Genomic Surveillance and Mutation Analysis of SARS-CoV-2 Variants among Patients in Saudi Arabia
The genome of severe acute respiratory coronavirus-2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19), has undergone a rapid evolution, resulting in the emergence of multiple SARS-CoV-2 variants with amino acid changes. This study aimed to sequence the whole genome of SARS...
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MDPI AG
2024-02-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/12/3/467 |
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| author | Feda A. Alsuwairi Asma N. Alsaleh Dalia A. Obeid Ahmed A. Al-Qahtani Reem S. Almaghrabi Basma M. Alahideb Maha A. AlAbdulkareem Madain S. Alsanea Layla A. Alharbi Sahar I. Althawadi Sara A. Altamimi Abeer N. Alshukairi Fatimah S. Alhamlan |
| author_facet | Feda A. Alsuwairi Asma N. Alsaleh Dalia A. Obeid Ahmed A. Al-Qahtani Reem S. Almaghrabi Basma M. Alahideb Maha A. AlAbdulkareem Madain S. Alsanea Layla A. Alharbi Sahar I. Althawadi Sara A. Altamimi Abeer N. Alshukairi Fatimah S. Alhamlan |
| author_sort | Feda A. Alsuwairi |
| collection | DOAJ |
| description | The genome of severe acute respiratory coronavirus-2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19), has undergone a rapid evolution, resulting in the emergence of multiple SARS-CoV-2 variants with amino acid changes. This study aimed to sequence the whole genome of SARS-CoV-2 and detect the variants present in specimens from Saudi Arabia. Furthermore, we sought to analyze and characterize the amino acid changes in the various proteins of the identified SARS-CoV-2 variants. A total of 1161 samples from patients diagnosed with COVID-19 in Saudi Arabia, between 1 April 2021 and 31 July 2023, were analyzed. Whole genome sequencing was employed for variant identification and mutation analysis. The statistical analysis was performed using the Statistical Analytical Software SAS, version 9.4, and GraphPad, version 9.0. This study identified twenty-three variants and subvariants of SARS-CoV-2 within the population, with the Omicron BA.1 (21K) variant (37.0%) and the Delta (21J) variant (12%) being the most frequently detected. Notably, the Omicron subvariants exhibited a higher mean mutation rate. Amino acid mutations were observed in twelve proteins. Among these, the spike (S), ORF1a, nucleocapsid (N), and ORF1b proteins showed a higher frequency of amino acid mutations compared to other the viral proteins. The S protein exhibited the highest incidence of amino acid mutations (47.6%). Conversely, the ORF3a, ORF8, ORF7a, ORF6, and ORF7b proteins appeared more conserved, demonstrating the lowest percentage and frequency of amino acid mutations. The investigation of structural protein regions revealed the N-terminal S1 subunit of the S protein to frequently harbor mutations, while the N-terminal domain of the envelope (E) protein displayed the lowest mutation frequency. This study provides insights into the variants and genetic diversity of SARS-CoV-2, underscoring the need for further research to comprehend its genome evolution and the occurrence of mutations. These findings are pertinent to the development of testing approaches, therapeutics, and vaccine strategies. |
| first_indexed | 2024-04-24T18:00:19Z |
| format | Article |
| id | doaj.art-45818b16583a49e29bb1b1ab96c2fb49 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-04-24T18:00:19Z |
| publishDate | 2024-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-45818b16583a49e29bb1b1ab96c2fb492024-03-27T13:55:33ZengMDPI AGMicroorganisms2076-26072024-02-0112346710.3390/microorganisms12030467Genomic Surveillance and Mutation Analysis of SARS-CoV-2 Variants among Patients in Saudi ArabiaFeda A. Alsuwairi0Asma N. Alsaleh1Dalia A. Obeid2Ahmed A. Al-Qahtani3Reem S. Almaghrabi4Basma M. Alahideb5Maha A. AlAbdulkareem6Madain S. Alsanea7Layla A. Alharbi8Sahar I. Althawadi9Sara A. Altamimi10Abeer N. Alshukairi11Fatimah S. Alhamlan12Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi ArabiaBotany and Microbiology Department, College of Science, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi ArabiaDepartment of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi ArabiaDepartment