Brazil currently has one of the fastest growing SARS-CoV-2 epidemics in the world. Owing to limited available data, assessments of the impact of non-pharmaceutical interventions (NPIs) on virus spread remain challenging. Using a mobility-driven transmission model, we show that NPIs reduced the reproduction number from >3 to 1–1.6 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 February11 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 travelled distances in national flights. This study sheds new light on the epidemic transmission and evolutionary trajectories of SARS-CoV-2 lineages in Brazil, and provide evidence that current interventions remain insufficient to keep virus transmission under control in the country.
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Candido, D., Claro, I., de Jesus, J., Souza, W., Moreira, F., Dellicour, S., Mellan, T., du Plessis, L., Pereira, R., Sales, F., Manuli, E., Thézé, J., Almeida, L., Menezes, M., Voloch, C., Fumagalli, M., Coletti, T., da Silva, C., Ramundo, M., Amorim, M., Hoeltgebaum, H., Mishra, S., Gill, M., Carvalho, L., Buss, L., Prete, C., Ashworth, J., Nakaya, H., Peixoto, P., Brady, O., Nicholls, S., Tanuri, A., Rossi, Á., Braga, C., Gerber, A., De C Guimarães, A., Gaburo, N., Alencar, C., Ferreira, A., Lima, C., Levi, J., Granato, C., Ferreira, G., Francisco, R., Granja, F., Garcia, M., Moretti, M., Perroud, M., Castiñeiras, T., Lazari, C., Hill, S., De Souza Santos, A., Simeoni, C., Forato, J., Sposito, A., Schreiber, A., Santos, M., De Sá, C., Souza, R., Resende-moreira, L., Teixeira, M., Hubner, J., Leme, P., Moreira, R., Nogueira, M., Ferguson, N., Costa, S., Proença-Modena, J., Vasconcelos, A., Bhatt, S., Lemey, P., Wu, C., Rambaut, A., Loman, N., Aguiar, R., Pybus, O., Sabino, E. & Faria, N. 2020, 'Evolution and epidemic spread of SARS-CoV-2 in Brazil', Science, 369(6508), pp. 1255-1260. https://doi.org/10.1126/science.abd2161