Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil

Marta Giovanetti; Svetoslav Nanev Slavov; Vagner Fonseca; Eduan Wilkinson; Houriiyah Tegally; José Salvatore Leister Patané; Vincent Louis Viala; Emmanuel James San; Evandra Strazza Rodrigues; Elaine Vieira Santos; Flavia Aburjaile; Joilson Xavier; Hegger Fritsch; Talita Emile Ribeiro Adelino; Felicidade Pereira; Arabela Leal; Felipe Campos de Melo Iani; Glauco de Carvalho Pereira; Cynthia Vazquez; Gladys Mercedes Estigarribia Sanabria; Elaine Cristina de Oliveira; Luiz Demarchi; Julio Croda; Rafael dos Santos Bezerra; Loyze Paola Oliveira de Lima; Claudia Renata dos Santos Barros; Elaine Cristina Marqueze; Jardelina de Souza Todao Bernardino; Debora Botequio Moretti; Ricardo Augusto Brassaloti; Raquel de Lello Rocha Campos Cassano; Pilar Drummond Sampaio Corrêa Mariani; João Paulo Kitajima; Bibiana Santos; Rodrigo Proto-Siqueira; Vlademir Vicente Cantarelli; Stephane Tosta; Vanessa Brandão Nardy; Luciana Reboredo de Oliveira da Silva; Marcela Kelly Astete Gómez; Jaqueline Gomes Lima; Adriana Aparecida Ribeiro; Natália Rocha Guimarães; Luiz Takao Watanabe; Luana Barbosa Da Silva; Raquel da Silva Ferreira; Mara Patricia F. da Penha; María José Ortega; Andrea Gómez de la Fuente; Shirley Villalba; Juan Torales; María Liz Gamarra; Carolina Aquino; Gloria Patricia Martínez Figueredo; Wellington Santos Fava; Ana Rita C. Motta-Castro; James Venturini; Sandra Maria do Vale Leone de Oliveira; Crhistinne Cavalheiro Maymone Gonçalves; Maria do Carmo Debur Rossa; Guilherme Nardi Becker; Mayra Presibella Giacomini; Nelson Quallio Marques; Irina Nastassja Riediger; Sonia Raboni; Gabriela Mattoso; Allan D. Cataneo; Camila Zanluca; Claudia N. Duarte dos Santos; Patricia Akemi Assato; Felipe Allan da Silva da Costa; Mirele Daiana Poleti; Jessika Cristina Chagas Lesbon; Elisangela Chicaroni Mattos; Cecilia Artico Banho; Lívia Sacchetto; Marília Mazzi Moraes; Rejane Maria Tommasini Grotto; Jayme A. Souza-Neto; Maurício Lacerda Nogueira; Heidge Fukumasu; Luiz Lehmann Coutinho; Rodrigo Tocantins Calado; Raul Machado Neto; Ana Maria Bispo de Filippis; Rivaldo Venancio da Cunha; Carla Freitas; Cassio Roberto Leonel Peterka; Cássia de Fátima Rangel Fernandes; Wildo Navegantes; Rodrigo Fabiano do Carmo Said; Carlos F. Campelo de A e Melo; Maria Almiron; José Lourenço; Tulio de Oliveira; Edward C. Holmes; Ricardo Haddad; Sandra Coccuzzo Sampaio; Maria Carolina Elias; Simone Kashima; Luiz Carlos Junior de Alcantara; Dimas Tadeu Covas; António Jorge Martins

