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

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 Paula C. de Guimarães; Nelson Gaburo; Cecila Salete Alencar; Alessandro C.S. Ferreira; Cristiano X. Lima; José Eduardo Levi; Celso Granato; Giulia M. Ferreira; Ronaldo S. Francisco; Fabiana Granja; Marcia T. Garcia; Maria Luiza Moretti; Mauricio W. Perroud; Terezinha M.P.P. Castiñeiras; Carolina S. Lazari; Sarah C. Hill; Andreza Aruska de Souza Santos; Camila L. Simeoni; Julia Forato; Andrei C. Sposito; Angelica Z. Schreiber; Magnun N.N. Santos; Camila Zolini de Sá; Renan P. Souza; Luciana C. Resende-Moreira; Mauro M. Teixeira; Josy Hubner; Patricia A.F. Leme; Rennan G. Moreira; Maurício L. Nogueira; Neil M. Ferguson; Silvia F. Costa; José Luiz Proenca-Modena; Ana Tereza R. Vasconcelos; Samir Bhatt; Philippe Lemey; Chieh Hsi Wu; Andrew Rambaut; Nick J. Loman; Renato S. Aguiar; Oliver G. Pybus; Ester C. Sabino; Nuno Rodrigues Faria

doi:10.1126/SCIENCE.ABD2161

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

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. AmorimHenrique 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 Paula C. de Guimarães, Nelson Gaburo, Cecila Salete Alencar, Alessandro C.S. Ferreira, Cristiano X. Lima, José Eduardo Levi, Celso Granato, Giulia M. Ferreira, Ronaldo S. Francisco, Fabiana Granja, Marcia T. Garcia, Maria Luiza Moretti, Mauricio W. Perroud, Terezinha M.P.P. Castiñeiras, Carolina S. Lazari, Sarah C. Hill, Andreza Aruska de Souza Santos, Camila L. Simeoni, Julia Forato, Andrei C. Sposito, Angelica Z. Schreiber, Magnun N.N. Santos, Camila Zolini de Sá, Renan P. Souza, Luciana C. Resende-Moreira, Mauro M. Teixeira, Josy Hubner, Patricia A.F. Leme, Rennan G. Moreira, Maurício L. Nogueira, Neil M. Ferguson, Silvia F. Costa, José Luiz Proenca-Modena, Ana Tereza R. Vasconcelos, Samir Bhatt, Philippe Lemey, Chieh Hsi Wu, Andrew Rambaut, Nick J. Loman, Renato S. Aguiar, Oliver G. Pybus, Ester C. Sabino, Nuno Rodrigues Faria

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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.

Originalsprog	Engelsk
Tidsskrift	Science
Vol/bind	369
Udgave nummer	6508
Sider (fra-til)	1255-1260
Antal sider	6
ISSN	0036-8075
DOI	https://doi.org/10.1126/SCIENCE.ABD2161
Status	Udgivet - 4 sep. 2020
Udgivet eksternt	Ja

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10.1126/SCIENCE.ABD2161Licens: CC BY

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Candido, D. S., Claro, I. M., de Jesus, J. G., Souza, W. M., Moreira, F. R. R., Dellicour, S., Mellan, T. A., du Plessis, L., Pereira, R. H. M., Sales, F. C. S., Manuli, E. R., Thézé, J., Almeida, L., Menezes, M. T., Voloch, C. M., Fumagalli, M. J., Coletti, T. M., da Silva, C. A. M., Ramundo, M. S., ... Faria, N. R. (2020). Evolution and epidemic spread of SARS-CoV-2 in Brazil. Science, 369(6508), 1255-1260. https://doi.org/10.1126/SCIENCE.ABD2161

