Genomic Evolution of the SARS-CoV-2 Omicron Variant in Córdoba, Argentina (2021–2022): Analysis of Uncommon and Prevalent Spike Mutations
Understanding the evolutionary patterns and geographic spread of SARS-CoV-2 variants, particularly Omicron, is essential for effective public health responses. This study focused on the genomic analysis of the Omicron variant in Cordoba, Argentina from 2021 to 2022. Phylogenetic analysis revealed th...
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2024-12-01
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| author | Nadia B. Olivero Victoria E. Zappia Pablo Gargantini Candela Human-Gonzalez Luciana Raya-Plasencia Judith Marquez Lucia Ortiz-Batsche Mirelys Hernandez-Morfa Paulo R. Cortes Danilo Ceschin Mariana Nuñez-Fernandez Daniel R. Perez José Echenique |
| author_facet | Nadia B. Olivero Victoria E. Zappia Pablo Gargantini Candela Human-Gonzalez Luciana Raya-Plasencia Judith Marquez Lucia Ortiz-Batsche Mirelys Hernandez-Morfa Paulo R. Cortes Danilo Ceschin Mariana Nuñez-Fernandez Daniel R. Perez José Echenique |
| author_sort | Nadia B. Olivero |
| collection | DOAJ |
| description | Understanding the evolutionary patterns and geographic spread of SARS-CoV-2 variants, particularly Omicron, is essential for effective public health responses. This study focused on the genomic analysis of the Omicron variant in Cordoba, Argentina from 2021 to 2022. Phylogenetic analysis revealed the dominant presence of BA.1 and BA.2 lineages, with BA.5 emerging earlier than BA.4, aligning with observations from other regions. Haplotype network analysis showed significant genetic divergence within Omicron samples, forming distinct clusters. In comparison to global datasets, we identified mutations in the Omicron genomes (A27S, Y145D, and L212I) situated within the NTD region of the Spike protein. These mutations, while not widespread globally, showed higher prevalence in our region. Of particular interest were the Y145D and L212I substitutions, previously unreported in Argentina. In silico analysis revealed that both mutations impact the binding affinity of T-cell epitopes to HLA type I and II alleles. Notably, these alleles are among the most common in the Argentinian population, with some associated with protection against and others with susceptibility to SARS-CoV-2 infection. These findings strongly suggest that these prevalent mutations likely influence the immunogenicity of the Spike protein and contribute to immune evasion mechanisms. This study provides valuable insights into the genomic dynamics of the Omicron variant in Cordoba, Argentina and highlights unique mutations with potential implications for COVID-19 vaccines. |
| format | Article |
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| institution | Kabale University |
| issn | 1999-4915 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj-art-d1403f1aae0a4c77a8ac1542d51d27822024-12-27T14:59:07ZengMDPI AGViruses1999-49152024-12-011612187710.3390/v16121877Genomic Evolution of the SARS-CoV-2 Omicron Variant in Córdoba, Argentina (2021–2022): Analysis of Uncommon and Prevalent Spike MutationsNadia B. Olivero0Victoria E. Zappia1Pablo Gargantini2Candela Human-Gonzalez3Luciana Raya-Plasencia4Judith Marquez5Lucia Ortiz-Batsche6Mirelys Hernandez-Morfa7Paulo R. Cortes8Danilo Ceschin9Mariana Nuñez-Fernandez10Daniel R. Perez11José Echenique12Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba X5000HUA, ArgentinaCentro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba X5000HUA, ArgentinaClínica Universitaria Reina Fabiola, Universidad Católica de Córdoba, Córdoba X5000HUA, ArgentinaCentro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba X5000HUA, ArgentinaCentro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba X5000HUA, ArgentinaClínica Universitaria Reina Fabiola, Universidad Católica de Córdoba, Córdoba X5000HUA, ArgentinaDepartment of Population Health, College of Veterinary Medicine, University