doi:10.1038/s41564-022-01191-z

Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil

Marta Giovanetti, Svetoslav Nanev Slavov, Vagner Fonseca, Eduan Wilkinson, Houriiyah Tegally, José Salvatore Leister Patané, Vincent Louis Viala, Emmanuel James San, Evandra Strazza Rodrigues, Elaine Vieira Santos, Flavia Aburjaile, Joilson Xavier, Hegger Fritsch, Talita Emile Ribeiro Adelino, Felicidade Pereira, Arabela Leal, Felipe Campos de Melo Iani, Glauco de Carvalho Pereira, Cynthia Vazquez, Gladys Mercedes Estigarribia SanabriaElaine Cristina de Oliveira, Luiz Demarchi, Julio Croda, Rafael dos Santos Bezerra, Loyze Paola Oliveira de Lima, Claudia Renata dos Santos Barros, Elaine Cristina Marqueze, Jardelina de Souza Todao Bernardino, Debora Botequio Moretti, Ricardo Augusto Brassaloti, Raquel de Lello Rocha Campos Cassano, Pilar Drummond Sampaio Corrêa Mariani, João Paulo Kitajima, Bibiana Santos, Rodrigo Proto-Siqueira, Vlademir Vicente Cantarelli, Stephane Tosta, Vanessa Brandão Nardy, Luciana Reboredo de Oliveira da Silva, Marcela Kelly Astete Gómez, Jaqueline Gomes Lima, Adriana Aparecida Ribeiro, Natália Rocha Guimarães, Luiz Takao Watanabe, Luana Barbosa Da Silva, Raquel da Silva Ferreira, Mara Patricia F. da Penha, María José Ortega, Andrea Gómez de la Fuente, Shirley Villalba, Juan Torales, María Liz Gamarra, Carolina Aquino, Gloria Patricia Martínez Figueredo, Wellington Santos Fava, Ana Rita C. Motta-Castro, James Venturini, Sandra Maria do Vale Leone de Oliveira, Crhistinne Cavalheiro Maymone Gonçalves, Maria do Carmo Debur Rossa, Guilherme Nardi Becker, Mayra Presibella Giacomini, Nelson Quallio Marques, Irina Nastassja Riediger, Sonia Raboni, Gabriela Mattoso, Allan D. Cataneo, Camila Zanluca, Claudia N. Duarte dos Santos, Patricia Akemi Assato, Felipe Allan da Silva da Costa, Mirele Daiana Poleti, Jessika Cristina Chagas Lesbon, Elisangela Chicaroni Mattos, Cecilia Artico Banho, Lívia Sacchetto, Marília Mazzi Moraes, Rejane Maria Tommasini Grotto, Jayme A. Souza-Neto, Maurício Lacerda Nogueira, Heidge Fukumasu, Luiz Lehmann Coutinho, Rodrigo Tocantins Calado, Raul Machado Neto, Ana Maria Bispo de Filippis, Rivaldo Venancio da Cunha, Carla Freitas, Cassio Roberto Leonel Peterka, Cássia de Fátima Rangel Fernandes, Wildo Navegantes, Rodrigo Fabiano do Carmo Said, Carlos F. Campelo de A e Melo, Maria Almiron, José Lourenço, Tulio de Oliveira, Edward C. Holmes, Ricardo Haddad, Sandra Coccuzzo Sampaio^*, Maria Carolina Elias^*, Simone Kashima^*, Luiz Carlos Junior de Alcantara^*, Dimas Tadeu Covas^*, António Jorge Martins

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

56 Citations (Scopus)

Abstract

The high numbers of COVID-19 cases and deaths in Brazil have made Latin America an epicentre of the pandemic. SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, but important gaps remain in our understanding of virus transmission dynamics at a national scale. We use 17,135 near-complete genomes sampled from 27 Brazilian states and bordering country Paraguay. From March to November 2020, we detected co-circulation of multiple viral lineages that were linked to multiple importations (predominantly from Europe). After November 2020, we detected large, local transmission clusters within the country. In the absence of effective restriction measures, the epidemic progressed, and in January 2021 there was emergence and onward spread, both within and abroad, of variants of concern and variants under monitoring, including Gamma (P.1) and Zeta (P.2). We also characterized a genomic overview of the epidemic in Paraguay and detected evidence of importation of SARS-CoV-2 ancestor lineages and variants of concern from Brazil. Our findings show that genomic surveillance in Brazil enabled assessment of the real-time spread of emerging SARS-CoV-2 variants.

