Introduction, Dispersal, and Predominance of SARS-CoV-2 Delta Variant in Rio Grande do Sul, Brazil: A Retrospective Analysis
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Published:2023-12-07
Issue:12
Volume:11
Page:2938
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ISSN:2076-2607
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Container-title:Microorganisms
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language:en
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Short-container-title:Microorganisms
Author:
y Castro Thaís Regina1, Piccoli Bruna C.1, Vieira Andressa A.1, Casarin Bruna C.1, Tessele Luíza F.1, Salvato Richard S.2, Gregianini Tatiana S.2, Martins Leticia G.2ORCID, Resende Paola Cristina3, Pereira Elisa C.3, Moreira Filipe R. R.4, de Jesus Jaqueline G.5ORCID, Seerig Ana Paula6, Lobato Marcos Antonio O.7, de Campos Marli M. A.8, Goularte Juliana S.9, da Silva Mariana S.9, Demoliner Meriane9ORCID, Filippi Micheli9ORCID, Pereira Vyctoria M. A. Góes9, Schwarzbold Alexandre V.10ORCID, Spilki Fernando R.9ORCID, Trindade Priscila A.1ORCID
Affiliation:
1. Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil 2. Centro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul (CEVS/SES-RS), Porto Alegre 90610-000, Brazil 3. Laboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz Institute, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-360, Brazil 4. Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-853, Brazil 5. Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05508-220, Brazil 6. Vigilância em Saúde, Secretaria Municipal da Saúde de Santa Maria, Santa Maria 97060-001, Brazil 7. Departamento de Saúde Coletiva, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil 8. Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil 9. Laboratório de Microbiologia Molecular, Universidade FEEVALE, Novo Hamburgo 93510-235, Brazil 10. Departamento de Clínica Médica, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil
Abstract
Mutations in the SARS-CoV-2 genome can alter the virus’ fitness, leading to the emergence of variants of concern (VOC). In Brazil, the Gamma variant dominated the pandemic in the first half of 2021, and from June onwards, the first cases of Delta infection were documented. Here, we investigate the introduction and dispersal of the Delta variant in the RS state by sequencing 1077 SARS-CoV-2-positive samples from June to October 2021. Of these samples, 34.7% were identified as Gamma and 65.3% as Delta. Notably, 99.2% of Delta sequences were clustered within the 21J lineage, forming a significant Brazilian clade. The estimated clock rate was 5.97 × 10−4 substitutions per site per year. The Delta variant was first reported on 17 June in the Vinhedos Basalto microregion and rapidly spread, accounting for over 70% of cases within nine weeks. Despite this, the number of cases and deaths remained stable, possibly due to vaccination, prior infections, and the continued mandatory mask use. In conclusion, our study provides insights into the Delta variant circulating in the RS state, highlighting the importance of genomic surveillance for monitoring viral evolution, even when the impact of new variants may be less severe in a given region.
Funder
Coordenação de Aperfeicoamento de Pessoal de Nível Superior Rede Corona-omica BR MCTI/FINEP affiliated to RedeVírus/MCTI FAPERGS AstraZeneca
Subject
Virology,Microbiology (medical),Microbiology
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