Genomic characterization of SARS-CoV-2 in Egypt
Introduction: The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread throughout the globe, causing a pandemic. In Egypt over 115,000 individuals were infected so far. Objective: In the present study, the objective is to perform a complete genome sequence of SAR...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2021-05-01
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| Series: | Journal of Advanced Research |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2090123220302381 |
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| author | Abdel-Rahman N. Zekri Khaled Easa Amer Mohammed M. Hafez Zeinab K. Hassan Ola S Ahmed Hany K. Soliman Abeer A. Bahnasy Wael Abdel Hamid Ahmad Gad Mahmoud Ali Wael Ali Hassan Mahmoud Samir Madboly Ahmad Abdel Raouf Ayman A. Khattab Mona Salah El Din Hamdy May Sherif Soliman Maha Hamdi El Sissy Sara Mohamed El khateeb Moushira Hosny Ezzelarab Lamiaa A. Fathalla Mohamed Abouelhoda |
| author_facet | Abdel-Rahman N. Zekri Khaled Easa Amer Mohammed M. Hafez Zeinab K. Hassan Ola S Ahmed Hany K. Soliman Abeer A. Bahnasy Wael Abdel Hamid Ahmad Gad Mahmoud Ali Wael Ali Hassan Mahmoud Samir Madboly Ahmad Abdel Raouf Ayman A. Khattab Mona Salah El Din Hamdy May Sherif Soliman Maha Hamdi El Sissy Sara Mohamed El khateeb Moushira Hosny Ezzelarab Lamiaa A. Fathalla Mohamed Abouelhoda |
| author_sort | Abdel-Rahman N. Zekri |
| collection | DOAJ |
| description | Introduction: The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread throughout the globe, causing a pandemic. In Egypt over 115,000 individuals were infected so far. Objective: In the present study, the objective is to perform a complete genome sequence of SAR-CoV2 isolated from Egyptian coronavirus disease (COVID-19) patients. Methods: Nasopharyngeal swabs were collected from 61 COVID-19 patients who attended at National Cancer Institute, Kasr Al-Aini Hospital and the army hospital. Viral RNA was extracted and whole genomic sequencing was conducted using Next Generation Sequencing. Results: In all cases, the sequenced virus has at least 99% identity to the reference Wuhan 1. The sequence analysis showed 204 distinct genome variations including 114 missense mutations, 72 synonymous mutations, 1 disruptive in-frame deletion, 7 downstream gene mutations, 6 upstream gene mutations, 3 frame-shift deletions, and 1 in-frame deletion. The most dominant clades were G/GH/GR/O and the dominant type is B. Conclusion: The whole genomic sequence of SARS-CoV2 showed 204 variations in the genomes of the Egyptian isolates, where the Asp614Gly (D614G) substitution is the most common among the samples (60/61). So far, there were no strikingly variations specific to the Egyptian population, at least for this set of samples. |
| first_indexed | 2024-12-21T20:29:24Z |
| format | Article |
| id | doaj.art-4f09527acd1b496cbb9b94bd87462caf |
| institution | Directory Open Access Journal |
| issn | 2090-1232 |
| language | English |
| last_indexed | 2024-12-21T20:29:24Z |
| publishDate | 2021-05-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Advanced Research |
| spelling | doaj.art-4f09527acd1b496cbb9b94bd87462caf2022-12-21T18:51:15ZengElsevierJournal of Advanced Research2090-12322021-05-0130123132Genomic characterization of SARS-CoV-2 in EgyptAbdel-Rahman N. Zekri0Khaled Easa Amer1Mohammed M. Hafez2Zeinab K. Hassan3Ola S Ahmed4Hany K. Soliman5Abeer A. Bahnasy6Wael Abdel Hamid7Ahmad Gad8Mahmoud Ali9Wael Ali Hassan10Mahmoud Samir Madboly11Ahmad Abdel Raouf12Ayman A. Khattab13Mona Salah El Din Hamdy14May Sherif Soliman15Maha Hamdi El Sissy16Sara Mohamed El khateeb17Moushira Hosny Ezzelarab18Lamiaa A. Fathalla19Mohamed Abouelhoda20Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, Egypt; Corresponding author.Egypt Center for Research and Regenerative Medicine