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 AP; Gaburo, N; Alencar, CS; Ferreira, ACS; Lima, CX; Levi, JE; Granato, C; Ferreira, GM; Francisco, RS; Granja, F; Garcia, MT; Moretti, ML; Perroud, MW; Castiñeiras, TMPP; Lazari, CS; Hill, SC; de Souza Santos, A; Simeoni, CL; Forato, J; Sposito, AC; Schreiber, AZ; Santos, MNN; de Sá, CZ; Souz...

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.

Citation

Candido, D. S., Claro, I. M., de Jesus, J. G., Souza, W. M., Moreira, F. R. R., Dellicour, S., Mellan, T. A., du Plessis, L., Pereira, R. H. M., Sales, F. C. S., Manuli, E. R., Thézé, J., Almeida, L., Menezes, M. T., Voloch, C. M., Fumagalli, M. J., Coletti, T. M., da Silva, C. A. M., Ramundo, M. S., Amorim, M. R., …Faria, N. (2020). Evolution and epidemic spread of SARS-CoV-2 in Brazil. Science, eabd2161. https://doi.org/10.1126/science.abd2161

• Journal Article Type: Article
• Acceptance Date: Jul 16, 2020
• Publication Date: Jul 23, 2020
• Deposit Date: Sep 3, 2020
• Publicly Available Date: Sep 3, 2020
• Journal: Science
• Print ISSN: 0036-8075
• Electronic ISSN: 1095-9203
• Publisher: American Association for the Advancement of Science
• Peer Reviewed: Peer Reviewed
• Pages: eabd2161
• DOI: https://doi.org/10.1126/science.abd2161
• Public URL: https://rvc-repository.worktribe.com/output/1376663
• Publisher URL: https://doi.org/10.1126/science.abd2161