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

• DOI: 10.1038/s41564-022-01191-z
• Publication Date: 2022-08-18T16:03:29Z
• Authors: Marta Giovanetti; Svetoslav Nanev S...; Vagner Fonseca; Eduan Wilkinson; Houriiyah Tegally; José Salvatore Le...; Vincent Louis Viala; Emmanuel James San; Evandra Strazza R...; Elaine Vieira Santos; Flavia Aburjaile; Joilson Xavier; Hegger Fritsch; Talita Emile Ribe...; Felicidade Pereira; Arabela Leal; Felipe Campos de ...; Glauco de Carvalh...; Cynthia Vazquez; Gladys Mercedes E...; Elaine Cristina d...; Luiz Demarchi; Julio Croda; Rafael dos Santos...; Loyze Paola Olive...; Antonio Jorge Mar...; Claudia Renata do...; Elaine Cristina M...; Jardelina de Souz...; Debora Botequio M...; Ricardo Augusto B...; Raquel de Lello R...; Pilar Drummond Sa...; João Paulo Kitajima; Bibiana Santos; Rodrigo Proto-Siq...; Vlademir Vicente ...; Stephane Tosta; Vanessa Brandão N...; Luciana Reboredo ...; Marcela Kelly Ast...; Jaqueline Gomes Lima; Adriana Aparecida...; Natália Rocha Gui...; Luiz Takao Watanabe; Luana Barbosa Da ...; Raquel da Silva F...; Mara Patricia F. ...; María José Ortega; Andrea Gómez de l...; Shirley Villalba; Juan Torales; María Liz Gamarra; Carolina Aquino; Gloria Patricia M...; Wellington Santos...; Ana Rita C. Motta...; James Venturini; Sandra Maria do V...; Crhistinne Cavalh...; Maria do Carmo De...; Guilherme Nardi B...; Mayra Presibella ...; Nelson Quallio Ma...; Irina Nastassja R...; Sonia Raboni; Gabriela Mattoso; Allan D. Cataneo; Camila Zanluca; Claudia N. Duarte...; Patricia Akemi As...; Felipe Allan da S...; Mirele Daiana Poleti; Jessika Cristina ...; Elisangela Chicar...; Cecilia Artico Banho; Lívia Sacchetto; Marília Mazzi Moraes; Rejane Maria Tomm...; Jayme A. Souza-Neto; Maurício Lacerda ...; Heidge Fukumasu; Luiz Lehmann Cout...; Rodrigo Tocantins...; Raul Machado Neto; Ana Maria Bispo d...; Rivaldo Venancio ...; Carla Freitas; Cassio Roberto Le...; Cássia de Fátima ...; Wildo Navegantes; Rodrigo Fabiano d...; Carlos F. Campelo...; Maria Almiron; José Lourenço; Tulio de Oliveira; Edward C. Holmes; Ricardo Haddad; Sandra Coccuzzo S...; Maria Carolina Elias; Simone Kashima; Luiz Carlos Junio...; Dimas Tadeu Covas
• Keywords: Pandemic

Abstract The high numbers of COVID-19 cases and deaths in Brazil have made Latin America an epicentre the pandemic. SARS-CoV-2 established sustained transmission early pandemic, but important gaps remain our understanding virus dynamics at a national scale. We use 17,135 near-complete genomes sampled from 27 Brazilian states bordering country Paraguay. From March to November 2020, we detected co-circulation multiple viral lineages that were linked importations (predominantly Europe). After large, local clusters within country. In absence effective restriction measures, epidemic progressed, January 2021 there was emergence onward spread, both abroad, variants concern under monitoring, including Gamma (P.1) Zeta (P.2). also characterized genomic overview Paraguay evidence importation ancestor Brazil. Our findings show surveillance enabled assessment real-time spread emerging variants.