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New genetic analysis reveals how coronavirus spread around Brazil, which is experiencing one of the world's fastest growing epidemics.

Results from a multinational project led by the Imperial College COVID-19 Response Team with 15 Brazilian Institutions, and the University of Oxford, has shed new insights on the virus's origins in Brazil and on 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 largest number in the world, and more than 80,000 deaths.

Largest genomic dataset from Latin America

Writing in the journal Science, the researchers generated a representative dataset of 427 new genomes sampled across Brazil.

This is the largest genomic dataset from Latin America and one of the largest in the world.

They combined genomic, mobility and epidemiological data to better understand the virus 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.

Introduction of virus to Brazil

Molecular analysis of the virus strains in Brazil reveals that there were more than 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 originates 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. 

Local spread during first epidemic phase

Genetic analysis estimated community transmission in Brazil’s large urban metropolis, such as São Paulo city, by late February, around the time of the first reported case in the country.

The early detection attests to the improved outbreak preparedness in the country and the rapid early implementation of molecular surveillance across Brazil.

The researchers from the WHO Collaborating Centre for Infectious Disease Modelling within the MRC Centre for Global Infectious Disease Analysis, the Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), in collaboration with Imperial’s Department of Mathematics, the University of Oxford and 15 Brazilian institutions including the University of São Paulo, also 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.

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.

'Largest genomic dataset in Latin America'

Professor Nuno Faria, UK principal investigator of the CADDE Project, Reader at Imperial College and University of Oxford, 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 analyse 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.”

Professor Ester Sabino, Brazil principal investigator of the CADDE Project and co-corresponding author of the study said “We generated the largest genomic dataset from Latin America by building an innovative and collaborative network across Brazil and the UK. This has important implications for early detection of virus resurgences, and our capacity to respond to new viral threats”.

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.

See the press release of this article