Paola Cristina Resende , Edson Delatorre , Tiago Gräf , Daiana Mir , Fernando do Couto Motta , Luciana Reis Appolinario , Anna Carolina Dias da Paixão , Maria Ogrzewalska , Braulia Caetano , Mirleide Cordeiro dos Santos , Jessylene de Almeida Ferreira , Edivaldo Costa Santos Junior , Sandro Patroca da Silva , Sandra Bianchini Fernandes , Lucas A Vianna , Larissa da Costa Souza , Jean F G Ferro , Vanessa B Nardy , Júlio Croda , Wanderson K Oliveira , André Abreu , Gonzalo Bello , Marilda M Siqueira
June 18 2020
Despite all efforts to control the COVID-19 spread, the SARS-CoV-2 reached South America within three months after its first detection in China, and Brazil became one of the hotspots of COVID-19 in the world. Several SARS-CoV-2 lineages have been identified and some local clusters have been described in this early pandemic phase in Western countries. Here we investigated the genetic diversity of SARS-CoV-2 during the early phase (late February to late April) of the epidemic in Brazil. Phylogenetic analyses revealed multiple introductions of SARS-CoV-2 in Brazil and the community transmission of a major B.1.1 lineage defined by two amino acid substitutions in the Nucleocapsid and ORF6. This SARS-CoV-2 Brazilian lineage was probably established during February 2020 and rapidly spread through the country, reaching different Brazilian regions by the middle of March 2020. Our study also supports occasional exportations of this Brazilian B.1.1 lineage to neighboring South American countries and to more distant countries before the implementation of international air travels restrictions in Brazil.