Original language	English
Pages (from-to)	1490-1500
Number of pages	11
Journal	Nature Microbiology
Volume	7
Issue number	9
DOIs	https://doi.org/10.1038/s41564-022-01191-z
Publication status	Published - Sept 2022
Externally published	Yes

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1038/s41564-022-01191-zLicence: CC BY

Cite this

Giovanetti, M., Slavov, S. N., Fonseca, V., Wilkinson, E., Tegally, H., Patané, J. S. L., Viala, V. L., San, E. J., Rodrigues, E. S., Santos, E. V., Aburjaile, F., Xavier, J., Fritsch, H., Adelino, T. E. R., Pereira, F., Leal, A., Iani, F. C. D. M., de Carvalho Pereira, G., Vazquez, C., ... Martins, A. J. (2022). Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil. Nature Microbiology, 7(9), 1490-1500. https://doi.org/10.1038/s41564-022-01191-z

@article{66b0a6eceb3a453ea0b1af135d770184,

title = "Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil",

abstract = "The high numbers of COVID-19 cases and deaths in Brazil have made Latin America an epicentre of the pandemic. SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, but important gaps remain in our understanding of virus transmission dynamics at a national scale. We use 17,135 near-complete genomes sampled from 27 Brazilian states and bordering country Paraguay. From March to November 2020, we detected co-circulation of multiple viral lineages that were linked to multiple importations (predominantly from Europe). After November 2020, we detected large, local transmission clusters within the country. In the absence of effective restriction measures, the epidemic progressed, and in January 2021 there was emergence and onward spread, both within and abroad, of variants of concern and variants under monitoring, including Gamma (P.1) and Zeta (P.2). We also characterized a genomic overview of the epidemic in Paraguay and detected evidence of importation of SARS-CoV-2 ancestor lineages and variants of concern from Brazil. Our findings show that genomic surveillance in Brazil enabled assessment of the real-time spread of emerging SARS-CoV-2 variants.",

author = "Marta Giovanetti and Slavov, {Svetoslav Nanev} and Vagner Fonseca and Eduan Wilkinson and Houriiyah Tegally and Patan{\'e}, {Jos{\'e} Salvatore Leister} and Viala, {Vincent Louis} and San, {Emmanuel James} and Rodrigues, {Evandra Strazza} and Santos, {Elaine Vieira} and Flavia Aburjaile and Joilson Xavier and Hegger Fritsch and Adelino, {Talita Emile Ribeiro} and Felicidade Pereira and Arabela Leal and Iani, {Felipe Campos de Melo} and {de Carvalho Pereira}, Glauco and Cynthia Vazquez and Sanabria, {Gladys Mercedes Estigarribia} and Oliveira, {Elaine Cristina de} and Luiz Demarchi and Julio Croda and {dos Santos Bezerra}, Rafael and {Paola Oliveira de Lima}, Loyze and {Renata dos Santos Barros}, Claudia and Marqueze, {Elaine Cristina} and {de Souza Todao Bernardino}, Jardelina and Moretti, {Debora Botequio} and Brassaloti, {Ricardo Augusto} and {de Lello Rocha Campos Cassano}, Raquel and Mariani, {Pilar Drummond Sampaio Corr{\^e}a} and Kitajima, {Jo{\~a}o Paulo} and Bibiana Santos and Rodrigo Proto-Siqueira and Cantarelli, {Vlademir Vicente} and Stephane Tosta and Nardy, {Vanessa Brand{\~a}o} and {Reboredo de Oliveira da Silva}, Luciana and G{\'o}mez, {Marcela Kelly Astete} and Lima, {Jaqueline Gomes} and Ribeiro, {Adriana Aparecida} and Guimar{\~a}es, {Nat{\'a}lia Rocha} and Watanabe, {Luiz Takao} and {Barbosa Da Silva}, Luana and {da Silva Ferreira}, Raquel and {da Penha}, {Mara Patricia F.} and Ortega, {Mar{\'i}a Jos{\'e}} and {de la Fuente}, {Andrea G{\'o}mez} and Shirley Villalba and Juan Torales and Gamarra, {Mar{\'i}a Liz} and Carolina Aquino and Figueredo, {Gloria Patricia Mart{\'i}nez} and Fava, {Wellington Santos} and Motta-Castro, {Ana Rita C.} and James Venturini and {do Vale Leone de Oliveira}, {Sandra Maria} and Gon{\c c}alves, {Crhistinne Cavalheiro Maymone} and {do Carmo Debur Rossa}, Maria and Becker, {Guilherme Nardi} and Giacomini, {Mayra Presibella} and Marques, {Nelson Quallio} and Riediger, {Irina Nastassja} and Sonia Raboni and Gabriela Mattoso and Cataneo, {Allan D.} and Camila Zanluca and {Duarte dos Santos}, {Claudia N.} and Assato, {Patricia Akemi} and {Allan da Silva da Costa}, Felipe and Poleti, {Mirele Daiana} and Lesbon, {Jessika Cristina Chagas} and Mattos, {Elisangela Chicaroni} and Banho, {Cecilia Artico} and L{\'i}via Sacchetto and Moraes, {Mar{\'i}lia Mazzi} and Grotto, {Rejane Maria Tommasini} and Souza-Neto, {Jayme A.} and Nogueira, {Maur{\'i}cio Lacerda} and Heidge Fukumasu and Coutinho, {Luiz Lehmann} and Calado, {Rodrigo Tocantins} and Neto, {Raul Machado} and {Bispo de Filippis}, {Ana Maria} and {Venancio da Cunha}, Rivaldo and Carla Freitas and Peterka, {Cassio Roberto Leonel} and {de F{\'a}tima Rangel Fernandes}, C{\'a}ssia and Wildo Navegantes and {do Carmo Said}, {Rodrigo Fabiano} and {Campelo de A e Melo}, {Carlos F.} and Maria Almiron and Jos{\'e} Louren{\c c}o and {de Oliveira}, Tulio and Holmes, {Edward C.} and Ricardo Haddad and Sampaio, {Sandra Coccuzzo} and Elias, {Maria Carolina} and Simone Kashima and {Junior de Alcantara}, {Luiz Carlos} and Covas, {Dimas Tadeu} and Martins, {Ant{\'o}nio Jorge}",

