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

Candido, Darlan S.; Claro, Ingra M.; de Jesus, Jaqueline G.; Souza, William M.; Moreira, Filipe R. R.; Dellicour, Simon; Mellan, Thomas A.; du Plessis, Louis; 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, Thaís M.; da Silva, Camila A. M.; Ramundo, Mariana S.; Amorim, Mariene R.; Hoeltgebaum, Henrique H.; Mishra, Swapnil; Gill, Mandev S.; Carvalho, Luiz M.; Buss, Lewis F.; Prete, Carlos A.; Ashworth, Jordan; Nakaya, Helder I.; Peixoto, Pedro S.; Brady, Oliver J.; Nicholls, Samuel M.; Tanuri, Amilcar; Rossi, Átila D.; Braga, Carlos K.V.; Gerber, Alexandra L.; de C. Guimarães, Ana 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, A; Simeoni, CL; Forato, J; Sposito, AC; Schreiber, AZ; Santos, MNN; de Sá, CZ; Souz...


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 AP de C. Guimarães

N Gaburo

CS Alencar

ACS Ferreira

CX Lima

JE Levi

C Granato

GM Ferreira

RS Francisco

F Granja

MT Garcia

ML Moretti

MW Perroud

TMPP Castiñeiras

CS Lazari

SC Hill

A de Souza Santos

CL Simeoni

J Forato

AC Sposito

AZ Schreiber

MNN Santos

CZ de Sá

RP Souza

LC Resende-Moreira

MM Teixeira

J Hubner

PAF Leme

RG Moreira

ML Nogueira

NM Ferguson

SF Costa

JL Proenca-Modena

ATR Vasconcelos

S Bhatt

P Lemey


A Rambaut

NJ Loman

RS Aguiar

OG Pybus

EC Sabino

NR Faria


Brazil currently has one of the fastest growing SARS-CoV-2 epidemics in the world. Owing to limited available data, assessments of the impact of non-pharmaceutical interventions (NPIs) on virus spread remain challenging. Using a mobility-driven transmission model, we show that NPIs reduced the reproduction number from >3 to 1–1.6 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 February11 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 travelled distances in national flights. This study sheds new light on the epidemic transmission and evolutionary trajectories of SARS-CoV-2 lineages in Brazil, and provide evidence that current interventions remain insufficient to keep virus transmission under control in the country.


Candido, D. S., Claro, I. M., de Jesus, J. G., Souza, W. M., Moreira, F. R. R., Dellicour, S., …Faria, N. (2020). Evolution and epidemic spread of SARS-CoV-2 in Brazil. Science, eabd2161.

Journal Article Type Article
Acceptance Date Jul 16, 2020
Publication Date Jul 23, 2020
Deposit Date Sep 3, 2020
Publicly Available Date Sep 3, 2020
Journal Science
Print ISSN 0036-8075
Publisher American Association for the Advancement of Science
Peer Reviewed Peer Reviewed
Pages eabd2161
Public URL
Publisher URL


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