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

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.

Authors

Darlan S Candido; Ingra M Claro; Jaqueline G de Jesus; William M Souza; Filipe R R Moreira; Simon Dellicour; Thomas A Mellan; Louis du Plessis; Rafael H M Pereira; Flavia C S Sales; Erika R Manuli; Julien Thézé; Luiz Almeida; Mariane T Menezes; Carolina M Voloch; Marcilio J Fumagalli; Thaís M Coletti; Camila A M da Silva; Mariana S Ramundo; Mariene R Amorim; Henrique H Hoeltgebaum; Swapnil Mishra; Mandev S Gill; Luiz M Carvalho; Lewis F Buss; Carlos A Prete; Jordan Ashworth; Helder I Nakaya; Pedro S Peixoto; Oliver J Brady; Samuel M Nicholls; Amilcar Tanuri; Átila D Rossi; Carlos K V Braga; Alexandra L Gerber; Ana Paula de C Guimarães; Nelson Gaburo; Cecila Salete Alencar; Alessandro C S Ferreira; Cristiano X Lima; José Eduardo Levi; Celso Granato; Giulia M Ferreira; Ronaldo S Francisco; Fabiana Granja; Marcia T Garcia; Maria Luiza Moretti; Mauricio W Perroud; Terezinha M P P Castiñeiras; Carolina S Lazari; Sarah C Hill; Andreza Aruska de Souza Santos; Camila L Simeoni; Julia Forato; Andrei C Sposito; Angelica Z Schreiber; Magnun N N Santos; Camila Zolini de Sá; Renan P Souza; Luciana C Resende-Moreira; Mauro M Teixeira; Josy Hubner; Patricia A F Leme; Rennan G Moreira; Maurício L Nogueira; Neil M Ferguson; Silvia F Costa; José Luiz Proenca-Modena; Ana Tereza R Vasconcelos; Samir Bhatt; Philippe Lemey; Chieh-Hsi Wu; Andrew Rambaut; Nick J Loman; Renato S Aguiar; Oliver G Pybus; Ester C Sabino; Nuno Rodrigues Faria

External link

https://pubmed.ncbi.nlm.nih.gov/32703910

Publication Year

2020

Publication Journal

Science

Associeted Project

Digital Epidemiology

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