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

The COVID-19 pandemic in Brazil is assessed using phylogenetic and phylogeographic analysis. The high numbers of COVID-19 cases and deaths in Brazil have made Latin America an epicentre 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 at a national scale. We use 17,135 near-complete genomes sampled from 27 Brazilian states and bordering country Paraguay. From March to 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 emergence and onward spread, both within and abroad, of variants of concern and variants under monitoring, 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 variants of concern from Brazil. Our findings show that genomic surveillance in Brazil enabled assessment of the real-time spread of emerging SARS-CoV-2 variants.

Automated summary

The COVID-19 pandemic in Brazil is assessed using phylogenetic and phylogeographic analysis. Multiple viral lineages were found to be circulating in Brazil with links to importations from Europe. Large local transmission clusters were detected within the country, and variants of concern and variants under monitoring emerged and spread both within and outside Brazil. Genomic surveillance in Brazil enabled real-time assessment of the spread of emerging SARS-CoV-2 variants.