note = "Publisher Copyright: {\textcopyright} 2022, The Author(s).",

year = "2022",

month = sep,

doi = "10.1038/s41564-022-01191-z",

language = "English",

volume = "7",

pages = "1490--1500",

journal = "Nature Microbiology",

issn = "2058-5276",

publisher = "Nature Research",

number = "9",

}

Giovanetti, M, Slavov, SN, Fonseca, V, Wilkinson, E, Tegally, H, Patané, JSL, Viala, VL, San, EJ, Rodrigues, ES, Santos, EV, Aburjaile, F, Xavier, J, Fritsch, H, Adelino, TER, Pereira, F, Leal, A, Iani, FCDM, de Carvalho Pereira, G, Vazquez, C, Sanabria, GME, Oliveira, ECD, Demarchi, L, Croda, J, dos Santos Bezerra, R, Paola Oliveira de Lima, L, Renata dos Santos Barros, C, Marqueze, EC, de Souza Todao Bernardino, J, Moretti, DB, Brassaloti, RA, de Lello Rocha Campos Cassano, R, Mariani, PDSC, Kitajima, JP, Santos, B, Proto-Siqueira, R, Cantarelli, VV, Tosta, S, Nardy, VB, Reboredo de Oliveira da Silva, L, Gómez, MKA, Lima, JG, Ribeiro, AA, Guimarães, NR, Watanabe, LT, Barbosa Da Silva, L, da Silva Ferreira, R, da Penha, MPF, Ortega, MJ, de la Fuente, AG, Villalba, S, Torales, J, Gamarra, ML, Aquino, C, Figueredo, GPM, Fava, WS, Motta-Castro, ARC, Venturini, J, do Vale Leone de Oliveira, SM, Gonçalves, CCM, do Carmo Debur Rossa, M, Becker, GN, Giacomini, MP, Marques, NQ, Riediger, IN, Raboni, S, Mattoso, G, Cataneo, AD, Zanluca, C, Duarte dos Santos, CN, Assato, PA, Allan da Silva da Costa, F, Poleti, MD, Lesbon, JCC, Mattos, EC, Banho, CA, Sacchetto, L, Moraes, MM, Grotto, RMT, Souza-Neto, JA, Nogueira, ML, Fukumasu, H, Coutinho, LL, Calado, RT, Neto, RM, Bispo de Filippis, AM, Venancio da Cunha, R, Freitas, C, Peterka, CRL, de Fátima Rangel Fernandes, C, Navegantes, W, do Carmo Said, RF, Campelo de A e Melo, CF, Almiron, M, Lourenço, J, de Oliveira, T, Holmes, EC, Haddad, R, Sampaio, SC, Elias, MC, Kashima, S, Junior de Alcantara, LC, Covas, DT & Martins, AJ 2022, 'Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil', Nature Microbiology, vol. 7, no. 9, pp. 1490-1500. https://doi.org/10.1038/s41564-022-01191-z

