Open AccessEvolution and epidemic spread of SARS-CoV-2 in Brazil
Author(s) -
Darlan S. Candido,
Ingra Morales Claro,
Jaqueline Góes de Jesus,
William Marciel de Souza,
Filipe Romero Rebello Moreira,
Simon Dellicour,
Thomas A. Mellan,
Louis du Plessis,
Rafael H. M. Pereira,
Flavia Cristina da Silva Sales,
Erika R. Manuli,
Julien Thézé,
Luiz Gonzaga Paula de Almeida,
Mariane Talon de Menezes,
Carolina Moreira Voloch,
Marcílio Jorge Fumagalli,
Thaís M. Coletti,
Camila Alves Maia da Silva,
Mariana Severo Ramundo,
Mariene R. Amorim,
Henrique Hoeltgebaum,
Swapnil Mishra,
Mandev S. Gill,
Luiz Max Carvalho,
Lewis Buss,
Carlos A. Prete,
Jordan Ashworth,
Helder I. Nakaya,
Pedro S. Peixoto,
Oliver J. Brady,
Samuel M. Nicholls,
Amílcar Tanuri,
Átila Duque Rossi,
Carlos Kauê Vieira Braga,
Alexandra Lehmkuhl Gerber,
Ana Paula de Campos Guimarães,
Nelson Gaburo,
Cecila Salete Alencar,
Alessandro Clayton de Souza Ferreira,
Cristiano Xavier Lima,
José Eduardo Levi,
Celso Granato,
Giulia Magalhães Ferreira,
Ronaldo da Silva Francisco,
Fabiana Granja,
Márcia Teixeira Garcia,
Maria Luíza Moretti,
Maurício Wesley Perroud,
Terezinha Marta Pereira Pinto Castiñeiras,
Carolina S. Lázari,
Sarah C. Hill,
Andreza Aruska de Souza Santos,
Camila L. Simeoni,
Julia Forato,
Andrei C. Spósito,
Angélica Zaninelli Schreiber,
Magnun Nueldo Nunes Santos,
Camila Zolini,
Renan P. Souza,
Luciana C. ResendeMoreira,
Mauro Martins Teixeira,
Jôsy Hubner,
Patrícia Asfora Falabella Leme,
Rennan Garcias Moreira,
Maurício Lacerda Nogueira,
Neil M. Ferguson,
Sílvia Figueiredo Costa,
José Luiz ProençaMódena,
Ana Tereza Ribeiro de Vasconcelos,
Samir Bhatt,
Philippe Lemey,
ChiehHsi Wu,
Andrew Rambaut,
Nicholas J. Loman,
Renato Santana Aguiar,
Oliver G. Pybus,
Éster Cerdeira Sabino,
Nuno R. Faria
Publication year - 2020
Publication title -
science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 12.556
H-Index - 1186
eISSN - 1095-9203
pISSN - 0036-8075
DOI - 10.1126/science.abd2161
Subject(s) - transmission (telecommunications) , clade , covid-19 , geography , pandemic , psychological intervention , demography , biology , virology , phylogenetics , medicine , disease , infectious disease (medical specialty) , genetics , outbreak , pathology , psychiatry , sociology , gene , electrical engineering , engineering
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.
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