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Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 lineages Gamma and P.2 in Brazil

2022; Cell Press; Volume: 25; Issue: 4 Linguagem: Inglês

10.1016/j.isci.2022.104156

2589-0042

Tiago Gräf, Gonzalo Bello, Felipe Gomes Naveca, Marcelo Ferreira da Costa Gomes, Vanessa Leiko Oikawa Cardoso, Alexandre Freitas da Silva, Filipe Zimmer Dezordi, Mirleide Cordeiro dos Santos, Mauro de Medeiros Oliveira, Érika Lopes Rocha Batista, Alessandro Leonardo Álvares Magalhães, Fernando Vinhal, Fábio Miyajima, Helisson Faoro, Ricardo Khouri, Gabriel Luz Wallau, Edson Delatorre, Marilda Mendonça Siqueira, Paola Cristina Resende, Tirza Mattos, Valdinete Alves do Nascimento, Victor Costa de Souza, André de Lima Guerra Corado, Fernanda Nascimento, George Silva, Matilde Mejía, Maria Júlia Brandão, Ágatha Costa, Karina Pessoa, Michele Silva de Jesus, Luciana Fé Gonçalves, Cristiano Fernandes, Valnete Andrade, Luana Soares Barbagelata, Ana Cecília Ribeiro Cruz, Andréa Ferreira da Costa, Lindomar dos Anjos Silva, Jucimária Dantas Galvão, Anderson Brandão Leite, Felicidade Mota Pereira, Thaís De Oliveira Costa, Joaquim Cesar Sousa, Lídio Gonçãlves Lima Neto, Haline Barroso, Dalane Loudal Florentino Teixeira, João Felipe Bezerra, Cássia Docena, Raul Emídio de Lima, Lílian Caroliny Amorim Silva, Gustavo Barbosa de Lima, Laís Ceschini Machado, Matheus Filgueira Bezerra, Marcelo Henrique Santos Paiva, Maria Eduarda Pessoa Lopes Dantas, Raíssa Liane Do Nascimento Pereira, Josélio Maria Galvão de Araújo, Cliomar A. Santos, Rodrigo Ribeiro‐Rodrigues, André Felipe Leal Bernardes, Felipe Campos de Melo Iani, Beatriz Grinsztejn, Valdiléa G. Veloso, Patrícia Brasil, Anna Carolina Dias Paixão, Luciana Appolinario, Renata Serrano Lopes, Fernando Couto Motta, Alice Sampaio Barreto da Rocha, Tainá Moreira Martins Venas, Elisa Cavalcante Pereira, Andréa Cony Cavalcanti, Leonardo da Costa Bastos, Luís Fernando de Macedo Brígido, Mauro de Medeiros Oliveira, Michelle Orane Schemberger, Andréia Akemi Suzukawa, Irina Nastassja Riediger, Maria do Carmo Debur, Richard Steiner Salvato, Tatiana Schäffer Gregianini, Darcita Büerger Rovaris, Sandra Bianchini Fernandes,

vaccines and immunoinformatics approaches

The COVID-19 epidemic in Brazil experienced two major lineage replacements until mid-2021. The first was driven by lineage P.2, in late 2020, and the second by lineage Gamma, in early 2021. To understand how these SARS-CoV-2 lineages spread in Brazil, we analyzed 11,724 genomes collected throughout the country between September 2020 and April 2021. Our findings indicate that lineage P.2 probably emerged in July 2020 in the Rio de Janeiro state and Gamma in November 2020 in the Amazonas state. Both states were the main hubs of viral disseminations to other Brazilian locations. We estimate that Gamma was 1.56–3.06 times more transmissible than P.2 in Rio de Janeiro and that the median effective reproductive number (Re) of Gamma varied according to the geographic context (Re = 1.59–3.55). In summary, our findings support that lineage Gamma was more transmissible and spread faster than P.2 in Brazil.