Genomic Analyses of Major SARS-CoV-2 Variants Predicting Multiple Regions of Pathogenic and Transmissive Importance
The rapid evolution of SARS-CoV-2 has fueled its global proliferation since its discovery in 2019, with several notable variants having been responsible for increases in cases of coronavirus disease 2019 (COVID-19). Analyses of codon bias and usage in these variants between phylogenetic clades or li...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2024-02-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/16/2/276 |
| _version_ | 1797296809470590976 |
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| author | Steven W. Brugger Julianne H. Grose Craig H. Decker Brett E. Pickett Mary F. Davis |
| author_facet | Steven W. Brugger Julianne H. Grose Craig H. Decker Brett E. Pickett Mary F. Davis |
| author_sort | Steven W. Brugger |
| collection | DOAJ |
| description | The rapid evolution of SARS-CoV-2 has fueled its global proliferation since its discovery in 2019, with several notable variants having been responsible for increases in cases of coronavirus disease 2019 (COVID-19). Analyses of codon bias and usage in these variants between phylogenetic clades or lineages may grant insights into the evolution of SARS-CoV-2 and identify target codons indicative of evolutionary or mutative trends that may prove useful in tracking or defending oneself against emerging strains. We processed a cohort of 120 SARS-CoV-2 genome sequences through a statistical and bioinformatic pipeline to identify codons presenting evidence of selective pressure as well as codon coevolution. We report the identification of two codon sites in the <i>orf8</i> and <i>N</i> genes demonstrating such evidence with real-world impacts on pathogenicity and transmissivity. |
| first_indexed | 2024-03-07T22:10:13Z |
| format | Article |
| id | doaj.art-73bd2d7930f94926bca570ba886d1117 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-07T22:10:13Z |
| publishDate | 2024-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-73bd2d7930f94926bca570ba886d11172024-02-23T15:37:41ZengMDPI AGViruses1999-49152024-02-0116227610.3390/v16020276Genomic Analyses of Major SARS-CoV-2 Variants Predicting Multiple Regions of Pathogenic and Transmissive ImportanceSteven W. Brugger0Julianne H. Grose1Craig H. Decker2Brett E. Pickett3Mary F. Davis4Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USADepartment of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USADepartment of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USADepartment of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USADepartment of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USAThe rapid evolution of SARS-CoV-2 has fueled its global proliferation since its discovery in 2019, with several notable variants having been responsible for increases in cases of coronavirus disease 2019 (COVID-19). Analyses of codon bias and usage in these variants between phylogenetic clades or lineages may grant insights into the evolution of SARS-CoV-2 and identify target codons indicative of evolutionary or mutative trends that may prove useful in tracking or defending oneself against emerging strains. We processed a cohort of 120 SARS-CoV-2 genome sequences through a statistical and bioinformatic pipeline to identify codons presenting evidence of selective pressure as well as codon coevolution. We report the identification of two codon sites in the <i>orf8</i> and <i>N</i> genes demonstrating such evidence with real-world impacts on pathogenicity and transmissivity.https://www.mdpi.com/1999-4915/16/2/276SARS-CoV-2genomicsbioinformaticscoevolutioncodon bias |
| spellingShingle | Steven W. Brugger Julianne H. Grose Craig H. Decker Brett E. Pickett Mary F. Davis Genomic Analyses of Major SARS-CoV-2 Variants Predicting Multiple Regions of Pathogenic and Transmissive Importance Viruses SARS-CoV-2 genomics bioinformatics coevolution codon bias |
| title | Genomic Analyses of Major SARS-CoV-2 Variants Predicting Multiple Regions of Pathogenic and Transmissive Importance |
| title_full | Genomic Analyses of Major SARS-CoV-2 Variants Predicting Multiple Regions of Pathogenic and Transmissive Importance |
| title_fullStr | Genomic Analyses of Major SARS-CoV-2 Variants Predicting Multiple Regions of Pathogenic and Transmissive Importance |
| title_full_unstemmed | Genomic Analyses of Major SARS-CoV-2 Variants Predicting Multiple Regions of Pathogenic and Transmissive Importance |
| title_short | Genomic Analyses of Major SARS-CoV-2 Variants Predicting Multiple Regions of Pathogenic and Transmissive Importance |
| title_sort | genomic analyses of major sars cov 2 variants predicting multiple regions of pathogenic and transmissive importance |
| topic | SARS-CoV-2 genomics bioinformatics coevolution codon bias |
| url | https://www.mdpi.com/1999-4915/16/2/276 |
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