Beta, Delta, and Omicron, Deadliest Among SARS-CoV-2 Variants: A Computational Repurposing Approach
SARS-CoV-2 has been highly susceptible to mutations since its emergence in Wuhan, China, and its subsequent propagation due to containing an RNA as its genome. The emergence of variants with improved transmissibility still poses a grave threat to global health. The spike protein mutation is mainly r...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
SAGE Publishing
2023-07-01
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| Series: | Evolutionary Bioinformatics |
| Online Access: | https://doi.org/10.1177/11769343231182258 |
| _version_ | 1797783028815101952 |
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| author | Mohammad Mamun Alam Sumaiya Binte Hannan Tanvir Ahmed Saikat Md Belayet Hasan Limon Md Raihan Topu Md Jowel Rana Asma Salauddin Sagar Bosu Mohammed Ziaur Rahman |
| author_facet | Mohammad Mamun Alam Sumaiya Binte Hannan Tanvir Ahmed Saikat Md Belayet Hasan Limon Md Raihan Topu Md Jowel Rana Asma Salauddin Sagar Bosu Mohammed Ziaur Rahman |
| author_sort | Mohammad Mamun Alam |
| collection | DOAJ |
| description | SARS-CoV-2 has been highly susceptible to mutations since its emergence in Wuhan, China, and its subsequent propagation due to containing an RNA as its genome. The emergence of variants with improved transmissibility still poses a grave threat to global health. The spike protein mutation is mainly responsible for higher transmissibility and risk severity. This study retrieved SARS-CoV-2 variants structural and nonstructural proteins (NSPs) sequences from several geographic locations, including Africa, Asia, Europe, Oceania, and North and South America. First, multiple sequence alignments with BioEdit and protein homology modeling were performed using the SWISS Model. Then the structure visualization and structural analysis were performed by superimposing against the Wuhan sequence by Pymol to retrieve the RMSD values. Sequence alignment revealed familiar, uncommon regional among variants and, interestingly, a few unique mutations in Beta, Delta, and Omicron. Structural analysis of such unique mutations revealed that they caused structural deviations in Beta, Delta, and Omicron spike proteins. In addition, these variants were more severe in terms of hospitalization, sickness, and higher mortality, which have a substantial relationship with the structural deviations because of those unique mutations. Such evidence provides insight into the SARS-CoV-2 spike protein vulnerability toward mutation and their structural and functional deviations, particularly in Beta, Delta, and Omicron, which might be the cause of their broader coverage. This knowledge can help us with regional vaccine strain selection, virus pathogenicity testing, diagnosis, and treatment with more specific vaccines. |
| first_indexed | 2024-03-13T00:19:18Z |
| format | Article |
| id | doaj.art-5cd844b766004fa3a79ca29acb3cb5e8 |
| institution | Directory Open Access Journal |
| issn | 1176-9343 |
| language | English |
| last_indexed | 2024-03-13T00:19:18Z |
| publishDate | 2023-07-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Evolutionary Bioinformatics |
| spelling | doaj.art-5cd844b766004fa3a79ca29acb3cb5e82023-07-11T16:33:40ZengSAGE PublishingEvolutionary Bioinformatics1176-93432023-07-011910.1177/11769343231182258Beta, Delta, and Omicron, Deadliest Among SARS-CoV-2 Variants: A Computational Repurposing ApproachMohammad Mamun AlamSumaiya Binte HannanTanvir Ahmed SaikatMd Belayet Hasan LimonMd Raihan TopuMd Jowel RanaAsma SalauddinSagar BosuMohammed Ziaur RahmanSARS-CoV-2 has been highly susceptible to mutations since its emergence in Wuhan, China, and its subsequent propagation due to containing an RNA as its genome. The emergence of variants with improved transmissibility still poses a grave threat to global health. The spike protein mutation is mainly responsible for higher transmissibility and risk severity. This study retrieved SARS-CoV-2 variants structural and nonstructural proteins (NSPs) sequences from several geographic locations, including Africa, Asia, Europe, Oceania, and North and South America. First, multiple sequence alignments with BioEdit and protein homology modeling were performed using the SWISS Model. Then the structure visualization and structural analysis were performed by superimposing against the Wuhan sequence by Pymol to retrieve the RMSD values. Sequence alignment revealed familiar, uncommon regional among variants and, interestingly, a few unique mutations in Beta, Delta, and Omicron. Structural analysis of such unique mutations revealed that they caused structural deviations in Beta, Delta, and Omicron spike proteins. In addition, these variants were more severe in terms of hospitalization, sickness, and higher mortality, which have a substantial relationship with the structural deviations because of those unique mutations. Such evidence provides insight into the SARS-CoV-2 spike protein vulnerability toward mutation and their structural and functional deviations, particularly in Beta, Delta, and Omicron, which might be the cause of their broader coverage. This knowledge can help us with regional vaccine strain selection, virus pathogenicity testing, diagnosis, and treatment with more specific vaccines.https://doi.org/10.1177/11769343231182258 |
| spellingShingle | Mohammad Mamun Alam Sumaiya Binte Hannan Tanvir Ahmed Saikat Md Belayet Hasan Limon Md Raihan Topu Md Jowel Rana Asma Salauddin Sagar Bosu Mohammed Ziaur Rahman Beta, Delta, and Omicron, Deadliest Among SARS-CoV-2 Variants: A Computational Repurposing Approach Evolutionary Bioinformatics |
| title | Beta, Delta, and Omicron, Deadliest Among SARS-CoV-2 Variants: A Computational Repurposing Approach |
| title_full | Beta, Delta, and Omicron, Deadliest Among SARS-CoV-2 Variants: A Computational Repurposing Approach |
| title_fullStr | Beta, Delta, and Omicron, Deadliest Among SARS-CoV-2 Variants: A Computational Repurposing Approach |
| title_full_unstemmed | Beta, Delta, and Omicron, Deadliest Among SARS-CoV-2 Variants: A Computational Repurposing Approach |
| title_short | Beta, Delta, and Omicron, Deadliest Among SARS-CoV-2 Variants: A Computational Repurposing Approach |
| title_sort | beta delta and omicron deadliest among sars cov 2 variants a computational repurposing approach |
| url | https://doi.org/10.1177/11769343231182258 |
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