Evolution and epidemic spread of SARS-CoV-2 in Brazil

Science. 2020 Sep 4;369(6508):1255-1260. doi: 10.1126/science.abd2161. Epub 2020 Jul 23.


Brazil currently has one of the fastest-growing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemics in the world. Because of limited available data, assessments of the impact of nonpharmaceutical interventions (NPIs) on this virus spread remain challenging. Using a mobility-driven transmission model, we show that NPIs reduced the reproduction number from >3 to 1 to 1.6 in São Paulo and Rio de Janeiro. Sequencing of 427 new genomes and analysis of a geographically representative genomic dataset identified >100 international virus introductions in Brazil. We estimate that most (76%) of the Brazilian strains fell in three clades that were introduced from Europe between 22 February and 11 March 2020. During the early epidemic phase, we found that SARS-CoV-2 spread mostly locally and within state borders. After this period, despite sharp decreases in air travel, we estimated multiple exportations from large urban centers that coincided with a 25% increase in average traveled distances in national flights. This study sheds new light on the epidemic transmission and evolutionary trajectories of SARS-CoV-2 lineages in Brazil and provides evidence that current interventions remain insufficient to keep virus transmission under control in this country.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Basic Reproduction Number
  • Bayes Theorem
  • Betacoronavirus / classification
  • Betacoronavirus / genetics*
  • Brazil / epidemiology
  • COVID-19
  • COVID-19 Testing
  • Cities / epidemiology
  • Clinical Laboratory Techniques
  • Coronavirus Infections / diagnosis
  • Coronavirus Infections / epidemiology*
  • Coronavirus Infections / prevention & control
  • Coronavirus Infections / transmission*
  • Coronavirus Infections / virology
  • Europe
  • Evolution, Molecular
  • Genome, Viral
  • Humans
  • Models, Genetic
  • Models, Statistical
  • Pandemics / prevention & control
  • Phylogeny
  • Phylogeography
  • Pneumonia, Viral / epidemiology*
  • Pneumonia, Viral / prevention & control
  • Pneumonia, Viral / transmission*
  • Pneumonia, Viral / virology
  • SARS-CoV-2
  • Spatio-Temporal Analysis
  • Travel
  • Urban Population

Associated data

  • Dryad/10.5061/dryad.rxwdbrv5z