BioProject

The high numbers of COVID-19 cases and deaths in Brazil have made Latin America an epicenter of the pandemic. More...

The high numbers of COVID-19 cases and deaths in Brazil have made Latin America an epicenter 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 on a national scale. We use 17,135 near-complete genomes sampled from 27 Brazilian states and the bordering country Paraguay. From March 2020-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 the emergence and onward spread, both within and abroad, of Variants of Concern (VOC) and Variants Under Monitoring (VUM), 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 VOC from Brazil. Our findings show that genomic surveillance in Brazil enabled the assessment of the real-time spread of emerging SARS-CoV-2 variants. Less...