Evolution and epidemic spread of SARS-CoV-2 in Brazil.
; Claro, Ingra M; de Jesus, Jaqueline G; Souza, William M; Moreira, Filipe RR; Dellicour, Simon; Mellan, Thomas A; du Plessis, Louis; Pereira, Rafael HM; Sales, Flavia CS; +69 more...Manuli, Erika R; Thézé, Julien; Almeida, Luiz; Menezes, Mariane T; Voloch, Carolina M; Fumagalli, Marcilio J; Coletti, Thaís M; da Silva, Camila AM; Ramundo, Mariana S; Amorim, Mariene R; Hoeltgebaum, Henrique H; Mishra, Swapnil; Gill, Mandev S; Carvalho, Luiz M; Buss, Lewis F; Prete, Carlos A; Ashworth, Jordan; Nakaya, Helder I; Peixoto, Pedro S; Brady, Oliver J; Nicholls, Samuel M; Tanuri, Amilcar; Rossi, Átila D; Braga, Carlos KV; Gerber, Alexandra L; de C Guimarães, Ana Paula; Gaburo, Nelson; Alencar, Cecila Salete; Ferreira, Alessandro CS; Lima, Cristiano X; Levi, José Eduardo; Granato, Celso; Ferreira, Giulia M; Francisco, Ronaldo S; Granja, Fabiana; Garcia, Marcia T; Moretti, Maria Luiza; Perroud, Mauricio W; Castiñeiras, Terezinha MPP; Lazari, Carolina S; Hill, Sarah C; de Souza Santos, Andreza Aruska; Simeoni, Camila L; Forato, Julia; Sposito, Andrei C; Schreiber, Angelica Z; Santos, Magnun NN; de Sá, Camila Zolini; Souza, Renan P; Resende-Moreira, Luciana C; Teixeira, Mauro M; Hubner, Josy; Leme, Patricia AF; Moreira, Rennan G; Nogueira, Maurício L; Brazil-UK Centre for Arbovirus Discovery, Diagnosis, Genomics an; Ferguson, Neil M; Costa, Silvia F; Proenca-Modena, José Luiz; Vasconcelos, Ana Tereza R; Bhatt, Samir; Lemey, Philippe; Wu, Chieh-Hsi; Rambaut, Andrew; Loman, Nick J; Aguiar, Renato S; Pybus, Oliver G; Sabino, Ester C; and Faria, Nuno Rodrigues
(2020)
Evolution and epidemic spread of SARS-CoV-2 in Brazil.
Science, 369 (6508).
pp. 1255-1260.
ISSN 0036-8075
DOI: 10.1126/science.abd2161
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.
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