Genomic epidemiology reveals the impact of national and international restrictions measures on 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 James Emmanuel , Rodrigues Evandra Strazza , Vieira Santos Elaine , Aburjaile Flavia , Xavier Joilson , Fritsch Hegger , Ribeiro Adelino Talita Emile , Pereira Felicidade , Leal Arabela , Campos de Melo Iani Felipe , de Carvalho Pereira Glauco , Vazquez Cynthia , Mercedes Estigarribia Sanabria Gladys , 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 , de Souza Todao Bernardino Jardelina , Moretti Debora Botequio , Brassaloti Ricardo Augusto , de Lello Rocha Campos Cassano Raquel , Drummond Sampaio Corrêa Mariani Pilar , Kitajima João Paulo , Santos Bibiana , Proto-Siqueira Rodrigo , Cantarelli Vlademir Vicente , Tosta Stephane , Brandão Nardy Vanessa , Reboredo de Oliveira da Silva Luciana , Astete Gómez Marcela Kelly , Lima Jaqueline Gomes , Ribeiro Adriana Aparecida , Guimarães Natália Rocha , Watanabe Luiz Takao , Barbosa Da Silva Luana , da Silva Ferreira Raquel , F. da Penha Mara Patricia , Ortega María José , Gómez de la Fuente Andrea , Villalba Shirley , Torales Juan , Gamarra María Liz , Aquino Carolina , Martínez Figueredo Gloria Patricia , Fava Wellington Santos , Motta-Castro Ana Rita C. , Venturini James , do Vale Leone de Oliveira Sandra Maria , Cavalheiro Maymone Gonçalves Crhistinne , Debur Rossa Maria do Carmo , Becker Guilherme Nardi , Presibella Mayra Marinho , Marques Nelson Quallio , Riediger Irina Nastassja , Raboni Sonia , Coelho Gabriela Mattoso , Cataneo Allan Henrique Depieri , Zanluca Camila , dos Santos Claudia N Duarte , Assato Patricia Akemi , Allan da Silva da Costa Felipe , Poleti Mirele Daiana , Chagas Lesbon Jessika Cristina , Mattos Elisangela Chicaroni , Banho Cecilia Artico , Sacchetto Lívia , Moraes Marília Mazzi , Tommasini Grotto Rejane Maria , 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 , Leonel Peterka Cassio Roberto , Rangel Fernandes Cássia de Fátima , de Araújo Wildo Navegantes , do Carmo Said Rodrigo Fabiano , Almiron Maria , Campelo de Albuquerque e Melo Carlos Frederico , Lourenço José , de Oliveira Tulio , Holmes Edward C. , Haddad Ricardo , Sampaio Sandra Coccuzzo , Elias Maria Carolina , Kashima Simone , de Alcantara Luiz Carlos Junior , Covas Dimas Tadeu 
Published: October 2021

Brazil has experienced some of the highest numbers of COVID-19 cases and deaths globally and from May 2021 made Latin America a pandemic epicenter. Although SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, important gaps remain in our understanding of virus transmission dynamics at the national scale. Here, we describe the genomic epidemiology of SARS-CoV-2 using near-full genomes sampled from 27 Brazilian states and a bordering country - Paraguay. We show that the early stage of the pandemic in Brazil was characterised by the co-circulation of multiple viral lineages, linked to multiple importations predominantly from Europe, and subsequently characterized by large local transmission clusters. As the epidemic progressed under an absence of effective restriction measures, there was a local emergence and onward international spread of Variants of Concern (VOC) and Variants Under Monitoring (VUM), including Gamma (P.1) and Zeta (P.2). In addition, we provide a preliminary genomic overview of the epidemic in Paraguay, showing evidence of importation from Brazil. These data reinforce the usefulness and need for the implementation of widespread genomic surveillance in South America as a toolkit for pandemic monitoring that provides a means to follow the real-time spread of emerging SARS-CoV-2 variants with possible implications for public health and immunization strategies.