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Volume 12
Issue 3
10.3390/microorganisms12030449
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Article

Epidemiology of the SARS-CoV-2 Omicron Variant Emergence in the Southeast Brazilian Population

by
Evandra Strazza Rodrigues
1,*,
Svetoslav Nanev Slavov
1,
Debora Glenda Lima de La Roque
1,
Elaine Vieira Santos
2,
Josiane Serrano Borges
1,
Mariane Evaristo
1,
Péricles Natan Mendes da Costa
1,
Juliana de Matos Maçonetto
1,
Adriana Aparecida Marques
1,
Anemarie Dinarte Baccarin
1,
Renata Aparecida Machado Oliveira
2,
Wilson Lau Junior
2,
Bruno Iglesias Benincasa
2,
Luana Martins de Andrade da Cruz
2,
Alex Ranieri Jerônimo Lima
2,
Gabriela Ribeiro
2,
Vincent Louis Viala
2,
Loyze Paola Oliveira de Lima
2,
Antonio Jorge Martins
2,
Claudia Renata dos Santos Barros
2,
Elaine Cristina Marqueze
2,
Jardelina de Souza Todao Bernardino
2,
Rejane Maria Tommasini Grotto
3,
Jayme A. Souza-Neto
4,
Vagner Fonseca
5,
Maurício Lacerda Nogueira
6,
Heidge Fukumasu
7,
Luiz Lehmann Coutinho
8,
Rodrigo Tocantins Calado
1,
Dimas Tadeu Covas
1,2,
Marta Giovanetti
9,10,
Luiz Carlos Junior Alcantara
9,
Sandra Coccuzzo Sampaio
2,
Maria Carolina Elias
2 and
Simone Kashima
1add Show full author list remove Hide full author list
1
Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-140, SP, Brazil
2
Butantan Institute, São Paulo 05585-000, SP, Brazil
3
School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, SP, Brazil
4
Department of Diagnostic Medicine/Pathobiology, Kansas State Veterinary Diagnostic Laboratory College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
5
Organização Pan-Americana da Saúde/Organização Mundial da Saúde, Brasília 70075-900, DF, Brazil
6
Medicine School of São José do Rio Preto (FAMERP), São José do Rio Preto 15090-000, SP, Brazil
7
Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga 05508-270, SP, Brazil
8
Centro de Genômica Funcional da ESALQ, University of São Paulo, Piracicaba 13418-900, SP, Brazil
9
Laboratorio de Flavivirus, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, RJ, Brazil
10
Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, 00128 Rome, Italy
*
Author to whom correspondence should be addressed.
Microorganisms 2024, 12(3), 449; https://doi.org/10.3390/microorganisms12030449
Submission received: 29 December 2023 / Revised: 9 February 2024 / Accepted: 10 February 2024 / Published: 23 February 2024
(This article belongs to the Special Issue COVID-19/SARS-CoV-2: Infection, Vaccination and Immune Response)
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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: SARS-CoV-2 genomic surveillance; Brazilian population; Omicron variant SARS-CoV-2 genomic surveillance; Brazilian population; Omicron variant

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MDPI and ACS Style

Rodrigues, E.S.; Slavov, S.N.; de La Roque, D.G.L.; Santos, E.V.; Borges, J.S.; Evaristo, M.; da Costa, P.N.M.; de Matos Maçonetto, J.; Marques, A.A.; Baccarin, A.D.; et al. Epidemiology of the SARS-CoV-2 Omicron Variant Emergence in the Southeast Brazilian Population. Microorganisms 2024, 12, 449. https://doi.org/10.3390/microorganisms12030449

AMA Style

Rodrigues ES, Slavov SN, de La Roque DGL, Santos EV, Borges JS, Evaristo M, da Costa PNM, de Matos Maçonetto J, Marques AA, Baccarin AD, et al. Epidemiology of the SARS-CoV-2 Omicron Variant Emergence in the Southeast Brazilian Population. Microorganisms. 2024; 12(3):449. https://doi.org/10.3390/microorganisms12030449

Chicago/Turabian Style

Rodrigues, Evandra Strazza, 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, and et al. 2024. "Epidemiology of the SARS-CoV-2 Omicron Variant Emergence in the Southeast Brazilian Population" Microorganisms 12, no. 3: 449. https://doi.org/10.3390/microorganisms12030449

APA Style

Rodrigues, E. S., Slavov, S. N., de La Roque, D. G. L., Santos, E. V., Borges, J. S., Evaristo, M., da Costa, P. N. M., de Matos Maçonetto, J., Marques, A. A., Baccarin, A. D., Oliveira, R. A. M., Junior, W. L., Benincasa, B. I., de Andrade da Cruz, L. M., Lima, A. R. J., Ribeiro, G., Viala, V. L., de Lima, L. P. O., Martins, A. J., ... Kashima, S. (2024). Epidemiology of the SARS-CoV-2 Omicron Variant Emergence in the Southeast Brazilian Population. Microorganisms, 12(3), 449. https://doi.org/10.3390/microorganisms12030449

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