SARS-CoV-2 genome variations and evolution patterns in Egypt: a multi-center study
Abstract A serious global public health emergency emerged late November 2019 in Wuhan City, China, by a new highly pathogenic virus, SARS-CoV-2. The virus evolution spread has been tracked by three developing databases: GISAID, Nextstrain and PANGO to understand its circulating variants. In this stu...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2022-08-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-022-18644-4 |
| _version_ | 1818082394946666496 |
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| author | Deena Jalal Mariam G. Elzayat Hend E. El-Shqanqery Aya A. Diab Abdelrahman Yahia Omar Samir Usama Bakry Khaled Amer Mostafa ElNaqeeb Wael Hassan Hala S. Talat Hala M. Farawela Mona S. Hamdy May S. Soliman Maha H. El Sissy Moushira H. Ezzelarab Sara M. El khateeb Lamyaa H. Soliman Sara E. Haddad Ashraf Hatem Mohamed S. Ismail Maha Hossam Tarek Mansour Lobna Shalaby Sonia Soliman Reem Hassan Mahmoud Hammad Ibrahim Abdo Sameh Magdeldin Alaa ElHaddad Sherif Abouelnaga Ahmed A. Sayed |
| author_facet | Deena Jalal Mariam G. Elzayat Hend E. El-Shqanqery Aya A. Diab Abdelrahman Yahia Omar Samir Usama Bakry Khaled Amer Mostafa ElNaqeeb Wael Hassan Hala S. Talat Hala M. Farawela Mona S. Hamdy May S. Soliman Maha H. El Sissy Moushira H. Ezzelarab Sara M. El khateeb Lamyaa H. Soliman Sara E. Haddad Ashraf Hatem Mohamed S. Ismail Maha Hossam Tarek Mansour Lobna Shalaby Sonia Soliman Reem Hassan Mahmoud Hammad Ibrahim Abdo Sameh Magdeldin Alaa ElHaddad Sherif Abouelnaga Ahmed A. Sayed |
| author_sort | Deena Jalal |
| collection | DOAJ |
| description | Abstract A serious global public health emergency emerged late November 2019 in Wuhan City, China, by a new highly pathogenic virus, SARS-CoV-2. The virus evolution spread has been tracked by three developing databases: GISAID, Nextstrain and PANGO to understand its circulating variants. In this study, 110 diagnosed positive COVID-19 patient’s samples, were collected from Kasr Al-Aini Hospital and the Children Cancer Hospital Egypt 57357 between May 2020 and January 2021, with clinical severity ranging from mild to severe. The viral genomes were sequenced by next generation sequencing, and phylogenetic analysis was performed to understand viral transmission dynamics. According to Nextstrain clades, most of our sequenced samples belonged to clades 20A and 20D, which in addition to clade 20B were present from the beginning of sample collection in May 2020. Clades 19A and 19B, on the other hand, appeared in the mid and late 2020 respectively, followed by the disappearance of clade 20B at the end of 2020. We identified a relatively high prevalence of the D614G spike protein variant and novel patterns of mutations associated together and with different clades. We also identified four mutations, spike H49Y, ORF3a H78Y, ORF8 E64stop and nucleocapsid E378V, associated with higher disease severity. Altogether, our study contributes genetic, phylogenetic, and clinical correlation data about the spread of the SARS-CoV-2 pandemic in Egypt. |
| first_indexed | 2024-12-10T19:21:25Z |
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| id | doaj.art-e8f154c00e2c476f924a0692b018394e |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-10T19:21:25Z |
| publishDate | 2022-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-e8f154c00e2c476f924a0692b018394e2022-12-22T01:36:28ZengNature PortfolioScientific Reports2045-23222022-08-011211910.1038/s41598-022-18644-4SARS-CoV-2 genome variations and evolution patterns in Egypt: a multi-center studyDeena Jalal0Mariam G. Elzayat1Hend E. El-Shqanqery2Aya A. Diab3Abdelrahman Yahia4Omar Samir5Usama Bakry6Khaled Amer7Mostafa ElNaqeeb8Wael Hassan9Hala S. Talat10Hala M. Farawela11Mona S. Hamdy12May S. Soliman13Maha H. El Sissy14Moushira H. Ezzelarab15Sara M. El khateeb16Lamyaa H. Soliman17Sara E. Haddad18Ashraf Hatem19Mohamed S. Ismail20Maha Hossam21Tarek Mansour22Lobna Shalaby23Sonia Soliman24Reem Hassan25Mahmoud Hammad26Ibrahim Abdo27Sameh Magdeldin28Alaa ElHaddad29Sherif Abouelnaga30Ahmed A. Sayed31Genomics Program, Department of Basic Research, Children’s Cancer Hospital Egypt 57357Genomics Program, Department of Basic Research, Children’s Cancer Hospital Egypt 57357Genomics Program, Department of Basic Research, Children’s Cancer Hospital Egypt 57357Genomics Program, Department of Basic Research, Children’s Cancer Hospital Egypt 57357Genomics Program, Department of Basic Research, Children’s Cancer Hospital Egypt 57357Genomics Program, Department of Basic Research, Children’s Cancer Hospital Egypt 57357Egypt Center for Research and Regenerative Medicine (ECRRM)Egypt Center for Research and Regenerative Medicine (ECRRM)Egypt Center for Research and