueira, Rodrigo; Cantarelli, Vlademir Vicente; Tosta, Stephane; Nardy, Vanessa Brandão; Reboredo de Oliveira da Silva, Luciana; Gómez, Marcela Kelly Astete; Lima, Jaqueline Gomes; Ribeiro, Adriana Aparecida; Guimarães, Natália Rocha; Watanabe, Luiz Takao; Barbosa Da Silva, Luana; da Silva Ferreira, Raquel; da Penha, Mara Patricia F.; Ortega, María José; de la Fuente, Andrea Gómez; Villalba, Shirley; Torales, Juan; Gamarra, María Liz; Aquino, Carolina; Figueredo, Gloria Patricia Martínez; Fava, Wellington Santos; Motta-Castro, Ana Rita C.; Venturini, James; do Vale Leone de Oliveira, Sandra Maria; Gonçalves, Crhistinne Cavalheiro Maymone; do Carmo Debur Rossa, Maria; 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; Allan da Silva da Costa, Felipe; Poleti, Mirele Daiana; Lesbon, Jessika Cristina Chagas; Mattos, Elisangela Chicaroni; Banho, Cecilia Artico; Sacchetto, Lívia; Moraes, Marília Mazzi; Grotto, Rejane Maria Tommasini; Souza-Neto, Jayme A.; Nogueira, Maurício Lacerda; Fukumasu, Heidge; Coutinho, Luiz Lehmann; Calado, Rodrigo Tocantins; Neto, Raul Machado; Bispo de Filippis, Ana Maria; Venancio da Cunha, Rivaldo; Freitas, Carla; Peterka, Cassio Roberto Leonel; de Fátima Rangel Fernandes, Cássia; Navegantes, Wildo; do Carmo Said, Rodrigo Fabiano; Campelo de A e Melo, Carlos F.; Almiron, Maria; Lourenço, José; de Oliveira, Tulio; Holmes, Edward C.; Haddad, Ricardo; Sampaio, Sandra Coccuzzo; Elias, Maria Carolina; Kashima, Simone; Junior de Alcantara, Luiz Carlos; Covas, Dimas Tadeu
Source
Nature Microbiology. 7(9):1490-1500
Subject
Language
English
ISSN
2058-5276
Abstract
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.
The COVID-19 pandemic in Brazil is assessed using phylogenetic and phylogeographic analysis.
The COVID-19 pandemic in Brazil is assessed using phylogenetic and phylogeographic analysis.