TY - JOUR

T1 - Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil

AU - Giovanetti, Marta

AU - Slavov, Svetoslav Nanev

AU - Fonseca, Vagner

AU - Wilkinson, Eduan

AU - Tegally, Houriiyah

AU - Patané, José Salvatore Leister

AU - Viala, Vincent Louis

AU - San, Emmanuel James

AU - Rodrigues, Evandra Strazza

AU - Santos, Elaine Vieira

AU - Aburjaile, Flavia

AU - Xavier, Joilson

AU - Fritsch, Hegger

AU - Adelino, Talita Emile Ribeiro

AU - Pereira, Felicidade

AU - Leal, Arabela

AU - Iani, Felipe Campos de Melo

AU - de Carvalho Pereira, Glauco

AU - Vazquez, Cynthia

AU - Sanabria, Gladys Mercedes Estigarribia

AU - Oliveira, Elaine Cristina de

AU - Demarchi, Luiz

AU - Croda, Julio

AU - dos Santos Bezerra, Rafael

AU - Paola Oliveira de Lima, Loyze

AU - Renata dos Santos Barros, Claudia

AU - Marqueze, Elaine Cristina

AU - de Souza Todao Bernardino, Jardelina

AU - Moretti, Debora Botequio

AU - Brassaloti, Ricardo Augusto

AU - de Lello Rocha Campos Cassano, Raquel

AU - Mariani, Pilar Drummond Sampaio Corrêa

AU - Kitajima, João Paulo

AU - Santos, Bibiana

AU - Proto-Siqueira, Rodrigo

AU - Cantarelli, Vlademir Vicente

AU - Tosta, Stephane

AU - Nardy, Vanessa Brandão

AU - Reboredo de Oliveira da Silva, Luciana

AU - Gómez, Marcela Kelly Astete

AU - Lima, Jaqueline Gomes

AU - Ribeiro, Adriana Aparecida

AU - Guimarães, Natália Rocha

AU - Watanabe, Luiz Takao

AU - Barbosa Da Silva, Luana

AU - da Silva Ferreira, Raquel

AU - da Penha, Mara Patricia F.

AU - Ortega, María José

AU - de la Fuente, Andrea Gómez

AU - Villalba, Shirley

AU - Torales, Juan

AU - Gamarra, María Liz

AU - Aquino, Carolina

AU - Figueredo, Gloria Patricia Martínez

AU - Fava, Wellington Santos

AU - Motta-Castro, Ana Rita C.

AU - Venturini, James

AU - do Vale Leone de Oliveira, Sandra Maria

AU - Gonçalves, Crhistinne Cavalheiro Maymone

AU - do Carmo Debur Rossa, Maria

AU - Becker, Guilherme Nardi

AU - Giacomini, Mayra Presibella

AU - Marques, Nelson Quallio

AU - Riediger, Irina Nastassja

AU - Raboni, Sonia

AU - Mattoso, Gabriela

AU - Cataneo, Allan D.