of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi ArabiaOrgan Transplant Center of Excellence, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi ArabiaDepartment of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi ArabiaDepartment of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi ArabiaDepartment of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi ArabiaDepartment of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi ArabiaDepartment of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi ArabiaDepartment of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi ArabiaCollege of Medicine, Alfaisal University, Riyadh 11533, Saudi ArabiaDepartment of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi ArabiaThe genome of severe acute respiratory coronavirus-2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19), has undergone a rapid evolution, resulting in the emergence of multiple SARS-CoV-2 variants with amino acid changes. This study aimed to sequence the whole genome of SARS-CoV-2 and detect the variants present in specimens from Saudi Arabia. Furthermore, we sought to analyze and characterize the amino acid changes in the various proteins of the identified SARS-CoV-2 variants. A total of 1161 samples from patients diagnosed with COVID-19 in Saudi Arabia, between 1 April 2021 and 31 July 2023, were analyzed. Whole genome sequencing was employed for variant identification and mutation analysis. The statistical analysis was performed using the Statistical Analytical Software SAS, version 9.4, and GraphPad, version 9.0. This study identified twenty-three variants and subvariants of SARS-CoV-2 within the population, with the Omicron BA.1 (21K) variant (37.0%) and the Delta (21J) variant (12%) being the most frequently detected. Notably, the Omicron subvariants exhibited a higher mean mutation rate. Amino acid mutations were observed in twelve proteins. Among these, the spike (S), ORF1a, nucleocapsid (N), and ORF1b proteins showed a higher frequency of amino acid mutations compared to other the viral proteins. The S protein exhibited the highest incidence of amino acid mutations (47.6%). Conversely, the ORF3a, ORF8, ORF7a, ORF6, and ORF7b proteins appeared more conserved, demonstrating the lowest percentage and frequency of amino acid mutations. The investigation of structural protein regions revealed the N-terminal S1 subunit of the S protein to frequently harbor mutations, while the N-terminal domain of the envelope (E) protein displayed the lowest mutation frequency. This study provides insights into the variants and genetic diversity of SARS-CoV-2, underscoring the need for further research to comprehend its genome evolution and the occurrence of mutations. These findings are pertinent to the development of testing approaches, therapeutics, and vaccine strategies.https://www.mdpi.com/2076-2607/12/3/467COVID-19SARS-CoV-2genomevariantsamino acidmutations |
| spellingShingle | Feda A. Alsuwairi Asma N. Alsaleh Dalia A. Obeid Ahmed A. Al-Qahtani Reem S. Almaghrabi Basma M. Alahideb Maha A. AlAbdulkareem Madain S. Alsanea Layla A. Alharbi Sahar I. Althawadi Sara A. Altamimi Abeer N. Alshukairi Fatimah S. Alhamlan Genomic Surveillance and Mutation Analysis of SARS-CoV-2 Variants among Patients in Saudi Arabia Microorganisms COVID-19 SARS-CoV-2 genome variants amino acid mutations |
| title | Genomic Surveillance and Mutation Analysis of SARS-CoV-2 Variants among Patients in Saudi Arabia |
| title_full | Genomic Surveillance and Mutation Analysis of SARS-CoV-2 Variants among Patients in Saudi Arabia |
| title_fullStr | Genomic Surveillance and Mutation Analysis of SARS-CoV-2 Variants among Patients in Saudi Arabia |
| title_full_unstemmed | Genomic Surveillance and Mutation Analysis of SARS-CoV-2 Variants among Patients in Saudi Arabia |
| title_short | Genomic Surveillance and Mutation Analysis of SARS-CoV-2 Variants among Patients in Saudi Arabia |
| title_sort | genomic surveillance and mutation analysis of sars cov 2 variants among patients in saudi arabia |
| topic | COVID-19 SARS-CoV-2 genome variants amino acid mutations |
| url | https://www.mdpi.com/2076-2607/12/3/467 |
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