Two Years of SARS-CoV-2 Omicron Genomic Evolution in Brazil (2022–2024): Subvariant Tracking and Assessment of Regional Sequencing Efforts
SARS-CoV-2, the virus responsible for COVID-19, has undergone significant genetic evolution since its emergence in 2019. This study examines the genomic diversity of SARS-CoV-2 in Brazil after the worst phase of the pandemic, the wider adoption of routine vaccination, and the abolishment of other no...
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2025-01-01
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| Online Access: | https://www.mdpi.com/1999-4915/17/1/64 |
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| author | Ueric José Borges de Souza Fernando Rosado Spilki Amilcar Tanuri Paulo Michel Roehe Fabrício Souza Campos |
| author_facet | Ueric José Borges de Souza Fernando Rosado Spilki Amilcar Tanuri Paulo Michel Roehe Fabrício Souza Campos |
| author_sort | Ueric José Borges de Souza |
| collection | DOAJ |
| description | SARS-CoV-2, the virus responsible for COVID-19, has undergone significant genetic evolution since its emergence in 2019. This study examines the genomic diversity of SARS-CoV-2 in Brazil after the worst phase of the pandemic, the wider adoption of routine vaccination, and the abolishment of other non-pharmacological preventive measures from July 2022 to July 2024 using 55,951 sequences retrieved from the GISAID database. The analysis focuses on the correlation between confirmed COVID-19 cases, sequencing efforts across Brazilian states, and the distribution and evolution of viral lineages. Our findings reveal significant regional disparities in genomic surveillance, with São Paulo and Rio de Janeiro recovering the largest number of genomes, while Tocantins and Amazonas showed higher sequencing rates relative to their reported case numbers, indicating proactive surveillance efforts. We identified 626 distinct SARS-CoV-2 lineages circulating in Brazil, with dominant subvariants shifting over time from BA.5 in 2022 to XBB and JN.1 in 2023–2024. The emergence of new subvariants in this new epidemiological scenario underscores the importance of ongoing genomic surveillance to track viral evolution and inform public health strategies, providing valuable information to update vaccines and implement other measures, such as lockdowns, mask usage, social distancing, health education, and self-testing. |
| format | Article |
| id | doaj-art-a7b6e2b77aaa4fb89d490299574c656b |
| institution | Kabale University |
| issn | 1999-4915 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | MDPI AG |
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| series | Viruses |
| spelling | doaj-art-a7b6e2b77aaa4fb89d490299574c656b2025-01-24T13:52:27ZengMDPI AGViruses1999-49152025-01-011716410.3390/v17010064Two Years of SARS-CoV-2 Omicron Genomic Evolution in Brazil (2022–2024): Subvariant Tracking and Assessment of Regional Sequencing EffortsUeric José Borges de Souza0Fernando Rosado Spilki1Amilcar Tanuri2Paulo Michel Roehe3Fabrício Souza Campos4Bioinformatics and Biotechnology Laboratory, Campus of Gurupi, Federal University of Tocantins, Gurupi 77410-570, BrazilMolecular Microbiology Laboratory, Feevale University, Novo Hamburgo 93525-075, BrazilLaboratory of Genetics and Immunology of Viral Infections, Department of Virology, Paulo de Góes Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, BrazilVirology Laboratory, Department of Microbiology, Immunology, and Parasitology, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90050-170, BrazilBioinformatics and Biotechnology Laboratory, Campus of Gurupi, Federal University of Tocantins, Gurupi 77410-570, BrazilSARS-CoV-2, the virus responsible for COVID-19, has undergone significant genetic evolution since its emergence in 2019. This study examines the genomic diversity of SARS-CoV-2 in Brazil after the worst phase of the pandemic, the wider adoption of routine vaccination, and the abolishment of other non-pharmacological preventive measures from July 2022 to July 2024 using 55,951 sequences retrieved from the GISAID database. The analysis focuses on the correlation between confirmed COVID-19 cases, sequencing efforts across Brazilian states, and the distribution and evolution of viral lineages. Our findings reveal significant regional disparities in genomic surveillance, with São Paulo and Rio de Janeiro recovering the largest number of genomes, while Tocantins and Amazonas showed higher sequencing rates relative to their reported case numbers, indicating proactive surveillance efforts. We identified 626 distinct SARS-CoV-2 lineages circulating in Brazil, with dominant subvariants shifting over time from BA.5 in 2022 to XBB and JN.1 in 2023–2024. The emergence of new subvariants in this new epidemiological scenario underscores the importance of ongoing genomic surveillance to track viral evolution and inform public health strategies, providing valuable information to update vaccines and implement other measures, such as lockdowns, mask usage, social distancing, health education, and self-testing.https://www.mdpi.com/1999-4915/17/1/64SARS-CoV-2genomic surveillanceomicron subvariantsCOVID-19lineage trackingpublic health |
| spellingShingle | Ueric José Borges de Souza Fernando Rosado Spilki Amilcar Tanuri Paulo Michel Roehe Fabrício Souza Campos Two Years of SARS-CoV-2 Omicron Genomic Evolution in Brazil (2022–2024): Subvariant Tracking and Assessment of Regional Sequencing Efforts Viruses SARS-CoV-2 genomic surveillance omicron subvariants COVID-19 lineage tracking public health |
| title | Two Years of SARS-CoV-2 Omicron Genomic Evolution in Brazil (2022–2024): Subvariant Tracking and Assessment of Regional Sequencing Efforts |
| title_full | Two Years of SARS-CoV-2 Omicron Genomic Evolution in Brazil (2022–2024): Subvariant Tracking and Assessment of Regional Sequencing Efforts |
| title_fullStr | Two Years of SARS-CoV-2 Omicron Genomic Evolution in Brazil (2022–2024): Subvariant Tracking and Assessment of Regional Sequencing Efforts |
| title_full_unstemmed | Two Years of SARS-CoV-2 Omicron Genomic Evolution in Brazil (2022–2024): Subvariant Tracking and Assessment of Regional Sequencing Efforts |
| title_short | Two Years of SARS-CoV-2 Omicron Genomic Evolution in Brazil (2022–2024): Subvariant Tracking and Assessment of Regional Sequencing Efforts |
| title_sort | two years of sars cov 2 omicron genomic evolution in brazil 2022 2024 subvariant tracking and assessment of regional sequencing efforts |
| topic | SARS-CoV-2 genomic surveillance omicron subvariants COVID-19 lineage tracking public health |
| url | https://www.mdpi.com/1999-4915/17/1/64 |
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