Introduction, Dispersal, and Predominance of SARS-CoV-2 Delta Variant in Rio Grande do Sul, Brazil: A Retrospective Analysis

Introduction, Dispersal, and Predominance of SARS-CoV-2 Delta Variant in Rio Grande do Sul, Brazil: A Retrospective Analysis

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...

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Bibliographic Details
Published in:Microorganisms (Basel) Vol. 11; no. 12; p. 2938
Main Authors: Y Castro, Thaís Regina, Piccoli, Bruna C, Vieira, Andressa A, Casarin, Bruna C, Tessele, Luíza F, Salvato, Richard S, Gregianini, Tatiana S, Martins, Leticia G, Resende, Paola Cristina, Pereira, Elisa C, Moreira, Filipe R R, de Jesus, Jaqueline G, Seerig, Ana Paula, Lobato, Marcos Antonio O, de Campos, Marli M A, Goularte, Juliana S, da Silva, Mariana S, Demoliner, Meriane, Filippi, Micheli, Pereira, Vyctoria M A Góes, Schwarzbold, Alexandre V, Spilki, Fernando R, Trindade, Priscila A
Format: Journal Article
Language:English
Published: Switzerland MDPI AG 01-12-2023
Subjects:
COVID-19
Datasets
Disease transmission
Dispersion
DNA sequencing
genome analysis
Genomes
genomic surveillance
Laboratories
Methods
Mutation
Nucleotide sequencing
Pandemics
Phylogenetics
phylogeny
Proteins
Severe acute respiratory syndrome coronavirus 2
Vaccination
variants of concern
Viral diseases
viral lineages
Brazil
Rio Grande do Sul Brazil
Rio de Janeiro Brazil
United States > US
Germany
India
phylogeny
viral lineages
variants of concern
genome analysis
genomic surveillance
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Summary: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 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.
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ISSN:2076-2607
2076-2607
DOI:10.3390/microorganisms11122938