Viruses (Jan 2023)
Retrospective Insights of the COVID-19 Epidemic in the Major Latin American City, São Paulo, Southeastern Brazil
- Patricia Akemi Assato,
- Luan Gaspar Clemente,
- Marta Giovanetti,
- Gabriela Ribeiro,
- Alex Ranieri Jeronimo Lima,
- Melissa Palmieri,
- Leonardo Nazario de Moraes,
- Simone Kashima,
- Heidge Fukumasu,
- Maurício Lacerda Nogueira,
- Luiz Carlos Junior Alcantara,
- Aline Lais Nicolodelli,
- Antonio Jorge Martins,
- Bruna Petry,
- Cecilia Artico Banho,
- Claudia Renata Dos Santos Barros,
- Cristina Tschorny Moncau-Gadbem,
- Debora Botequio Moretti,
- Debora Glenda Lima De La Roque,
- Elaine Cristina Marqueze,
- Elisangela Chicaroni Mattos,
- Fabiana Erica Vilanova Da Silva,
- Felipe Allan Da Silva Da Costa,
- Giselle Cacherik,
- Jardelina De Souza Todao Bernardino,
- Jessika Cristina Chagas Lesbon,
- Lívia Sacchetto,
- Loyze Paola Oliveira De Lima,
- Luiz Artur Vieira Caldeira,
- Maiara Martininghi,
- Marília Mazzi Moraes,
- Mirele Daiana Poleti,
- Pedro De Queiroz Cattony Neto,
- Raquel De Lello Rocha Campos Cassano,
- Ricardo Augusto Brassaloti,
- Svetoslav Nanev Slavov,
- Vincent Louis Viala,
- Luiz Lehmann Coutinho,
- Rejane Maria Tommasini Grotto,
- Raul Machado Neto,
- Dimas Tadeu Covas,
- Sandra Coccuzzo Sampaio,
- Maria Carolina Elias,
- Jayme A. Souza-Neto
Affiliations
- Patricia Akemi Assato
- School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, Brazil
- Luan Gaspar Clemente
- Centro de Genômica Funcional da ESALQ, University of São Paulo, Piracicaba 13418-900, Brazil
- Marta Giovanetti
- Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro 21040-360, Brazil
- Gabriela Ribeiro
- Butantan Institute, Sao Paulo 05508-040, Brazil
- Alex Ranieri Jeronimo Lima
- Butantan Institute, Sao Paulo 05508-040, Brazil
- Melissa Palmieri
- Health Surveillance Coordination, Sao Paulo Municipal Health Department—Coordenadoria de Vigilância em Saúde—Secretaria Municipal de São Paulo, Sao Paulo 05579-000, Brazil
- Leonardo Nazario de Moraes
- School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, Brazil
- Simone Kashima
- Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14051-140, Brazil
- Heidge Fukumasu
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga 13635-900, Brazil
- Maurício Lacerda Nogueira
- Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto 15090-000, Brazil
- Luiz Carlos Junior Alcantara
- Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro 21040-360, Brazil
- Aline Lais Nicolodelli
- Primary Care Coordination/Sao Paulo Municipal Health Department—Coordenadoria de Atenção Básica—Secretaria Municipal de São Paulo, Sao Paulo 05579-000, Brazil
- Antonio Jorge Martins
- Butantan Institute, Sao Paulo 05508-040, Brazil
- Bruna Petry
- Centro de Genômica Funcional da ESALQ, University of São Paulo, Piracicaba 13418-900, Brazil
- Cecilia Artico Banho
- Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto 15090-000, Brazil
- Claudia Renata Dos Santos Barros
- Butantan Institute, Sao Paulo 05508-040, Brazil
- Cristina Tschorny Moncau-Gadbem
- Centro de Genômica Funcional da ESALQ, University of São Paulo, Piracicaba 13418-900, Brazil
- Debora Botequio Moretti
- Butantan Institute, Sao Paulo 05508-040, Brazil
- Debora Glenda Lima De La Roque
- Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14051-140, Brazil
- Elaine Cristina Marqueze
- Butantan Institute, Sao Paulo 05508-040, Brazil
- Elisangela Chicaroni Mattos
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga 13635-900, Brazil
- Fabiana Erica Vilanova Da Silva
- Primary Care Coordination/Sao Paulo Municipal Health Department—Coordenadoria de Atenção Básica—Secretaria Municipal de São Paulo, Sao Paulo 05579-000, Brazil
- Felipe Allan Da Silva Da Costa
- School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, Brazil
- Giselle Cacherik
