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

By Darlan da Silva Candido, Ingra Morales Claro, Jaqueline Goes de Jesus, William Marciel Souza, Filipe Romero Rebello Moreira, Simon Dellicour, Thomas A Mellan, Louis Raymond du Plessis, Rafael Henrique Moraes Pereira, Flavia Cristina da Silva Sales, Erika Regina Manuli, Julien Theze, Luis Almeida, Mariane Talon de Menezes, Carolina Moreira Voloch, Marcilio Jorge Fumagalli, Thais de Moura Coletti, Camila Alves Maia Silva, Mariana Severo Ramundo, Mariene Ribeiro Amorim, Henrique Hoeltgebaum, Swapnil Mishra, Mandev Gill, Luiz Max Carvalho, Lewis F Buss, Carlos A. Prete, Jordan Ashworth, Helder I Nakaya, Pedro da Silva Peixoto, Oliver J Brady, Samuel M. Nicholls, Amilcar Tanuri, Atila Duque Rossi, Carlos K. V. Braga, Alexandra Gerber, Ana Paula Guimaraes, Nelson Gaburo, Cecilia Salete Alencar, Alessandro Clayton de Souza Ferreira, Cristiano Xavier Lima, Jose Eduardo Levi, Celso Granato, Giula Magalhaes Ferreira, Ronaldo da Silva Francisco Junior, Fabiana Granja, Marcia Teixeira Garcia, Maria Luiza Moretti, Mauricio Wesley Perroud, Terezinha M. P. P. Castineiras, Carolina Dos Santos Lazari, Sarah C. Hill, Andreza Aruska de Souza Santos, Camila Lopes Simeoni, Julia Forato, Andrei Carvalho Sposito, Angelica Zaninelli Schreiber, Magnun Nueldo Nunes Santos, Camila Zolini Sa, Renan Pedra de Souza, Luciana Cunha Resende Moreira, Mauro Martins Teixeira, Josy Hubner, Patricia Asfora Falabella Leme, Rennan Garcias Moreira, Mauricio Lacerda Nogueira, CADDE-Genomic-Network, Neil Ferguson, Silvia Figueiredo Costa, Jose Luiz Proenca-Modena, Ana Tereza Ribeiro de Vasconcelos, Samir Bhatt, Philippe Lemey, Chieh-Hsi Wu, Andrew Rambaut, Nicholas James Loman, Renato Santana Aguiar, Oliver G. Pybus, Ester C. Sabino, Nuno R. Faria

Posted 12 Jun 2020
medRxiv DOI: 10.1101/2020.06.11.20128249

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 Sao 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.

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