Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil
Authors: 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 
Published: August 2022

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.