Genomic and epidemiological data sheds light on phases of the SARS-CoV-2 epidemic in Brazil

Results from a multinational project have shed new insights on SARS-CoV-2 origins in Brazil and how the transmission of the virus is unfolding in the country. 

Brazil currently has one of the fastest growing coronavirus epidemics in the world. As of 22 July 2020, Brazil had reported more than 2,118,000 cases (the second highest case tally in the world), and more than 80,000 deaths.

Researchers at the Department of Zoology, in collaboration with 15 Brazilian Institutions and the Imperial College COVID-19 Response Team, have generated a representative dataset of 427 new genomes sampled across Brazil. Published this week in Science, this is the largest genomic dataset from Latin America and one of the largest in the world. The team combined genomic, mobility and epidemiological data to better understand SARS-CoV-2 transmission at different scales and to investigate the impact of non-pharmaceutical interventions (NPIs) in virus transmission and spread in the country.

The researchers found that NPIs, such as school closures and store closures during late March, helped to reduce the reproduction (R) number from greater than 3 in São Paulo and Rio de Janeiro, to close to 1 in both states.

However, since restrictions were lifted the R number in both states remains above 1 – meaning the epidemic is growing.

Molecular analysis of the virus strains in Brazil reveals that there were >100 international introductions of the virus to the country. Most of these introductions were well-connected states such as São Paulo (36% of all imports), Minas Gerais (24%), Ceará (10%) and Rio de Janeiro (8%).

Only a handful of these introductions resulted in sustained onwards transmission across the country. Most ongoing virus transmission originated from three main virus clades that were introduced from Europe before the reduction in international flights.

Strains of the virus in Brazil can mainly (76%) be grouped into three clades (groups), and were introduced to the country around late February and early March, suggesting that international travel restrictions initiated after this period would have had limited impact.

The researchers estimate that during the first epidemic phase, the virus spread mostly locally and within-state borders. In contrast, the second phase was characterised by long-distance movement and the ignition of the epidemic outside the southeast region of Brazil. 

Dr Nuno Faria, UK principal investigator of the CADDE Project and co-corresponding author of the study, said “Genome sequencing is increasingly becoming part of the toolkit for the response to infectious epidemics and can have a direct impact on public health. We generated 427 new SARS-CoV-2 genomes from across Brazil and we analysed these together with mobility and epidemiological data to investigate how SARS-CoV-2 spread and transmission changed in response to control measures implemented in the country.”

The researchers say that there is now an urgent need to prevent future virus transmission by expanding rapid and accessible diagnostic screening, contact tracing, quarantining of new cases and coordinated social and physical distancing measures across the country.


The research was supported by the UK-Brazil CADDE Partnership funded by Medical Research Council (MRC)-São Paulo Research Foundation (FAPESP), National Council for Scientific and Technological Development (CNPq), Financiadora de Estudos e Projetos (FINEP), Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ) and Wellcome Trust.