Genomic epidemiology reveals how restriction measures shaped the SARS-CoV-2 epidemic in Brazil
2021
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 | de Melo Iani, Felipe Campos | de Carvalho Pereira, Glauco | Vazquez, Cynthia | Sanabria, Gladys Mercedes Estigarribia | de Oliveira, Elaine Cristina | Demarchi, Luiz | Croda, Julio | dos Santos Bezerra, Rafael | de Lima, Loyze Paola Oliveira | 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 | Mariani, Pilar Drummond Sampaio Corrêa | Kitajima, João Paulo | Santos, Bibiana | Proto-Siqueira, Rodrigo | Cantarelli, Vlademir Vicente | Tosta, Stephane | Nardy, Vanessa Brandão | da Silva, Luciana Reboredo de Oliveira | Gómez, Marcela Kelly Astete | Lima, Jaqueline Gomes | Ribeiro, Adriana Aparecida | Guimarães, Natália Rocha | Watanabe, Luiz Takao | Da Silva, Luana Barbosa | 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 | de Oliveira, Sandra Maria do Vale Leone | Gonçalves, Crhistinne Cavalheiro Maymone | do Carmo Debur Rossa, Maria | 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 Costa, Felipe 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 | Neto, Raul Machado | de Filippis, Ana Maria Bispo | da Cunha, Rivaldo Venancio | Freitas, Carla | Peterka, Cassio Roberto Leonel | de Fátima Rangel Fernandes, Cássia | de Araújo, Wildo Navegantes | do Carmo Said, Rodrigo Fabiano | Almiron, Maria | de Albuquerque e Melo, Carlos Frederico Campelo | 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
Abstract Brazil has experienced some of the highest numbers of COVID-19 infections and deaths globally and made Latin America a pandemic epicenter from May 2021. Although SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, important gaps remain in our understanding of local virus transmission dynamics. Here, we describe the genomic epidemiology of SARS-CoV-2 using near-full genomes sampled from 27 Brazilian states and an adjacent 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, the absence of effective restriction measures led to the local emergence and international spread of Variants of Concern (VOC) and under monitoring (VUM), including the Gamma (P.1) and Zeta (P.2) variants. In addition, we provide a preliminary genomic overview of the epidemic in Paraguay, showing evidence of importation from Brazil. These data reinforce the need for the implementation of widespread genomic surveillance in South America as a toolkit for pandemic monitoring and providing a means to follow the real-time spread of emerging SARS-CoV-2 variants with possible implications for public health and immunization strategies.
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