ECRRM, EgyptCancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, EgyptCancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, EgyptCancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, EgyptCancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, EgyptSurgical Pathology Department National Cancer Institute, Cairo University, 11796, EgyptMilitary Central Laboratories, EgyptMilitary Central Laboratories, EgyptEgypt Center for Research and Regenerative Medicine ECRRM, EgyptEgypt Center for Research and Regenerative Medicine ECRRM, EgyptEgypt Center for Research and Regenerative Medicine ECRRM, EgyptEgypt Center for Research and Regenerative Medicine ECRRM, EgyptEgypt Center for Research and Regenerative Medicine ECRRM, EgyptClinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, EgyptClinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, EgyptClinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, EgyptClinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, EgyptClinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, EgyptClinical Pathology Department, National Cancer Institute, Cairo University 11796, EgyptSystems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo 12613, Egypt; Co-corresponding author.Introduction: The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread throughout the globe, causing a pandemic. In Egypt over 115,000 individuals were infected so far. Objective: In the present study, the objective is to perform a complete genome sequence of SAR-CoV2 isolated from Egyptian coronavirus disease (COVID-19) patients. Methods: Nasopharyngeal swabs were collected from 61 COVID-19 patients who attended at National Cancer Institute, Kasr Al-Aini Hospital and the army hospital. Viral RNA was extracted and whole genomic sequencing was conducted using Next Generation Sequencing. Results: In all cases, the sequenced virus has at least 99% identity to the reference Wuhan 1. The sequence analysis showed 204 distinct genome variations including 114 missense mutations, 72 synonymous mutations, 1 disruptive in-frame deletion, 7 downstream gene mutations, 6 upstream gene mutations, 3 frame-shift deletions, and 1 in-frame deletion. The most dominant clades were G/GH/GR/O and the dominant type is B. Conclusion: The whole genomic sequence of SARS-CoV2 showed 204 variations in the genomes of the Egyptian isolates, where the Asp614Gly (D614G) substitution is the most common among the samples (60/61). So far, there were no strikingly variations specific to the Egyptian population, at least for this set of samples.http://www.sciencedirect.com/science/article/pii/S2090123220302381Sars-CoV2Next generation sequencingReal time PCRNasopharyngeal swab |
| spellingShingle | Abdel-Rahman N. Zekri Khaled Easa Amer Mohammed M. Hafez Zeinab K. Hassan Ola S Ahmed Hany K. Soliman Abeer A. Bahnasy Wael Abdel Hamid Ahmad Gad Mahmoud Ali Wael Ali Hassan Mahmoud Samir Madboly Ahmad Abdel Raouf Ayman A. Khattab Mona Salah El Din Hamdy May Sherif Soliman Maha Hamdi El Sissy Sara Mohamed El khateeb Moushira Hosny Ezzelarab Lamiaa A. Fathalla Mohamed Abouelhoda Genomic characterization of SARS-CoV-2 in Egypt Journal of Advanced Research Sars-CoV2 Next generation sequencing Real time PCR Nasopharyngeal swab |
| title | Genomic characterization of SARS-CoV-2 in Egypt |
| title_full | Genomic characterization of SARS-CoV-2 in Egypt |
| title_fullStr | Genomic characterization of SARS-CoV-2 in Egypt |
| title_full_unstemmed | Genomic characterization of SARS-CoV-2 in Egypt |
| title_short | Genomic characterization of SARS-CoV-2 in Egypt |
| title_sort | genomic characterization of sars cov 2 in egypt |
| topic | Sars-CoV2 Next generation sequencing Real time PCR Nasopharyngeal swab |
| url | http://www.sciencedirect.com/science/article/pii/S2090123220302381 |
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