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

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

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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Brazil-UK Centre for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE) Genomic Network
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Claro, Ingra M.
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Wu, Chieh Hsi
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Brazil-UK Centre for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE) Genomic Network (2020) Evolution and epidemic spread of SARS-CoV-2 in Brazil. Science, 369 (6508), 1255-1260. (doi:10.1126/SCIENCE.ABD2161).

Record type: Article

Abstract

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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Evolution and epidemic spread of SARS-CoV-2 in Brazil.full - Accepted Manuscript
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Accepted/In Press date: 16 July 2020
Published date: September 2020
Additional Information: Publisher Copyright: © 2020 American Association for the Advancement of Science. All rights reserved. Copyright: Copyright 2020 Elsevier B.V., All rights reserved.

Identifiers

Local EPrints ID: 449616
URI: http://eprints.soton.ac.uk/id/eprint/449616
ISSN: 0036-8075
PURE UUID: 54196b6b-b0cc-4510-b491-3891660f1b14
ORCID for Chieh Hsi Wu: ORCID iD orcid.org/0000-0001-9386-725X

Catalogue record

Date deposited: 09 Jun 2021 16:30
Last modified: 17 Mar 2024 04:00

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Contributors

Author: Darlan S. Candido
Author: Ingra M. Claro
Author: Jaqueline G. de Jesus
Author: William M. Souza
Author: Filipe R.R. Moreira
Author: Simon Dellicour
Author: Thomas A. Mellan
Author: Louis du Plessis
Author: Rafael H.M. Pereira
Author: Flavia C.S. Sales
Author: Erika R. Manuli
Author: Julien Thézé
Author: Luiz Almeida
Author: Mariane T. Menezes
Author: Carolina M. Voloch
Author: Marcilio J. Fumagalli
Author: Thaís M. Coletti
Author: Camila A.M. da Silva
Author: Mariana S. Ramundo
Author: Mariene R. Amorim
Author: Henrique H. Hoeltgebaum
Author: Swapnil Mishra
Author: Mandev S. Gill
Author: Luiz M. Carvalho
Author: Lewis F. Buss
Author: Carlos A. Prete
Author: Jordan Ashworth
Author: Helder I. Nakaya
Author: Pedro S. Peixoto
Author: Oliver J. Brady
Author: Samuel M. Nicholls
Author: Amilcar Tanuri
Author: Átila D. Rossi
Author: Carlos K.V. Braga
Author: Alexandra L. Gerber
Author: Ana Paula C. de Guimarães
Author: Nelson Gaburo
Author: Cecila Salete Alencar
Author: Alessandro C.S. Ferreira
Author: Cristiano X. Lima
Author: José Eduardo Levi
Author: Celso Granato
Author: Giulia M. Ferreira
Author: Ronaldo S. Francisco
Author: Fabiana Granja
Author: Marcia T. Garcia
Author: Maria Luiza Moretti
Author: Mauricio W. Perroud
Author: Neil M. Ferguson
Author: Chieh Hsi Wu ORCID iD
Corporate Author: Brazil-UK Centre for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE) Genomic Network

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