摘要：SummaryThe 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.Graphical abstractDisplay OmittedHighlights•Lineages P.2 and Gamma probably emerged around July and November 2020, respectively•Lineages P.2 and Gamma mostly spread from Rio de Janeiro and Amazonas, respectively•Gamma was locally transmitted in most Brazilian states by December 2020•Gamma spread faster and was more transmissible than P.2Biological sciences; Viral microbiology; Phylogeny