- Primary Care Coordination/Sao Paulo Municipal Health Department—Coordenadoria de Atenção Básica—Secretaria Municipal de São Paulo, Sao Paulo 05579-000, Brazil
- Jardelina De Souza Todao Bernardino
- Butantan Institute, Sao Paulo 05508-040, Brazil
- Jessika Cristina Chagas Lesbon
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga 13635-900, Brazil
- Lívia Sacchetto
- Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto 15090-000, Brazil
- Loyze Paola Oliveira De Lima
- Butantan Institute, Sao Paulo 05508-040, Brazil
- Luiz Artur Vieira Caldeira
- Health Surveillance Coordination, Sao Paulo Municipal Health Department—Coordenadoria de Vigilância em Saúde—Secretaria Municipal de São Paulo, Sao Paulo 05579-000, Brazil
- Maiara Martininghi
- Health Surveillance Coordination, Sao Paulo Municipal Health Department—Coordenadoria de Vigilância em Saúde—Secretaria Municipal de São Paulo, Sao Paulo 05579-000, Brazil
- Marília Mazzi Moraes
- Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto 15090-000, Brazil
- Mirele Daiana Poleti
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga 13635-900, Brazil
- Pedro De Queiroz Cattony Neto
- Butantan Institute, Sao Paulo 05508-040, Brazil
- Raquel De Lello Rocha Campos Cassano
- Centro de Genômica Funcional da ESALQ, University of São Paulo, Piracicaba 13418-900, Brazil
- Ricardo Augusto Brassaloti
- Centro de Genômica Funcional da ESALQ, University of São Paulo, Piracicaba 13418-900, Brazil
- Svetoslav Nanev Slavov
- Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14051-140, Brazil
- Vincent Louis Viala
- Butantan Institute, Sao Paulo 05508-040, Brazil
- Luiz Lehmann Coutinho
- Centro de Genômica Funcional da ESALQ, University of São Paulo, Piracicaba 13418-900, Brazil
- Rejane Maria Tommasini Grotto
- School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, Brazil
- Raul Machado Neto
- Butantan Institute, Sao Paulo 05508-040, Brazil
- Dimas Tadeu Covas
- Butantan Institute, Sao Paulo 05508-040, Brazil
- Sandra Coccuzzo Sampaio
- Butantan Institute, Sao Paulo 05508-040, Brazil
- Maria Carolina Elias
- Butantan Institute, Sao Paulo 05508-040, Brazil
- Jayme A. Souza-Neto
- School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, Brazil
- DOI
- https://doi.org/10.3390/v15020327
- Journal volume & issue
-
Vol. 15,
no. 2
p. 327
Abstract
São Paulo is the financial center of Brazil, with a population of over 12 million, that receives travelers from all over the world for business and tourism. It was the first city in Brazil to report a case of COVID-19 that rapidly spread across the city despite the implementation of the restriction measures. Despite many reports, much is still unknown regarding the genomic diversity and transmission dynamics of this virus in the city of São Paulo. Thus, in this study, we provide a retrospective overview of the COVID-19 epidemic in São Paulo City, Southeastern, Brazil, by generating a total of 9995 near-complete genome sequences from all the city’s different macro-regions (North, West, Central, East, South, and Southeast). Our analysis revealed that multiple independent introduction events of different variants (mainly Gamma, Delta, and Omicron) occurred throughout time. Additionally, our estimates of viral movement within the different macro-regions further suggested that the East and the Southeast regions were the largest contributors to the Gamma and Delta viral exchanges to other regions. Meanwhile, the North region had a higher contribution to the dispersion of the Omicron variant. Together, our results reinforce the importance of increasing SARS-CoV-2 genomic monitoring within the city and the country to track the real-time evolution of the virus and to detect earlier any eventual emergency of new variants of concern that could undermine the fight against COVID-19 in Brazil and worldwide.
Keywords
