The University of Southampton
University of Southampton Institutional Repository

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.

0036-8075
1255-1260
Candido, Darlan S.
bead69ce-6ff9-4c26-b94a-76b3259db061
Claro, Ingra M.
0916982c-d089-4453-8e21-ff0015aad1df
de Jesus, Jaqueline G.
41f1adc7-7bfd-4feb-8e2f-cd25a7201d2b
Souza, William M.
3cc9cfcb-ad2c-47ff-ae24-73d94fa9471b
Moreira, Filipe R.R.
91f00f4c-e362-4b5e-ae24-22337610b515
Dellicour, Simon
f026e785-71e3-4ef1-b87f-04b6864e6a3b
Mellan, Thomas A.
54e87349-33a8-42cb-8991-f71748651a17
du Plessis, Louis
b73c550f-9e6a-44af-b09a-c863c45efb8e
Pereira, Rafael H.M.
706c79b9-0228-4ca3-90e2-0d904dd7de8a
Sales, Flavia C.S.
c42bc4f3-2e8a-415f-af85-fe6354e2d5cd
Manuli, Erika R.
222df51f-6ccb-4605-ac9d-b92bef1d3247
Thézé, Julien
08b09d7b-1b76-49a2-8794-759ff6e68a64
Almeida, Luiz
ab944446-5a5e-4b55-a30b-1e0203f7eae5
Menezes, Mariane T.
014835ac-f584-4668-9bea-ad29a012d52f
Voloch, Carolina M.
f9a7c2e9-428c-425a-8ad2-1c1918552942
Fumagalli, Marcilio J.
f33997ea-fa0f-4d37-9b0b-8936fd3f31a1
Coletti, Thaís M.
b53cdd74-f6ba-4ec0-85d4-f7dc7455c157
da Silva, Camila A.M.
d80733cf-c610-4865-864a-6717f2bcb6a6
Ramundo, Mariana S.
4faa19b4-cb4d-4760-8896-b9b12a82daf3
Amorim, Mariene R.
728e526b-5525-4e35-bb69-bd5c6e97069b
Hoeltgebaum, Henrique H.
97104f70-f854-45d8-89c5-ccdb30d79c9c
Mishra, Swapnil
46a21337-415e-415e-a572-82b633e9231a
Gill, Mandev S.
e70557e5-796f-4be9-b3f4-de5b95d2a426
Carvalho, Luiz M.
1026b6dd-b40c-4633-82b9-0b636b42df98
Buss, Lewis F.
53ab8102-943b-4b6f-a976-1b7100c41266
Prete, Carlos A.
41bc411d-67f3-480e-b7d6-108359394dd4
Ashworth, Jordan
ba1642ab-cabb-42be-a03d-5579c213dc50
Nakaya, Helder I.
7a31277e-0711-4ccb-8c72-13d710f5d216
Peixoto, Pedro S.
bdc28fe6-2268-4f2f-aa4f-f800c8523683
Brady, Oliver J.
2acbd374-26d3-4e56-9e19-558eef1d4f9b
Nicholls, Samuel M.
24c36632-713e-4169-a136-be81509f844c
Tanuri, Amilcar
45494d21-7978-47d8-99e3-63f358b75bf7
Rossi, Átila D.
f6c82b05-032a-473f-a60f-5f9ce7f80d0e
Braga, Carlos K.V.
7dbcbb1b-85f4-40c1-b67b-fb25572dc63a
Gerber, Alexandra L.
499b0f54-e0b7-4997-bb50-7b2c7146f6dd
de Guimarães, Ana Paula C.
55f81c89-82c0-47bc-9ae8-bafd8189b8ab
Gaburo, Nelson
fcd4041b-61c4-4a6b-8496-1b59ebcc82ca
Alencar, Cecila Salete
ea00b1ad-24e9-476d-8ae2-cc529b11c30a
Ferreira, Alessandro C.S.
4c6e6bc3-c699-4286-80de-ff954cecd882
Lima, Cristiano X.
14ea0fee-1b39-4a38-94ef-d9fdfd67e815
Levi, José Eduardo
aa45f5d0-fbb6-412a-a880-4b4a9dca3a87
Granato, Celso
0ab45549-e62d-4dd5-931d-af1d96fcf304
Ferreira, Giulia M.
ac3d3299-ceab-4f1d-bd67-5037eaf68c38
Francisco, Ronaldo S.
4d62c8d4-281c-4e34-9903-a1ee343d9d7c
Granja, Fabiana
dc4baa49-1f1b-4ac0-b363-18502345720f
Garcia, Marcia T.
4b78bebf-5676-4418-8728-8e61904e5f56
Moretti, Maria Luiza
21e525c1-0fe1-43fb-9085-8cfb3d1d56e5
Perroud, Mauricio W.
857005ea-f735-4073-be17-3e2ddd46c966
Ferguson, Neil M.
915d5afc-55f3-4157-95bd-df5410ad91a8
Wu, Chieh Hsi
ace630c6-2095-4ade-b657-241692f6b4d3
Brazil-UK Centre for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE) Genomic Network
Candido, Darlan S.
bead69ce-6ff9-4c26-b94a-76b3259db061
Claro, Ingra M.
0916982c-d089-4453-8e21-ff0015aad1df
de Jesus, Jaqueline G.
41f1adc7-7bfd-4feb-8e2f-cd25a7201d2b
Souza, William M.
3cc9cfcb-ad2c-47ff-ae24-73d94fa9471b
Moreira, Filipe R.R.
91f00f4c-e362-4b5e-ae24-22337610b515
Dellicour, Simon
f026e785-71e3-4ef1-b87f-04b6864e6a3b
Mellan, Thomas A.
54e87349-33a8-42cb-8991-f71748651a17
du Plessis, Louis
b73c550f-9e6a-44af-b09a-c863c45efb8e
Pereira, Rafael H.M.