AU - Zanluca, Camila

AU - Duarte dos Santos, Claudia N.

AU - Assato, Patricia Akemi

AU - Allan da Silva da Costa, Felipe

AU - Poleti, Mirele Daiana

AU - Lesbon, Jessika Cristina Chagas

AU - Mattos, Elisangela Chicaroni

AU - Banho, Cecilia Artico

AU - Sacchetto, Lívia

AU - Moraes, Marília Mazzi

AU - Grotto, Rejane Maria Tommasini

AU - Souza-Neto, Jayme A.

AU - Nogueira, Maurício Lacerda

AU - Fukumasu, Heidge

AU - Coutinho, Luiz Lehmann

AU - Calado, Rodrigo Tocantins

AU - Neto, Raul Machado

AU - Bispo de Filippis, Ana Maria

AU - Venancio da Cunha, Rivaldo

AU - Freitas, Carla

AU - Peterka, Cassio Roberto Leonel

AU - de Fátima Rangel Fernandes, Cássia

AU - Navegantes, Wildo

AU - do Carmo Said, Rodrigo Fabiano

AU - Campelo de A e Melo, Carlos F.

AU - Almiron, Maria

AU - Lourenço, José

AU - de Oliveira, Tulio

AU - Holmes, Edward C.

AU - Haddad, Ricardo

AU - Sampaio, Sandra Coccuzzo

AU - Elias, Maria Carolina

AU - Kashima, Simone

AU - Junior de Alcantara, Luiz Carlos

AU - Covas, Dimas Tadeu

AU - Martins, António Jorge

PY - 2022/9

Y1 - 2022/9

N2 - The high numbers of COVID-19 cases and deaths in Brazil have made Latin America an epicentre of the pandemic. SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, but important gaps remain in our understanding of virus transmission dynamics at a national scale. We use 17,135 near-complete genomes sampled from 27 Brazilian states and bordering country Paraguay. From March to November 2020, we detected co-circulation of multiple viral lineages that were linked to multiple importations (predominantly from Europe). After November 2020, we detected large, local transmission clusters within the country. In the absence of effective restriction measures, the epidemic progressed, and in January 2021 there was emergence and onward spread, both within and abroad, of variants of concern and variants under monitoring, including Gamma (P.1) and Zeta (P.2). We also characterized a genomic overview of the epidemic in Paraguay and detected evidence of importation of SARS-CoV-2 ancestor lineages and variants of concern from Brazil. Our findings show that genomic surveillance in Brazil enabled assessment of the real-time spread of emerging SARS-CoV-2 variants.

AB - The high numbers of COVID-19 cases and deaths in Brazil have made Latin America an epicentre of the pandemic. SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, but important gaps remain in our understanding of virus transmission dynamics at a national scale. We use 17,135 near-complete genomes sampled from 27 Brazilian states and bordering country Paraguay. From March to November 2020, we detected co-circulation of multiple viral lineages that were linked to multiple importations (predominantly from Europe). After November 2020, we detected large, local transmission clusters within the country. In the absence of effective restriction measures, the epidemic progressed, and in January 2021 there was emergence and onward spread, both within and abroad, of variants of concern and variants under monitoring, including Gamma (P.1) and Zeta (P.2). We also characterized a genomic overview of the epidemic in Paraguay and detected evidence of importation of SARS-CoV-2 ancestor lineages and variants of concern from Brazil. Our findings show that genomic surveillance in Brazil enabled assessment of the real-time spread of emerging SARS-CoV-2 variants.

UR - http://www.scopus.com/inward/record.url?scp=85136302306&partnerID=8YFLogxK

U2 - 10.1038/s41564-022-01191-z

DO - 10.1038/s41564-022-01191-z

M3 - Article

C2 - 35982313

AN - SCOPUS:85136302306

SN - 2058-5276

VL - 7

SP - 1490

EP - 1500

JO - Nature Microbiology

JF - Nature Microbiology

IS - 9

ER -

Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil

Abstract

UN SDGs

Access to Document

Other files and links

Fingerprint

Cite this