Molecular evolutionary model based on phylogenetic and mutation analysis of SARS-CoV-2 spike protein sequences from Asian countries: A phylogenomic approach
The lethal pathogenic severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection has caused the COVID-19 pandemic, posing serious risks to people. The clove-like spike (S) protein that distinguishes coronaviruses from other viruses is important for viral pathogenicity, evolution, and tra...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-01-01
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| Series: | Informatics in Medicine Unlocked |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352914823000631 |
| _version_ | 1797845079369449472 |
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| author | Kamaleldin B. Said Ahmed Alsolami Fawaz Alshammari Khalid Farhan Alshammari Meshari Alazmi Tulika Bhardwaj Mohammad Zeeshan Najm Rajeev Singh Mohd Adnan Kausar |
| author_facet | Kamaleldin B. Said Ahmed Alsolami Fawaz Alshammari Khalid Farhan Alshammari Meshari Alazmi Tulika Bhardwaj Mohammad Zeeshan Najm Rajeev Singh Mohd Adnan Kausar |
| author_sort | Kamaleldin B. Said |
| collection | DOAJ |
| description | The lethal pathogenic severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection has caused the COVID-19 pandemic, posing serious risks to people. The clove-like spike (S) protein that distinguishes coronaviruses from other viruses is important for viral pathogenicity, evolution, and transmission. The investigation of the unique structural mutations of the SARS-CoV-2 spike protein among 34 Asian countries, as well as the resulting phylogenetic relationship, provided critical information in understanding the pathogenesis. This can be utilized for the discovery of possible treatments and vaccine development. The current study analyzed and depicted phylogenetic and evolutionary models useful for understanding SARS-CoV-2 human-human transmission dynamics in Asian regions with shared land borders. Further, integrated bioinformatics analysis was performed to predict the pathogenic potential and stability of 53 mutational positions among 34 coronavirus strains. Mutations at positions N969K, D614G and S884F have deleterious effects on protein function. These findings are crucial because the Asian mutations could potentially provide a vaccine candidate with co-protection against all SARS-CoV-2 strains. This region is vulnerable because of the high population density and the volume of domestic and international travel for business and tourism. These discoveries would also aid in the development of plans for governments and the general populace to implement all required biocontainment protocols common to all countries. |
| first_indexed | 2024-04-09T17:32:43Z |
| format | Article |
| id | doaj.art-a0dc3ba2c08443138374c605d08bb9e7 |
| institution | Directory Open Access Journal |
| issn | 2352-9148 |
| language | English |
| last_indexed | 2024-04-09T17:32:43Z |
| publishDate | 2023-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Informatics in Medicine Unlocked |
| spelling | doaj.art-a0dc3ba2c08443138374c605d08bb9e72023-04-18T04:08:58ZengElsevierInformatics in Medicine Unlocked2352-91482023-01-0138101221Molecular evolutionary model based on phylogenetic and mutation analysis of SARS-CoV-2 spike protein sequences from Asian countries: A phylogenomic approachKamaleldin B. Said0Ahmed Alsolami1Fawaz Alshammari2Khalid Farhan Alshammari3Meshari Alazmi4Tulika Bhardwaj5Mohammad Zeeshan Najm6Rajeev Singh7Mohd Adnan Kausar8Department of Pathology and Microbiology, College of Medicine, University of Ha'il, Ha'il, 55476, Saudi Arabia; Corresponding author.Department of Internal Medicine, College of Medicine, University of Ha'il, Ha'il, 55476, Saudi ArabiaDepartment of Dermatology, College of Medicine, University of Ha'il, Ha'il, 55476, Saudi ArabiaDepartment of Internal Medicine, College of Medicine at University of Ha'il, Ha'il, 2440, Saudi ArabiaDepartment of Information and Computer Science, College of Computer Science and Engineering, University of Ha'il, Ha'il, 81481, Saudi ArabiaDepartment of Agriculture, Food and Nutritional Sciences, University of Alberta, Edmonton, AB, T6G 2P5, CanadaSchool of Biosciences, Apeejay Stya University, Sohna, Gurugram, 122003, IndiaDepartment of Environmental Science, Jamia Millia Islamia (Central University), New Delhi, 110025, IndiaDepartment of Biochemistry, College of Medicine, University of Ha'il, Ha'il, 2440, Saudi ArabiaThe lethal pathogenic severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection has caused the COVID-19 pandemic, posing serious risks to people. The clove-like spike (S) protein that distinguishes coronaviruses from other viruses is important for viral pathogenicity, evolution, and transmission. The investigation of the unique structural mutations of the SARS-CoV-2 spike protein among 34 Asian countries, as well as the resulting phylogenetic relationship, provided critical information in understanding the pathogenesis. This can be utilized for the discovery of possible treatments and vaccine development. The current study analyzed and depicted phylogenetic and evolutionary models useful for understanding SARS-CoV-2 human-human transmission dynamics in Asian regions with shared land borders. Further, integrated bioinformatics analysis was performed to predict the pathogenic potential and stability of 53 mutational positions among 34 coronavirus strains. Mutations at positions N969K, D614G and S884F have deleterious effects on protein function. These findings are crucial because the Asian mutations could potentially provide a vaccine candidate with co-protection against all SARS-CoV-2 strains. This region is vulnerable because of the high population density and the volume of domestic and international travel for business and tourism. These discoveries would also aid in the development of plans for governments and the general populace to implement all required biocontainment protocols common to all countries.http://www.sciencedirect.com/science/article/pii/S2352914823000631SARS-CoV-2Genetic variabilityPhylogenomic analysisSpike proteinMutational analysisEvolutionary conservation analysis |
| spellingShingle | Kamaleldin B. Said Ahmed Alsolami Fawaz Alshammari Khalid Farhan Alshammari Meshari Alazmi Tulika Bhardwaj Mohammad Zeeshan Najm Rajeev Singh Mohd Adnan Kausar Molecular evolutionary model based on phylogenetic and mutation analysis of SARS-CoV-2 spike protein sequences from Asian countries: A phylogenomic approach Informatics in Medicine Unlocked SARS-CoV-2 Genetic variability Phylogenomic analysis Spike protein Mutational analysis Evolutionary conservation analysis |
| title | Molecular evolutionary model based on phylogenetic and mutation analysis of SARS-CoV-2 spike protein sequences from Asian countries: A phylogenomic approach |
| title_full | Molecular evolutionary model based on phylogenetic and mutation analysis of SARS-CoV-2 spike protein sequences from Asian countries: A phylogenomic approach |
| title_fullStr | Molecular evolutionary model based on phylogenetic and mutation analysis of SARS-CoV-2 spike protein sequences from Asian countries: A phylogenomic approach |
| title_full_unstemmed | Molecular evolutionary model based on phylogenetic and mutation analysis of SARS-CoV-2 spike protein sequences from Asian countries: A phylogenomic approach |
| title_short | Molecular evolutionary model based on phylogenetic and mutation analysis of SARS-CoV-2 spike protein sequences from Asian countries: A phylogenomic approach |
| title_sort | molecular evolutionary model based on phylogenetic and mutation analysis of sars cov 2 spike protein sequences from asian countries a phylogenomic approach |
| topic | SARS-CoV-2 Genetic variability Phylogenomic analysis Spike protein Mutational analysis Evolutionary conservation analysis |
| url | http://www.sciencedirect.com/science/article/pii/S2352914823000631 |
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