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


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.

SUBMITTER: Giovanetti M 

PROVIDER: S-EPMC9417986 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature

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

Giovanetti Marta M   Slavov Svetoslav Nanev SN   Fonseca Vagner V   Wilkinson Eduan E   Tegally Houriiyah H   Patané José Salvatore Leister JSL   Viala Vincent Louis VL   San Emmanuel James EJ   Rodrigues Evandra Strazza ES   Santos Elaine Vieira EV   Aburjaile Flavia F   Xavier Joilson J   Fritsch Hegger H   Adelino Talita Emile Ribeiro TER   Pereira Felicidade F   Leal Arabela A   Iani Felipe Campos de Melo FCM   de Carvalho Pereira Glauco G   Vazquez Cynthia C   Sanabria Gladys Mercedes Estigarribia GME   Oliveira Elaine Cristina de EC   Demarchi Luiz L   Croda Julio J   Dos Santos Bezerra Rafael R   Paola Oliveira de Lima Loyze L   Martins Antonio Jorge AJ   Renata Dos Santos Barros Claudia C   Marqueze Elaine Cristina EC   de Souza Todao Bernardino Jardelina J   Moretti Debora Botequio DB   Brassaloti Ricardo Augusto RA   de Lello Rocha Campos Cassano Raquel R   Mariani Pilar Drummond Sampaio Corrêa PDSC   Kitajima João Paulo JP   Santos Bibiana B   Proto-Siqueira Rodrigo R   Cantarelli Vlademir Vicente VV   Tosta Stephane S   Nardy Vanessa Brandão VB   Reboredo de Oliveira da Silva Luciana L   Gómez Marcela Kelly Astete MKA   Lima Jaqueline Gomes JG   Ribeiro Adriana Aparecida AA   Guimarães Natália Rocha NR   Watanabe Luiz Takao LT   Barbosa Da Silva Luana L   da Silva Ferreira Raquel R   da Penha Mara Patricia F MPF   Ortega María José MJ   de la Fuente Andrea Gómez AG   Villalba Shirley S   Torales Juan J   Gamarra María Liz ML   Aquino Carolina C   Figueredo Gloria Patricia Martínez GPM   Fava Wellington Santos WS   Motta-Castro Ana Rita C ARC   Venturini James J   do Vale Leone de Oliveira Sandra Maria SM   Gonçalves Crhistinne Cavalheiro Maymone CCM   do Carmo Debur Rossa Maria M   Becker Guilherme Nardi GN   Giacomini Mayra Presibella MP   Marques Nelson Quallio NQ   Riediger Irina Nastassja IN   Raboni Sonia S   Mattoso Gabriela G   Cataneo Allan D AD   Zanluca Camila C   Duarte Dos Santos Claudia N CN   Assato Patricia Akemi PA   Allan da Silva da Costa Felipe F   Poleti Mirele Daiana MD   Lesbon Jessika Cristina Chagas JCC   Mattos Elisangela Chicaroni EC   Banho Cecilia Artico CA   Sacchetto Lívia L   Moraes Marília Mazzi MM   Grotto Rejane Maria Tommasini RMT   Souza-Neto Jayme A JA   Nogueira Maurício Lacerda ML   Fukumasu Heidge H   Coutinho Luiz Lehmann LL   Calado Rodrigo Tocantins RT   Neto Raul Machado RM   Bispo de Filippis Ana Maria AM   Venancio da Cunha Rivaldo R   Freitas Carla C   Peterka Cassio Roberto Leonel CRL   de Fátima Rangel Fernandes Cássia C   Navegantes Wildo W   do Carmo Said Rodrigo Fabiano RF   Campelo de A E Melo Carlos F CF   Almiron Maria M   Lourenço José J   de Oliveira Tulio T   Holmes Edward C EC   Haddad Ricardo R   Sampaio Sandra Coccuzzo SC   Elias Maria Carolina MC   Kashima Simone S   Junior de Alcantara Luiz Carlos LC   Covas Dimas Tadeu DT  

Nature microbiology 20220818 9


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  ...[more]

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