of Georgia, Athens 30692, GA, USACentro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba X5000HUA, ArgentinaCentro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba X5000HUA, ArgentinaInstituto Universitario de Ciencias Biomedicas de Córdoba (IUCBC), Centro de Investigacion en Medicina Traslacional “Severo R. Amuchastegui” (CIMETSA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba X5000HUA, ArgentinaCentro de Química Aplicada, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba X5000HUA, ArgentinaDepartment of Population Health, College of Veterinary Medicine, University of Georgia, Athens 30692, GA, USACentro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba X5000HUA, ArgentinaUnderstanding the evolutionary patterns and geographic spread of SARS-CoV-2 variants, particularly Omicron, is essential for effective public health responses. This study focused on the genomic analysis of the Omicron variant in Cordoba, Argentina from 2021 to 2022. Phylogenetic analysis revealed the dominant presence of BA.1 and BA.2 lineages, with BA.5 emerging earlier than BA.4, aligning with observations from other regions. Haplotype network analysis showed significant genetic divergence within Omicron samples, forming distinct clusters. In comparison to global datasets, we identified mutations in the Omicron genomes (A27S, Y145D, and L212I) situated within the NTD region of the Spike protein. These mutations, while not widespread globally, showed higher prevalence in our region. Of particular interest were the Y145D and L212I substitutions, previously unreported in Argentina. In silico analysis revealed that both mutations impact the binding affinity of T-cell epitopes to HLA type I and II alleles. Notably, these alleles are among the most common in the Argentinian population, with some associated with protection against and others with susceptibility to SARS-CoV-2 infection. These findings strongly suggest that these prevalent mutations likely influence the immunogenicity of the Spike protein and contribute to immune evasion mechanisms. This study provides valuable insights into the genomic dynamics of the Omicron variant in Cordoba, Argentina and highlights unique mutations with potential implications for COVID-19 vaccines.https://www.mdpi.com/1999-4915/16/12/1877SARS-CoV-2OmicronHLA allelesT-cell epitopesCordobaArgentina |
| spellingShingle | Nadia B. Olivero Victoria E. Zappia Pablo Gargantini Candela Human-Gonzalez Luciana Raya-Plasencia Judith Marquez Lucia Ortiz-Batsche Mirelys Hernandez-Morfa Paulo R. Cortes Danilo Ceschin Mariana Nuñez-Fernandez Daniel R. Perez José Echenique Genomic Evolution of the SARS-CoV-2 Omicron Variant in Córdoba, Argentina (2021–2022): Analysis of Uncommon and Prevalent Spike Mutations Viruses SARS-CoV-2 Omicron HLA alleles T-cell epitopes Cordoba Argentina |
| title | Genomic Evolution of the SARS-CoV-2 Omicron Variant in Córdoba, Argentina (2021–2022): Analysis of Uncommon and Prevalent Spike Mutations |
| title_full | Genomic Evolution of the SARS-CoV-2 Omicron Variant in Córdoba, Argentina (2021–2022): Analysis of Uncommon and Prevalent Spike Mutations |
| title_fullStr | Genomic Evolution of the SARS-CoV-2 Omicron Variant in Córdoba, Argentina (2021–2022): Analysis of Uncommon and Prevalent Spike Mutations |
| title_full_unstemmed | Genomic Evolution of the SARS-CoV-2 Omicron Variant in Córdoba, Argentina (2021–2022): Analysis of Uncommon and Prevalent Spike Mutations |
| title_short | Genomic Evolution of the SARS-CoV-2 Omicron Variant in Córdoba, Argentina (2021–2022): Analysis of Uncommon and Prevalent Spike Mutations |
| title_sort | genomic evolution of the sars cov 2 omicron variant in cordoba argentina 2021 2022 analysis of uncommon and prevalent spike mutations |
| topic | SARS-CoV-2 Omicron HLA alleles T-cell epitopes Cordoba Argentina |
| url | https://www.mdpi.com/1999-4915/16/12/1877 |
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