Regenerative Medicine (ECRRM)Egypt Center for Research and Regenerative Medicine (ECRRM)Department of Pediatric Medicine, Kasr Al-Aini School of Medicine, Cairo UniversityDepartment of Clinical and Chemical Pathology, Kasr Al-Aini School of Medicine, Cairo UniversityDepartment of Clinical and Chemical Pathology, Kasr Al-Aini School of Medicine, Cairo UniversityDepartment of Clinical and Chemical Pathology, Kasr Al-Aini School of Medicine, Cairo UniversityDepartment of Clinical and Chemical Pathology, Kasr Al-Aini School of Medicine, Cairo UniversityDepartment of Clinical and Chemical Pathology, Kasr Al-Aini School of Medicine, Cairo UniversityDepartment of Clinical and Chemical Pathology, Kasr Al-Aini School of Medicine, Cairo UniversityDepartment of Clinical and Chemical Pathology, Kasr Al-Aini School of Medicine, Cairo UniversityDepartment of Clinical and Chemical Pathology, Kasr Al-Aini School of Medicine, Cairo UniversityDepartment of Pulmonary Medicine, Kasr Al-Aini School of Medicine, Cairo UniversityDepartment of Pulmonary Medicine, Kasr Al-Aini School of Medicine, Cairo UniversityDepartment of Internal Medicine, Kasr Al-Aini School of Medicine, Cairo UniversityVirology and Immunology Department, National Cancer Institute, Cairo UniversityInfectious Disease Unit, Children’s Cancer Hospital Egypt 57357Department of Clinical Pathology, Children’s Cancer Hospital Egypt 57357Department of Clinical and Chemical Pathology, Kasr Al-Aini School of Medicine, Cairo UniversityDepartment of Pediatric Oncology, National Cancer Institute, Cairo UniversityDepartment of Clinical Pharmacy, Children’s Cancer Hospital Egypt 57357Proteomics and Metabolomics Unit, Department of Basic Research, Children’s Cancer Hospital Egypt 57357Department of Pediatric Oncology, National Cancer Institute, Cairo UniversityDepartment of Pediatric Oncology, National Cancer Institute, Cairo UniversityGenomics Program, Department of Basic Research, Children’s Cancer Hospital Egypt 57357Abstract A serious global public health emergency emerged late November 2019 in Wuhan City, China, by a new highly pathogenic virus, SARS-CoV-2. The virus evolution spread has been tracked by three developing databases: GISAID, Nextstrain and PANGO to understand its circulating variants. In this study, 110 diagnosed positive COVID-19 patient’s samples, were collected from Kasr Al-Aini Hospital and the Children Cancer Hospital Egypt 57357 between May 2020 and January 2021, with clinical severity ranging from mild to severe. The viral genomes were sequenced by next generation sequencing, and phylogenetic analysis was performed to understand viral transmission dynamics. According to Nextstrain clades, most of our sequenced samples belonged to clades 20A and 20D, which in addition to clade 20B were present from the beginning of sample collection in May 2020. Clades 19A and 19B, on the other hand, appeared in the mid and late 2020 respectively, followed by the disappearance of clade 20B at the end of 2020. We identified a relatively high prevalence of the D614G spike protein variant and novel patterns of mutations associated together and with different clades. We also identified four mutations, spike H49Y, ORF3a H78Y, ORF8 E64stop and nucleocapsid E378V, associated with higher disease severity. Altogether, our study contributes genetic, phylogenetic, and clinical correlation data about the spread of the SARS-CoV-2 pandemic in Egypt.https://doi.org/10.1038/s41598-022-18644-4 |
| spellingShingle | Deena Jalal Mariam G. Elzayat Hend E. El-Shqanqery Aya A. Diab Abdelrahman Yahia Omar Samir Usama Bakry Khaled Amer Mostafa ElNaqeeb Wael Hassan Hala S. Talat Hala M. Farawela Mona S. Hamdy May S. Soliman Maha H. El Sissy Moushira H. Ezzelarab Sara M. El khateeb Lamyaa H. Soliman Sara E. Haddad Ashraf Hatem Mohamed S. Ismail Maha Hossam Tarek Mansour Lobna Shalaby Sonia Soliman Reem Hassan Mahmoud Hammad Ibrahim Abdo Sameh Magdeldin Alaa ElHaddad Sherif Abouelnaga Ahmed A. Sayed SARS-CoV-2 genome variations and evolution patterns in Egypt: a multi-center study Scientific Reports |
| title | SARS-CoV-2 genome variations and evolution patterns in Egypt: a multi-center study |
| title_full | SARS-CoV-2 genome variations and evolution patterns in Egypt: a multi-center study |
| title_fullStr | SARS-CoV-2 genome variations and evolution patterns in Egypt: a multi-center study |
| title_full_unstemmed | SARS-CoV-2 genome variations and evolution patterns in Egypt: a multi-center study |
| title_short | SARS-CoV-2 genome variations and evolution patterns in Egypt: a multi-center study |
| title_sort | sars cov 2 genome variations and evolution patterns in egypt a multi center study |
| url | https://doi.org/10.1038/s41598-022-18644-4 |
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