Evolution and epidemic spread of SARS-CoV-2 in Brazil.
Candido DS., Claro IM., de Jesus JG., Souza WM., Moreira FRR., Dellicour S., Mellan TA., du Plessis L., Pereira RHM., Sales FCS., Manuli ER., Thézé J., Almeida L., Menezes MT., Voloch CM., Fumagalli MJ., Coletti TM., da Silva CAM., Ramundo MS., Amorim MR., Hoeltgebaum HH., Mishra S., Gill MS., Carvalho LM., Buss LF., Prete CA., Ashworth J., Nakaya HI., Peixoto PS., Brady OJ., Nicholls SM., Tanuri A., Rossi ÁD., Braga CKV., Gerber AL., de C Guimarães 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 AA., Simeoni CL., Forato J., Sposito AC., Schreiber AZ., Santos MNN., de Sá CZ., Souza RP., Resende-Moreira LC., Teixeira MM., Hubner J., Leme PAF., Moreira RG., Nogueira ML., Brazil-UK Centre for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE) Genomic Network None., Ferguson NM., Costa SF., Proenca-Modena JL., Vasconcelos ATR., Bhatt S., Lemey P., Wu C-H., Rambaut A., Loman NJ., Aguiar RS., Pybus OG., Sabino EC., Faria NR.
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.