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

Candido, Darlan S.; Claro, Ingra M.; de Jesus, Jaqueline G.; Souza, William M.; Moreira, Filipe R. R.; Dellicour, Simon; Mellan, Thomas A.; du Plessis, Louis; Pereira, Rafael H. M.; Sales, Flavia C. S.; Manuli, Erika R.; Thézé, Julien; Almeida, Luiz; Menezes, Mariane T.; Voloch, Carolina M.; Fumagalli, Marcilio J.; Coletti, Thaís M.; da Silva, Camila A. M.; 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 K.V.; Gerber, Alexandra L.; de C. Guimarães, Ana Paula; Gaburo, Nelson; Alencar, Cecila Salete; Ferreira, Alessandro C.S.; 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 M. P. P.; Lazari, Carolina S.; Hill, Sarah C.; de Souza Santos, Andreza Aruska; Simeoni, Camila L.; Forato, Julia; Sposito, Andrei C.; Schreiber, Angelica Z.; Santos, Magnun N. N.; de Sá, Camila Zolini; Souza, Renan P.; Resende-Moreira, Luciana C.; Teixeira, Mauro M.; Hubner, Josy; Leme, Patricia A. F.; Moreira, Rennan G; Nogueira, Maurício L.; 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.; Faria, Nuno Rodrigues

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.