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

Autor: 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
Jazyk: angličtina
Rok vydání: 2024
Předmět:
Zdroj: Microorganisms, Vol 12, Iss 3, p 449 (2024)
Druh dokumentu: article
ISSN: 12030449
2076-2607
DOI: 10.3390/microorganisms12030449
Popis: 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.
Databáze: Directory of Open Access Journals
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