Some common deleterious mutations are shared in SARS-CoV-2 genomes from deceased COVID-19 patients across continents
Abstract The identification of deleterious mutations in different variants of SARS-CoV-2 and their roles in the morbidity of COVID-19 patients has yet to be thoroughly investigated. To unravel the spectrum of mutations and their effects within SARS-CoV-2 genomes, we analyzed 5,724 complete genomes f...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-10-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-45517-1 |
| _version_ | 1827770613745319936 |
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| author | Md. Aminul Islam Abdullah Al Marzan Md. Sakil Arman Shatila Shahi Tahsin Islam Sakif Maqsud Hossain Tofazzal Islam M. Nazmul Hoque |
| author_facet | Md. Aminul Islam Abdullah Al Marzan Md. Sakil Arman Shatila Shahi Tahsin Islam Sakif Maqsud Hossain Tofazzal Islam M. Nazmul Hoque |
| author_sort | Md. Aminul Islam |
| collection | DOAJ |
| description | Abstract The identification of deleterious mutations in different variants of SARS-CoV-2 and their roles in the morbidity of COVID-19 patients has yet to be thoroughly investigated. To unravel the spectrum of mutations and their effects within SARS-CoV-2 genomes, we analyzed 5,724 complete genomes from deceased COVID-19 patients sourced from the GISAID database. This analysis was conducted using the Nextstrain platform, applying a generalized time-reversible model for evolutionary phylogeny. These genomes were compared to the reference strain (hCoV-19/Wuhan/WIV04/2019) using MAFFT v7.470. Our findings revealed that SARS-CoV-2 genomes from deceased individuals belonged to 21 Nextstrain clades, with clade 20I (Alpha variant) being the most predominant, followed by clade 20H (Beta variant) and clade 20J (Gamma variant). The majority of SARS-CoV-2 genomes from deceased patients (33.4%) were sequenced in North America, while the lowest percentage (0.98%) came from Africa. The ‘G’ clade was dominant in the SARS-CoV-2 genomes of Asian, African, and North American regions, while the ‘GRY’ clade prevailed in Europe. In our analysis, we identified 35,799 nucleotide (NT) mutations throughout the genome, with the highest frequency (11,402 occurrences) found in the spike protein. Notably, we observed 4150 point-specific amino acid (AA) mutations in SARS-CoV-2 genomes, with D614G (20%) and N501Y (14%) identified as the top two deleterious mutations in the spike protein on a global scale. Furthermore, we detected five common deleterious AA mutations, including G18V, W45S, I33T, P30L, and Q418H, which play a key role in defining each clade of SARS-CoV-2. Our novel findings hold potential value for genomic surveillance, enabling the monitoring of the evolving pattern of SARS-CoV-2 infection, its emerging variants, and their impact on the development of effective vaccination and control strategies. |
| first_indexed | 2024-03-11T12:42:04Z |
| format | Article |
| id | doaj.art-c55609b934b34175ad6ffcbe6e7546b2 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-11T12:42:04Z |
| publishDate | 2023-10-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-c55609b934b34175ad6ffcbe6e7546b22023-11-05T12:14:34ZengNature PortfolioScientific Reports2045-23222023-10-0113111410.1038/s41598-023-45517-1Some common deleterious mutations are shared in SARS-CoV-2 genomes from deceased COVID-19 patients across continentsMd. Aminul Islam0Abdullah Al Marzan1Md. Sakil Arman2Shatila Shahi3Tahsin Islam Sakif4Maqsud Hossain5Tofazzal Islam6M. Nazmul Hoque7Advanced Molecular Lab, Department of Microbiology, President Abdul Hamid Medical CollegeAdvanced Molecular Lab, Department of Microbiology, President Abdul Hamid Medical CollegeDepartment of Biochemistry and Molecular Biology, Shahjalal University of Science and TechnologyDepartment of Biochemistry and Molecular Biology, Shahjalal University of Science and TechnologyLane Department of Computer Science and Electrical Engineering, West Virginia UniversityUniversity of NottinghamInstitute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural UniversityMolecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural UniversityAbstract The identification of deleterious mutations in different variants of SARS-CoV-2 and their roles in the morbidity of COVID-19 patients has yet to be thoroughly investigated. To unravel the spectrum of mutations and their effects within SARS-CoV-2 genomes, we analyzed 5,724 complete genomes from deceased COVID-19 patients sourced from the GISAID database. This analysis was conducted using the Nextstrain platform, applying a generalized time-reversible model for evolutionary phylogeny. These genomes were compared to the reference strain (hCoV-19/Wuhan/WIV04/2019) using MAFFT v7.470. Our findings revealed that SARS-CoV-2 genomes from deceased individuals belonged to 21 Nextstrain clades, with clade 20I (Alpha variant) being the most predominant, followed by clade 20H (Beta variant) and clade 20J (Gamma variant). The majority of SARS-CoV-2 genomes from deceased patients (33.4%) were sequenced in North America, while the lowest percentage (0.98%) came from Africa. The ‘G’ clade was dominant in the SARS-CoV-2 genomes of Asian, African, and North American regions, while the ‘GRY’ clade prevailed in Europe. In our analysis, we identified 35,799 nucleotide (NT) mutations throughout the genome, with the highest frequency (11,402 occurrences) found in the spike protein. Notably, we observed 4150 point-specific amino acid (AA) mutations in SARS-CoV-2 genomes, with D614G (20%) and N501Y (14%) identified as the top two deleterious mutations in the spike protein on a global scale. Furthermore, we detected five common deleterious AA mutations, including G18V, W45S, I33T, P30L, and Q418H, which play a key role in defining each clade of SARS-CoV-2. Our novel findings hold potential value for genomic surveillance, enabling the monitoring of the evolving pattern of SARS-CoV-2 infection, its emerging variants, and their impact on the development of effective vaccination and control strategies.https://doi.org/10.1038/s41598-023-45517-1 |
| spellingShingle | Md. Aminul Islam Abdullah Al Marzan Md. Sakil Arman Shatila Shahi Tahsin Islam Sakif Maqsud Hossain Tofazzal Islam M. Nazmul Hoque Some common deleterious mutations are shared in SARS-CoV-2 genomes from deceased COVID-19 patients across continents Scientific Reports |
| title | Some common deleterious mutations are shared in SARS-CoV-2 genomes from deceased COVID-19 patients across continents |
| title_full | Some common deleterious mutations are shared in SARS-CoV-2 genomes from deceased COVID-19 patients across continents |
| title_fullStr | Some common deleterious mutations are shared in SARS-CoV-2 genomes from deceased COVID-19 patients across continents |
| title_full_unstemmed | Some common deleterious mutations are shared in SARS-CoV-2 genomes from deceased COVID-19 patients across continents |
| title_short | Some common deleterious mutations are shared in SARS-CoV-2 genomes from deceased COVID-19 patients across continents |
| title_sort | some common deleterious mutations are shared in sars cov 2 genomes from deceased covid 19 patients across continents |
| url | https://doi.org/10.1038/s41598-023-45517-1 |
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