The Epidemiological Scenario of the SARS-CoV-2 Omicron Emergence in the Southeast Brazilian Population

Evandra Strazza Rodrigues; Svetoslav N. Slavov; Debora Glenda Lima De La-Roque; Elaine Vieira Santos; Josiane Serrano Borges; Mariane Evaristo; Pericles Natan Mendes Da Costa; Juliana Matos; Adriana Marques; Anemarie Dinarte Baccarin; Renata Aparecida Machado Oliveira; Wilson Lau Junior; Bruno Iglesias Benincasa; Luana Martins de Andrade Da Cruz; Alex R. J. 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 Todão 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 Júnior Alcantara; Sandra Coccuzzo Sampaio; Maria Carolina Elias; Simone K. Haddad

doi:10.20944/preprints202401.0196.v1

A peer-reviewed article of this Preprint also exists.

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.; dos Santos Barros, C.R.; Marqueze, E.C.; de Souza Todao Bernardino, J.; Grotto, R.M.T.; Souza-Neto, J.A.; Fonseca, V.; Nogueira, M.L.; Fukumasu, H.; Coutinho, L.L.; Calado, R.T.; Covas, D.T.; Giovanetti, M.; Alcantara, L.C.J.; Sampaio, S.C.; Elias, M.C.; Kashima, S. Epidemiology of the SARS-CoV-2 Omicron Variant Emergence in the Southeast Brazilian Population. Microorganisms 2024, 12, 449. 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.; dos Santos Barros, C.R.; Marqueze, E.C.; de Souza Todao Bernardino, J.; Grotto, R.M.T.; Souza-Neto, J.A.; Fonseca, V.; Nogueira, M.L.; Fukumasu, H.; Coutinho, L.L.; Calado, R.T.; Covas, D.T.; Giovanetti, M.; Alcantara, L.C.J.; Sampaio, S.C.; Elias, M.C.; Kashima, S. Epidemiology of the SARS-CoV-2 Omicron Variant Emergence in the Southeast Brazilian Population. Microorganisms 2024, 12, 449.

Abstract

Background: To describe epidemiological characteristics and perform a SARS-CoV-2 genomic surveillance in the southeastern region of São Paulo state. Methods: During the first months of 2022, we compared weekly SARS-CoV-2 infection prevalence considering age, Ct value and variants lineages. Results: An increase in the number of SARS-CoV-2 positive cases until the fourth epidemiological week were observed. From the 4th 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 growing increase in SARS-CoV-2 infection within the age group 0-10 throughout the epidemiological weeks, from 2.8% in the 1st epidemiological week to 9.2% in the 8th epidemiological week. We further observed significantly higher Ct values within younger patients 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 sublineage by that time. Our results suggest the initial dissemination steps of the Omicron’s sublinage BA.2 into the younger group, due specific genomic features of the detected sequences. Conclusion: These data provide interesting results related to the spread, emerging and evolution of the Omicron variant in the Southeast Brazilian population.

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Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

The Epidemiological Scenario of the SARS-CoV-2 Omicron Emergence in the Southeast Brazilian Population

Abstract

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