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


Author
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;  Pereira, Glauco de Carvalho;  Vazquez, Cynthia;  Sanabria, Gladys Mercedes Estigarribia;  Oliveira, Elaine Cristina de;  Demarchi, Luiz;  Croda, Julio;  Bezerra, Rafael dos Santos;  Lima, Loyze Paola Oliveira de ;  Barros, Claudia Renata dos Santos ;  Marqueze, Elaine Cristina ;  Bernardino, Jardelina de Souza Todão ;  Moretti, Debora Botequio ;  Brassaloti, Ricardo Augusto;  Cassano, Raquel de Lello Rocha Campos;  Mariani, Pilar Drummond Sampaio Corrêa;  Kitajima, João Paulo;  Santos, Bibiana;  Proto-Siqueira, Rodrigo;  Cantarelli, Vlademir Vicente;  Tosta, Stephane;  Nardy, Vanessa Brandão;  Silva, Luciana Reboredo de Oliveira da;  Gómez, Marcela Kelly Astete;  Lima, Jaqueline Gomes;  Ribeiro, Adriana Aparecida;  Guimarães, Natália Rocha;  Watanabe, Luiz Takao;  Silva, Luana Barbosa Da;  Ferreira, Raquel da Silva;  Penha, Mara Patricia F. da;  Ortega, María José;  Fuente, Andrea Gómez de la;  Villalba, Shirley;  Torales, Juan;  Gamarra, María Liz;  Aquino, Carolina;  Figueredo, Gloria Patricia Martínez;  Fava, Wellington Santos;  Motta-Castro, Ana Rita C.;  Venturini, James;  Oliveira, Sandra Maria do Vale Leone de;  Gonçalves, Crhistinne Cavalheiro Maymone;  Rossa, Maria do Carmo Debur;  Becker, Guilherme Nardi;  Giacomini, Mayra Presibella;  Marques, Nelson Quallio;  Riediger, Irina Nastassja;  Raboni, Sonia;  Mattoso, Gabriela;  Cataneo, Allan D.;  Zanluca, Camila;  Santos, Claudia N. Duarte dos;  Assato, Patricia Akemi;  Costa, Felipe Allan da Silva da;  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;  Machado Neto, Raul ;  Filippis, Ana Maria Bispo de;  Cunha, Rivaldo Venancio da;  Freitas, Carla;  Peterka, Cassio Roberto Leonel;  Fernandes, Cássia de Fátima Rangel;  Navegantes, Wildo;  Said, Rodrigo Fabiano do Carmo;  Melo, Carlos F. Campelo de A e;  Almiron, Maria;  Lourenço, José;  Oliveira, Tulio de;  Holmes, Edward C.;  Haddad, Ricardo ;  Sampaio, Sandra Coccuzzo ;  Elias, Maria Carolina ;  Kashima, Simone;  Alcantara, Luiz Carlos Junior de;  Covas, Dimas Tadeu 
Publication type
Article
Language
English
Access rights
Open access
Terms of use
CC BY
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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.
Reference
Slavov SN, Fonseca V, Wilkinson E, Tegally H, Patané JSL, Viala VL, et al. Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil. Nat Microbiol. 2022; in press. doi:10.1038/s41564-022-01191-z.
Link to cite this reference
https://repositorio.butantan.gov.br/handle/butantan/4488
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Issue Date
2022


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