Viruses, Vol. 15, Pages 327: Retrospective Insights of the COVID-19 Epidemic in the Major Latin American City, São Paulo, Southeastern Brazil

Viruses, Vol. 15, Pages 327: Retrospective Insights of the COVID-19 Epidemic in the Major Latin American City, São Paulo, Southeastern Brazil

Viruses doi: 10.3390/v15020327

Authors: 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

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.