Microorganisms (Feb 2024)
Epidemiology of the SARS-CoV-2 Omicron Variant Emergence in the Southeast Brazilian Population
- Evandra Strazza Rodrigues,
- Svetoslav Nanev Slavov,
- Debora Glenda Lima de La Roque,
- Elaine Vieira Santos,
- Josiane Serrano Borges,
- Mariane Evaristo,
- Péricles Natan Mendes da Costa,
- Juliana de Matos Maçonetto,
- Adriana Aparecida Marques,
- Anemarie Dinarte Baccarin,
- Renata Aparecida Machado Oliveira,
- Wilson Lau Junior,
- Bruno Iglesias Benincasa,
- Luana Martins de Andrade da Cruz,
- Alex Ranieri Jerônimo Lima,
- Gabriela Ribeiro,
- Vincent Louis Viala,
- Loyze Paola Oliveira de Lima,
- Antonio Jorge Martins,
- Claudia Renata dos Santos Barros,
- Elaine Cristina Marqueze,
- Jardelina de Souza Todao Bernardino,
- Rejane Maria Tommasini Grotto,
- Jayme A. Souza-Neto,
- Vagner Fonseca,
- Maurício Lacerda Nogueira,
- Heidge Fukumasu,
- Luiz Lehmann Coutinho,
- Rodrigo Tocantins Calado,
- Dimas Tadeu Covas,
- Marta Giovanetti,
- Luiz Carlos Junior Alcantara,
- Sandra Coccuzzo Sampaio,
- Maria Carolina Elias,
- Simone Kashima
Affiliations
- Evandra Strazza Rodrigues
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-140, SP, Brazil
- Svetoslav Nanev Slavov
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-140, SP, Brazil
- Debora Glenda Lima de La Roque
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-140, SP, Brazil
- Elaine Vieira Santos
- Butantan Institute, São Paulo 05585-000, SP, Brazil
- Josiane Serrano Borges
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-140, SP, Brazil
- Mariane Evaristo
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-140, SP, Brazil
- Péricles Natan Mendes da Costa
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-140, SP, Brazil
- Juliana de Matos Maçonetto
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-140, SP, Brazil
- Adriana Aparecida Marques
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-140, SP, Brazil
- Anemarie Dinarte Baccarin
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-140, SP, Brazil
- Renata Aparecida Machado Oliveira
- Butantan Institute, São Paulo 05585-000, SP, Brazil
- Wilson Lau Junior
- Butantan Institute, São Paulo 05585-000, SP, Brazil
- Bruno Iglesias Benincasa
- Butantan Institute, São Paulo 05585-000, SP, Brazil
- Luana Martins de Andrade da Cruz
- Butantan Institute, São Paulo 05585-000, SP, Brazil
- Alex Ranieri Jerônimo Lima
- Butantan Institute, São Paulo 05585-000, SP, Brazil
- Gabriela Ribeiro
- Butantan Institute, São Paulo 05585-000, SP, Brazil
- Vincent Louis Viala
- Butantan Institute, São Paulo 05585-000, SP, Brazil
- Loyze Paola Oliveira de Lima
- Butantan Institute, São Paulo 05585-000, SP, Brazil
- Antonio Jorge Martins
- Butantan Institute, São Paulo 05585-000, SP, Brazil
- Claudia Renata dos Santos Barros
- Butantan Institute, São Paulo 05585-000, SP, Brazil
- Elaine Cristina Marqueze
- Butantan Institute, São Paulo 05585-000, SP, Brazil
- Jardelina de Souza Todao Bernardino
- Butantan Institute, São Paulo 05585-000, SP, Brazil
- Rejane Maria Tommasini Grotto
- School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, SP, Brazil
- Jayme A. Souza-Neto
- Department of Diagnostic Medicine/Pathobiology, Kansas State Veterinary Diagnostic Laboratory College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
- Vagner Fonseca
- Organização Pan-Americana da Saúde/Organização Mundial da Saúde, Brasília 70075-900, DF, Brazil
- Maurício Lacerda Nogueira
- Medicine School of São José do Rio Preto (FAMERP), São José do Rio Preto 15090-000, SP, Brazil
- Heidge Fukumasu
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga 05508-270, SP, Brazil
- Luiz Lehmann Coutinho
- Centro de Genômica Funcional da ESALQ, University of São Paulo, Piracicaba 13418-900, SP, Brazil
- Rodrigo Tocantins Calado
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-140, SP, Brazil
- Dimas Tadeu Covas
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-140, SP, Brazil
- Marta Giovanetti
- Laboratorio de Flavivirus, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, RJ, Brazil
- Luiz Carlos Junior Alcantara
- Laboratorio de Flavivirus, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, RJ, Brazil
- Sandra Coccuzzo Sampaio
- Butantan Institute, São Paulo 05585-000, SP, Brazil
- Maria Carolina Elias
- Butantan Institute, São Paulo 05585-000, SP, Brazil
- Simone Kashima
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-140, SP, Brazil
- DOI
- https://doi.org/10.3390/microorganisms12030449
- Journal volume & issue
-
Vol. 12,
no. 3
p. 449
Abstract
The aim of this study was to describe epidemiological characteristics and perform SARS-CoV-2 genomic surveillance in the southeastern region of São Paulo State. During the first months of 2022, we compared weekly SARS-CoV-2 infection prevalence considering age, Ct value, and variants’ lineages. An increase in the number of SARS-CoV-2-positive cases until the fourth epidemiological week of 2022 was observed. From the fourth epidemiological week onwards, the number of tests for SARS-CoV-2 diagnosis began to decrease, but the number of positive samples for SARS-CoV-2 remained high, reaching its most expressive level with a rate of 60% of infected individual cases. In this period, we observed a progressive increase in SARS-CoV-2 infection within the 0–10 age group throughout the epidemiological weeks, from 2.8% in the first epidemiological week to 9.2% in the eighth epidemiological week of 2022. We further observed significantly higher Ct values within younger patient samples compared to other older age groups. According to lineage assignment, SARS-CoV-2 (BA.1) was the most prevalent (74.5%) in the younger group, followed by BA.1.1 (23%), BA.2 (1.7%), and Delta (1%). Phylogenetic analysis showed that BA.2 sequences clustered together, indicating sustained transmission of this Omicron VOC sub-lineage by that time. Our results suggest the initial dissemination steps of the Omicron’s sub-linage BA.2 into the younger group, due to specific genomic features of the detected sequences. These data provide interesting results related to the spread, emergence, and evolution of the Omicron variant in the southeast Brazilian population.
Keywords