Candido, DS, Claro, IM, de Jesus, JG, Souza, WM, Moreira, FRR, Dellicour, S, Mellan, TA, du Plessis, L, Pereira, RHM, Sales, FCS, Manuli, ER, Thézé, J, Almeida, L, Menezes, MT, Voloch, CM, Fumagalli, MJ, Coletti, TM, da Silva, CAM, Ramundo, MS, Amorim, MR, Hoeltgebaum, HH, Mishra, S, Gill, MS, Carvalho, LM, Buss, LF, Prete, CA, Ashworth, J, Nakaya, HI, Peixoto, PS, Brady, OJ, Nicholls, SM, Tanuri, A, Rossi, ÁD, Braga, CKV, Gerber, AL, de Guimarães, APC, 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, AA, Simeoni, CL, Forato, J, Sposito, AC, Schreiber, AZ, Santos, MNN, de Sá, CZ, Souza, RP, Resende-Moreira, LC, Teixeira, MM, Hubner, J, Leme, PAF, Moreira, RG, Nogueira, ML, Ferguson, NM, Costa, SF, Proenca-Modena, JL, Vasconcelos, ATR, Bhatt, S, Lemey, P, Wu, CH, Rambaut, A, Loman, NJ, Aguiar, RS, Pybus, OG, Sabino, EC & Faria, NR 2020, 'Evolution and epidemic spread of SARS-CoV-2 in Brazil', Science, bind 369, nr. 6508, s. 1255-1260. https://doi.org/10.1126/SCIENCE.ABD2161

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title = "Evolution and epidemic spread of SARS-CoV-2 in Brazil",

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 S{\~a}o 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.",

author = "Candido, {Darlan S.} and Claro, {Ingra M.} and {de Jesus}, {Jaqueline G.} and Souza, {William M.} and Moreira, {Filipe R.R.} and Simon Dellicour and Mellan, {Thomas A.} and {du Plessis}, Louis and Pereira, {Rafael H.M.} and Sales, {Flavia C.S.} and Manuli, {Erika R.} and Julien Th{\'e}z{\'e} and Luiz Almeida and Menezes, {Mariane T.} and Voloch, {Carolina M.} and Fumagalli, {Marcilio J.} and Coletti, {Tha{\'i}s M.} and {da Silva}, {Camila A.M.} and Ramundo, {Mariana S.} and Amorim, {Mariene R.} and Hoeltgebaum, {Henrique H.} and Swapnil Mishra and Gill, {Mandev S.} and Carvalho, {Luiz M.} and Buss, {Lewis F.} and Prete, {Carlos A.} and Jordan Ashworth and Nakaya, {Helder I.} and Peixoto, {Pedro S.} and Brady, {Oliver J.} and Nicholls, {Samuel M.} and Amilcar Tanuri and Rossi, {{\'A}tila D.} and Braga, {Carlos K.V.} and Gerber, {Alexandra L.} and {de Guimar{\~a}es}, {Ana Paula C.} and Nelson Gaburo and Alencar, {Cecila Salete} and Ferreira, {Alessandro C.S.} and Lima, {Cristiano X.} and Levi, {Jos{\'e} Eduardo} and Celso Granato and Ferreira, {Giulia M.} and Francisco, {Ronaldo S.} and Fabiana Granja and Garcia, {Marcia T.} and Moretti, {Maria Luiza} and Perroud, {Mauricio W.} and Casti{\~n}eiras, {Terezinha M.P.P.} and Lazari, {Carolina S.} and Hill, {Sarah C.} and {de Souza Santos}, {Andreza Aruska} and Simeoni, {Camila L.} and Julia Forato and Sposito, {Andrei C.} and Schreiber, {Angelica Z.} and Santos, {Magnun N.N.} and {de S{\'a}}, {Camila Zolini} and Souza, {Renan P.} and Resende-Moreira, {Luciana C.} and Teixeira, {Mauro M.} and Josy Hubner and Leme, {Patricia A.F.} and Moreira, {Rennan G.} and Nogueira, {Maur{\'i}cio L.} and Ferguson, {Neil M.} and Costa, {Silvia F.} and Proenca-Modena, {Jos{\'e} Luiz} and Vasconcelos, {Ana Tereza R.} and Samir Bhatt and Philippe Lemey and Wu, {Chieh Hsi} and Andrew Rambaut and Loman, {Nick J.} and Aguiar, {Renato S.} and Pybus, {Oliver G.} and Sabino, {Ester C.} and Faria, {Nuno Rodrigues}",

