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. 2023 Dec 7;11(12):2938.
doi: 10.3390/microorganisms11122938.

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

Thaís Regina Y Castro  1 , Bruna C Piccoli  1 , Andressa A Vieira  1 , Bruna C Casarin  1 , Luíza F Tessele  1 , Richard S Salvato  2 , Tatiana S Gregianini  2 , Leticia G Martins  2 , Paola Cristina Resende  3 , Elisa C Pereira  3 , Filipe R R Moreira  4 , Jaqueline G de Jesus  5 , Ana Paula Seerig  6 , Marcos Antonio O Lobato  7 , Marli M A de Campos  8 , Juliana S Goularte  9 , Mariana S da Silva  9 , Meriane Demoliner  9 , Micheli Filippi  9 , Vyctoria M A Góes Pereira  9 , Alexandre V Schwarzbold  10 , Fernando R Spilki  9 , Priscila A Trindade  1
Affiliations

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

Thaís Regina Y Castro et al. Microorganisms. .

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.

Keywords: genome analysis; genomic surveillance; phylogeny; variants of concern; viral lineages.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

Figures

Figure 1
Figure 1
Diagram of the study methodology.
Figure 2
Figure 2
COVID-19 overview in the Rio Grande do Sul state, Brazil, during epidemiological weeks 26 to 40 of 2021. (A) number of confirmed cases, deaths, and (B) vaccinated individuals.
Figure 3
Figure 3
Replacement of Gamma variant by Delta variant considering the sequenced samples in this study.
Figure 4
Figure 4
Genetic composition of SARS-CoV-2 lineages in Rio Grande do Sul from June to October 2021. (A) absolute variation number in lineages’ frequencies across epidemiological weeks, as classified by Pangolin version 4.1.1; (B) lineages’ variation frequencies in relative terms.
Figure 5
Figure 5
Mutational profile and variant frequency in the coding region of SARS-CoV-2 Gamma (A) and Delta (B) variants.
Figure 6
Figure 6
Maximum likelihood phylogeny constructed with proportional data set (n = 10,013). In this study, 63.9% of the Delta cases sequenced clustered into a large Brazilian clade (highlighted in gray), covering 3025 sequences (A). Temporal signal analysis of the large Brazilian clade through root-to-tip regression (B). Clock rate distribution using 10% of the large Brazilian clade sequences (C).
Figure 7
Figure 7
SARS-CoV-2 genomic surveillance in Rio Grande do Sul, Brazil, from June to October 2021. Gamma retraction (A) and Delta variant dispersal (B) across the state of Rio Grande do Sul considering the H = health microregions in each epidemiological week sampled in our study.
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