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 the i...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-12-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/11/12/2938 |
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| author | Thaís Regina y Castro Bruna C. Piccoli Andressa A. Vieira Bruna C. Casarin Luíza F. Tessele Richard S. Salvato Tatiana S. Gregianini Leticia G. Martins Paola Cristina Resende Elisa C. Pereira Filipe R. R. Moreira Jaqueline G. de Jesus Ana Paula Seerig Marcos Antonio O. Lobato Marli M. A. de Campos Juliana S. Goularte Mariana S. da Silva Meriane Demoliner Micheli Filippi Vyctoria M. A. Góes Pereira Alexandre V. Schwarzbold Fernando R. Spilki Priscila A. Trindade |
| author_facet | Thaís Regina y Castro Bruna C. Piccoli Andressa A. Vieira Bruna C. Casarin Luíza F. Tessele Richard S. Salvato Tatiana S. Gregianini Leticia G. Martins Paola Cristina Resende Elisa C. Pereira Filipe R. R. Moreira Jaqueline G. de Jesus Ana Paula Seerig Marcos Antonio O. Lobato Marli M. A. de Campos Juliana S. Goularte Mariana S. da Silva Meriane Demoliner Micheli Filippi Vyctoria M. A. Góes Pereira Alexandre V. Schwarzbold Fernando R. Spilki Priscila A. Trindade |
| author_sort | Thaís Regina y Castro |
| collection | DOAJ |
| description | 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<sup>−4</sup> 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. |
| first_indexed | 2024-03-08T20:30:48Z |
| format | Article |
| id | doaj.art-511666d653164a9da239eff4c6cefb40 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-08T20:30:48Z |
| publishDate | 2023-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-511666d653164a9da239eff4c6cefb402023-12-22T14:26:08ZengMDPI AGMicroorganisms2076-26072023-12-011112293810.3390/microorganisms11122938Introduction, Dispersal, and Predominance of SARS-CoV-2 Delta Variant in Rio Grande do Sul, Brazil: A Retrospective AnalysisThaís Regina y Castro0Bruna C. Piccoli1Andressa A. Vieira2Bruna C. Casarin3Luíza F. Tessele4Richard S. Salvato5Tatiana S. Gregianini6Leticia G. Martins7Paola Cristina Resende8Elisa C. Pereira9Filipe R. R. Moreira10Jaqueline G. de Jesus11Ana Paula Seerig12Marcos Antonio O. Lobato13Marli M. A. de Campos14Juliana S. Goularte15Mariana S. da Silva16Meriane Demoliner17Micheli Filippi18Vyctoria M. A. Góes Pereira19Alexandre V. Schwarzbold20Fernando R. Spilki21Priscila A. Trindade22Laboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, BrazilLaboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, BrazilLaboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, BrazilLaboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, BrazilLaboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, BrazilCentro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul (CEVS/SES-RS), Porto Alegre 90610-000, BrazilCentro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul (CEVS/SES-RS), Porto Alegre 90610-000, BrazilCentro Estadual de Vigilância em Saúde, Secretaria Estadual da Saúde do Rio Grande do Sul (CEVS/SES-RS), Porto Alegre 90610-000, BrazilLaboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz Institute, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-360, BrazilLaboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz Institute, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-360, BrazilDepartamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-853, BrazilInstituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05508-220, BrazilVigilância em Saúde, Secretaria Municipal da Saúde de Santa Maria, Santa Maria 97060-001, BrazilDepartamento de Saúde Coletiva, Universidade Federal de Santa Maria, Santa Maria 97105-900, BrazilDepartamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, BrazilLaboratório de Microbiologia Molecular, Universidade FEEVALE, Novo Hamburgo 93510-235, BrazilLaboratório de Microbiologia Molecular, Universidade FEEVALE, Novo Hamburgo 93510-235, BrazilLaboratório de Microbiologia Molecular, Universidade FEEVALE, Novo Hamburgo 93510-235, BrazilLaboratório de Microbiologia Molecular, Universidade FEEVALE, Novo Hamburgo 93510-235, BrazilLaboratório de Microbiologia Molecular, Universidade FEEVALE, Novo Hamburgo 93510-235, BrazilDepartamento de Clínica Médica, Universidade Federal de Santa Maria, Santa Maria 97105-900, BrazilLaboratório de Microbiologia Molecular, Universidade FEEVALE, Novo Hamburgo 93510-235, BrazilLaboratório de Biologia Molecular e Bioinformática Aplicadas a Microbiologia Clínica, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Santa Maria, Santa Maria 97105-900, BrazilMutations 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<sup>−4</sup> 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.https://www.mdpi.com/2076-2607/11/12/2938genomic surveillanceviral lineagesvariants of concerngenome analysisphylogeny |
| spellingShingle | Thaís Regina y Castro Bruna C. Piccoli Andressa A. Vieira Bruna C. Casarin Luíza F. Tessele Richard S. Salvato Tatiana S. Gregianini Leticia G. Martins Paola Cristina Resende Elisa C. Pereira Filipe R. R. Moreira Jaqueline G. de Jesus Ana Paula Seerig Marcos Antonio O. Lobato Marli M. A. de Campos Juliana S. Goularte Mariana S. da Silva Meriane Demoliner Micheli Filippi Vyctoria M. A. Góes Pereira Alexandre V. Schwarzbold Fernando R. Spilki Priscila A. Trindade Introduction, Dispersal, and Predominance of SARS-CoV-2 Delta Variant in Rio Grande do Sul, Brazil: A Retrospective Analysis Microorganisms genomic surveillance viral lineages variants of concern genome analysis phylogeny |
| title | Introduction, Dispersal, and Predominance of SARS-CoV-2 Delta Variant in Rio Grande do Sul, Brazil: A Retrospective Analysis |
| title_full | Introduction, Dispersal, and Predominance of SARS-CoV-2 Delta Variant in Rio Grande do Sul, Brazil: A Retrospective Analysis |
| title_fullStr | Introduction, Dispersal, and Predominance of SARS-CoV-2 Delta Variant in Rio Grande do Sul, Brazil: A Retrospective Analysis |
| title_full_unstemmed | Introduction, Dispersal, and Predominance of SARS-CoV-2 Delta Variant in Rio Grande do Sul, Brazil: A Retrospective Analysis |
| title_short | Introduction, Dispersal, and Predominance of SARS-CoV-2 Delta Variant in Rio Grande do Sul, Brazil: A Retrospective Analysis |
| title_sort | introduction dispersal and predominance of sars cov 2 delta variant in rio grande do sul brazil a retrospective analysis |
| topic | genomic surveillance viral lineages variants of concern genome analysis phylogeny |
| url | https://www.mdpi.com/2076-2607/11/12/2938 |
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