Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil
-
Published:2022-08-18
Issue:9
Volume:7
Page:1490-1500
-
ISSN:2058-5276
-
Container-title:Nature Microbiology
-
language:en
-
Short-container-title:Nat Microbiol
Author:
Giovanetti Marta, Slavov Svetoslav Nanev, Fonseca VagnerORCID, Wilkinson EduanORCID, Tegally Houriiyah, Patané José Salvatore Leister, Viala Vincent LouisORCID, San Emmanuel JamesORCID, Rodrigues Evandra Strazza, Santos Elaine Vieira, Aburjaile FlaviaORCID, Xavier JoilsonORCID, Fritsch Hegger, Adelino Talita Emile RibeiroORCID, Pereira Felicidade, Leal Arabela, Iani Felipe Campos de MeloORCID, de Carvalho Pereira Glauco, Vazquez Cynthia, Sanabria Gladys Mercedes Estigarribia, Oliveira Elaine Cristina de, Demarchi LuizORCID, Croda JulioORCID, dos Santos Bezerra Rafael, Paola Oliveira de Lima Loyze, Martins Antonio Jorge, Renata dos Santos Barros Claudia, Marqueze Elaine CristinaORCID, de Souza Todao Bernardino Jardelina, Moretti Debora BotequioORCID, 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 SoniaORCID, Mattoso Gabriela, Cataneo Allan D., Zanluca CamilaORCID, 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 LíviaORCID, Moraes Marília MazziORCID, Grotto Rejane Maria Tommasini, Souza-Neto Jayme A., Nogueira Maurício LacerdaORCID, Fukumasu Heidge, Coutinho Luiz LehmannORCID, 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 WildoORCID, do Carmo Said Rodrigo Fabiano, Campelo de A e Melo Carlos F.ORCID, Almiron Maria, Lourenço JoséORCID, de Oliveira Tulio, Holmes Edward C.ORCID, Haddad Ricardo, Sampaio Sandra Coccuzzo, Elias Maria CarolinaORCID, Kashima Simone, Junior de Alcantara Luiz CarlosORCID, Covas Dimas Tadeu
Abstract
AbstractThe 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.
Funder
International Centre for Genetic Engineering and Biotechnology U.S. Department of Health & Human Services | NIH | Center for Information Technology WHO | Pan American Health Organization
Publisher
Springer Science and Business Media LLC
Subject
Cell Biology,Microbiology (medical),Genetics,Applied Microbiology and Biotechnology,Immunology,Microbiology
Reference54 articles.
1. Coronavirus Disease (COVID-19) Situation Reports (WHO, 20 June 2022); https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports 2. COVID-19 Map (Johns Hopkins Coronavirus Resource Center, 20 June 2022); https://coronavirus.jhu.edu/map.html 3. COVID-19 Situation Reports (Pan American Health Organization (PAHO)/WHO, 20 June 2022); https://www.paho.org/en/covid-19-situation-reports 4. Candido, D. S. et al. Evolution and epidemic spread of SARS-CoV-2 in Brazil. Science 369, 1255–1260 (2020). 5. Xavier, J. et al. The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing. Emerg. Microbes Infect. 9, 1824–1834 (2020).
Cited by
60 articles.
订阅此论文施引文献
订阅此论文施引文献，注册后可以免费订阅5篇论文的施引文献，订阅后可以查看论文全部施引文献
|
|