706c79b9-0228-4ca3-90e2-0d904dd7de8a
Sales, Flavia C.S.
c42bc4f3-2e8a-415f-af85-fe6354e2d5cd
Manuli, Erika R.
222df51f-6ccb-4605-ac9d-b92bef1d3247
Thézé, Julien
08b09d7b-1b76-49a2-8794-759ff6e68a64
Almeida, Luiz
ab944446-5a5e-4b55-a30b-1e0203f7eae5
Menezes, Mariane T.
014835ac-f584-4668-9bea-ad29a012d52f
Voloch, Carolina M.
f9a7c2e9-428c-425a-8ad2-1c1918552942
Fumagalli, Marcilio J.
f33997ea-fa0f-4d37-9b0b-8936fd3f31a1
Coletti, Thaís M.
b53cdd74-f6ba-4ec0-85d4-f7dc7455c157
da Silva, Camila A.M.
d80733cf-c610-4865-864a-6717f2bcb6a6
Ramundo, Mariana S.
4faa19b4-cb4d-4760-8896-b9b12a82daf3
Amorim, Mariene R.
728e526b-5525-4e35-bb69-bd5c6e97069b
Hoeltgebaum, Henrique H.
97104f70-f854-45d8-89c5-ccdb30d79c9c
Mishra, Swapnil
46a21337-415e-415e-a572-82b633e9231a
Gill, Mandev S.
e70557e5-796f-4be9-b3f4-de5b95d2a426
Carvalho, Luiz M.
1026b6dd-b40c-4633-82b9-0b636b42df98
Buss, Lewis F.
53ab8102-943b-4b6f-a976-1b7100c41266
Prete, Carlos A.
41bc411d-67f3-480e-b7d6-108359394dd4
Ashworth, Jordan
ba1642ab-cabb-42be-a03d-5579c213dc50
Nakaya, Helder I.
7a31277e-0711-4ccb-8c72-13d710f5d216
Peixoto, Pedro S.
bdc28fe6-2268-4f2f-aa4f-f800c8523683
Brady, Oliver J.
2acbd374-26d3-4e56-9e19-558eef1d4f9b
Nicholls, Samuel M.
24c36632-713e-4169-a136-be81509f844c
Tanuri, Amilcar
45494d21-7978-47d8-99e3-63f358b75bf7
Rossi, Átila D.
f6c82b05-032a-473f-a60f-5f9ce7f80d0e
Braga, Carlos K.V.
7dbcbb1b-85f4-40c1-b67b-fb25572dc63a
Gerber, Alexandra L.
499b0f54-e0b7-4997-bb50-7b2c7146f6dd
de Guimarães, Ana Paula C.
55f81c89-82c0-47bc-9ae8-bafd8189b8ab
Gaburo, Nelson
fcd4041b-61c4-4a6b-8496-1b59ebcc82ca
Alencar, Cecila Salete
ea00b1ad-24e9-476d-8ae2-cc529b11c30a
Ferreira, Alessandro C.S.
4c6e6bc3-c699-4286-80de-ff954cecd882
Lima, Cristiano X.
14ea0fee-1b39-4a38-94ef-d9fdfd67e815
Levi, José Eduardo
aa45f5d0-fbb6-412a-a880-4b4a9dca3a87
Granato, Celso
0ab45549-e62d-4dd5-931d-af1d96fcf304
Ferreira, Giulia M.
ac3d3299-ceab-4f1d-bd67-5037eaf68c38
Francisco, Ronaldo S.
4d62c8d4-281c-4e34-9903-a1ee343d9d7c
Granja, Fabiana
dc4baa49-1f1b-4ac0-b363-18502345720f
Garcia, Marcia T.
4b78bebf-5676-4418-8728-8e61904e5f56
Moretti, Maria Luiza
21e525c1-0fe1-43fb-9085-8cfb3d1d56e5
Perroud, Mauricio W.
857005ea-f735-4073-be17-3e2ddd46c966
Ferguson, Neil M.
915d5afc-55f3-4157-95bd-df5410ad91a8
Wu, Chieh Hsi
ace630c6-2095-4ade-b657-241692f6b4d3

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.

Text
Evolution and epidemic spread of SARS-CoV-2 in Brazil.full - Accepted Manuscript
Restricted to Repository staff only
Request a copy

More information

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

Catalogue record

Date deposited: 09 Jun 2021 16:30
Last modified: 14 Sep 2021 17:49

Export record

Altmetrics

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
Corporate Author: Brazil-UK Centre for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE) Genomic Network

University divisions

Download statistics

Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.

View more statistics

Atom RSS 1.0 RSS 2.0

Contact ePrints Soton: eprints@soton.ac.uk

ePrints Soton supports OAI 2.0 with a base URL of http://eprints.soton.ac.uk/cgi/oai2

This repository has been built using EPrints software, developed at the University of Southampton, but available to everyone to use.

We use cookies to ensure that we give you the best experience on our website. If you continue without changing your settings, we will assume that you are happy to receive cookies on the University of Southampton website.

×