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

Candido, Darlan S. and Claro, Ingra M. and de Jesus, Jaqueline G. and Souza, William M. and Moreira, Filipe R. R. and Dellicour, Simon and Mellan, Thomas A. and du Plessis, Louis and Pereira, Rafael H. M. and Sales, Flavia C. S. and Manuli, Erika R. and Thézé, Julien and Almeida, Luiz and Menezes, Mariane T. and Voloch, Carolina M. and Fumagalli, Marcilio J. and Coletti, Thaís M. and da Silva, Camila A. M. and Ramundo, Mariana S. and Amorim, Mariene R. and Hoeltgebaum, Henrique H. and Mishra, Swapnil and Gill, Mandev S. and Carvalho, Luiz M. and Buss, Lewis F. and Prete, Carlos A. and Ashworth, Jordan and Nakaya, Helder I. and Peixoto, Pedro S. and Brady, Oliver J. and Nicholls, Samuel M. and Tanuri, Amilcar and Rossi, Átila D. and Braga, Carlos K.V. and Gerber, Alexandra L. and de C. Guimarães, Ana AP and Gaburo, N and Alencar, CS and Ferreira, ACS and Lima, CX and Levi, JE and Granato, C and Ferreira, GM and Francisco, RS and Granja, F and Garcia, MT and Moretti, ML and Perroud, MW and Castiñeiras, TMPP and Lazari, CS and Hill, SC and de Souza Santos, A and Simeoni, CL and Forato, J and Sposito, AC and Schreiber, AZ and Santos, MNN and de Sá, CZ and Souza, RP and Resende-Moreira, LC and Teixeira, MM and Hubner, J and Leme, PAF and Moreira, RG and Nogueira, ML and Ferguson, NM and Costa, SF and Proenca-Modena, JL and Vasconcelos, ATR and Bhatt, S and Lemey, P and Wu, CH and Rambaut, A and Loman, NJ and Aguiar, RS and Pybus, OG and Sabino, EC and Faria, NR (2020) Evolution and epidemic spread of SARS-CoV-2 in Brazil. Science. eabd2161. ISSN 0036-8075

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Official URL: https://doi.org/10.1126/science.abd2161

Abstract

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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