year = "2020",

month = sep,

day = "4",

doi = "10.1126/SCIENCE.ABD2161",

language = "English",

volume = "369",

pages = "1255--1260",

journal = "Science",

issn = "0036-8075",

publisher = "American Association for the Advancement of Science",

number = "6508",

}

TY - JOUR

T1 - Evolution and epidemic spread of SARS-CoV-2 in Brazil

AU - Candido, Darlan S.

AU - Claro, Ingra M.

AU - de Jesus, Jaqueline G.

AU - Souza, William M.

AU - Moreira, Filipe R.R.

AU - Dellicour, Simon

AU - Mellan, Thomas A.

AU - du Plessis, Louis

AU - Pereira, Rafael H.M.

AU - Sales, Flavia C.S.

AU - Manuli, Erika R.

AU - Thézé, Julien

AU - Almeida, Luiz

AU - Menezes, Mariane T.

AU - Voloch, Carolina M.

AU - Fumagalli, Marcilio J.

AU - Coletti, Thaís M.

AU - da Silva, Camila A.M.

AU - Ramundo, Mariana S.

AU - Amorim, Mariene R.

AU - Hoeltgebaum, Henrique H.

AU - Mishra, Swapnil

AU - Gill, Mandev S.

AU - Carvalho, Luiz M.

AU - Buss, Lewis F.

AU - Prete, Carlos A.

AU - Ashworth, Jordan

AU - Nakaya, Helder I.

AU - Peixoto, Pedro S.

AU - Brady, Oliver J.

AU - Nicholls, Samuel M.

AU - Tanuri, Amilcar

AU - Rossi, Átila D.

AU - Braga, Carlos K.V.

AU - Gerber, Alexandra L.

AU - de Guimarães, Ana Paula C.

AU - Gaburo, Nelson

AU - Alencar, Cecila Salete

AU - Ferreira, Alessandro C.S.

AU - Lima, Cristiano X.

AU - Levi, José Eduardo

AU - Granato, Celso

AU - Ferreira, Giulia M.

AU - Francisco, Ronaldo S.

AU - Granja, Fabiana

AU - Garcia, Marcia T.

AU - Moretti, Maria Luiza

AU - Perroud, Mauricio W.

AU - Castiñeiras, Terezinha M.P.P.

AU - Lazari, Carolina S.

AU - Hill, Sarah C.

AU - de Souza Santos, Andreza Aruska

AU - Simeoni, Camila L.

AU - Forato, Julia

AU - Sposito, Andrei C.

AU - Schreiber, Angelica Z.

AU - Santos, Magnun N.N.

AU - de Sá, Camila Zolini

AU - Souza, Renan P.

AU - Resende-Moreira, Luciana C.

AU - Teixeira, Mauro M.

AU - Hubner, Josy

AU - Leme, Patricia A.F.

AU - Moreira, Rennan G.

AU - Nogueira, Maurício L.

AU - Ferguson, Neil M.

AU - Costa, Silvia F.

AU - Proenca-Modena, José Luiz

AU - Vasconcelos, Ana Tereza R.

AU - Bhatt, Samir

AU - Lemey, Philippe

AU - Wu, Chieh Hsi

AU - Rambaut, Andrew

AU - Loman, Nick J.

AU - Aguiar, Renato S.

AU - Pybus, Oliver G.

AU - Sabino, Ester C.

AU - Faria, Nuno Rodrigues

PY - 2020/9/4

Y1 - 2020/9/4

N2 - 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.

AB - 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.

U2 - 10.1126/SCIENCE.ABD2161

DO - 10.1126/SCIENCE.ABD2161

M3 - Journal article

C2 - 32703910

SN - 0036-8075

VL - 369

SP - 1255

EP - 1260

JO - Science

JF - Science

IS - 6508

ER -