Evolution and epidemic spread of SARS-CoV-2 in Brazil
Authors: Candido Darlan S. , Claro Ingra M. , de Jesus Jaqueline G. , Souza William M. , Moreira Filipe R. R. , Dellicour Simon , Mellan Thomas A. , Plessis Louis du , 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 Thais M. , Silva Camila A. M. , Ramundo Mariana S. , Amorim Mariene R. , Hoeltgebaum Henrique , Mishra Swapnil , Gill Mandev S. , Carvalho Luiz M. , Buss Lewis F. , Prete Carlos A. , Ashworth Jordan , Nakaya Helder , Peixoto Pedro S. , Brady Oliver J. , Nicholls Samuel M. , Tanuri Amilcar , Rossi Átila D. , Braga Carlos K.V. , Gerber Alexandra L. , Guimarães Ana Paula , Gaburo Nelson , Alencar Cecila S. , Ferreira Alessandro C.S. , Lima Cristiano X. , Levi José Eduardo , Granato Celso , Ferreira Giula M. , Francisco Ronaldo S. , Granja Fabiana , Garcia Marcia T. , Moretti Maria Luiza , Perroud Mauricio W. , Castineiras Terezinha M. P. P. , Lazari Carolina S. , Hill Sarah C. , de Souza Santos Andreza A. , 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 Lacerda ,   CADDE-Genomic-Network, 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 
Published: June 2020

Brazil currently has one of the fastest growing SARS-CoV-2 epidemics in the world. Due to limited available data, assessments of the impact of non-pharmaceutical interventions (NPIs) on virus transmission and epidemic spread remain challenging. We investigate the impact of NPIs in Brazil using epidemiological, mobility and genomic data. Mobility-driven transmission models for São Paulo and Rio de Janeiro cities show that the reproduction number (Rt) reached below 1 following NPIs but slowly increased to values between 1 to 1.3 (1.0–1.6). Genome sequencing of 427 new genomes and analysis of a geographically representative genomic dataset from 21 of the 27 Brazilian states identified >100 international introductions of SARS-CoV-2 in Brazil. We estimate that three clades introduced from Europe emerged between 22 and 27 February 2020, and were already well-established before the implementation of NPIs and travel bans. During this first phase of the epidemic establishment of SARS-CoV-2 in Brazil, we find that the virus spread mostly locally and within-state borders. Despite sharp decreases in national air travel during this period, we detected a 25% increase in the average distance travelled by air passengers during this time period. This coincided with the spread of SARS-CoV-2 from large urban centers to the rest of the country. In conclusion, our results shed light on the role of large and highly connected populated centres in the rapid ignition and establishment of SARS-CoV-2, and provide evidence that current interventions remain insufficient to keep virus transmission under control in Brazil.

One Sentence Summary

Joint analysis of genomic, mobility and epidemiological novel data provide unique insight into the spread and transmission of the rapidly evolving epidemic of SARS-CoV-2 in Brazil.