SARS-CoV-2 genome variations and evolution patterns in Egypt: a multi-center study.

Autor: Jalal D; Genomics Program, Department of Basic Research, Children's Cancer Hospital Egypt 57357, Cairo, Egypt., Elzayat MG; Genomics Program, Department of Basic Research, Children's Cancer Hospital Egypt 57357, Cairo, Egypt., El-Shqanqery HE; Genomics Program, Department of Basic Research, Children's Cancer Hospital Egypt 57357, Cairo, Egypt., Diab AA; Genomics Program, Department of Basic Research, Children's Cancer Hospital Egypt 57357, Cairo, Egypt., Yahia A; Genomics Program, Department of Basic Research, Children's Cancer Hospital Egypt 57357, Cairo, Egypt., Samir O; Genomics Program, Department of Basic Research, Children's Cancer Hospital Egypt 57357, Cairo, Egypt., Bakry U; Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt., Amer K; Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt., ElNaqeeb M; Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt., Hassan W; Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt., Talat HS; Department of Pediatric Medicine, Kasr Al-Aini School of Medicine, Cairo University, Cairo, Egypt., Farawela HM; Department of Clinical and Chemical Pathology, Kasr Al-Aini School of Medicine, Cairo University, Cairo, Egypt., Hamdy MS; Department of Clinical and Chemical Pathology, Kasr Al-Aini School of Medicine, Cairo University, Cairo, Egypt., Soliman MS; Department of Clinical and Chemical Pathology, Kasr Al-Aini School of Medicine, Cairo University, Cairo, Egypt., El Sissy MH; Department of Clinical and Chemical Pathology, Kasr Al-Aini School of Medicine, Cairo University, Cairo, Egypt., Ezzelarab MH; Department of Clinical and Chemical Pathology, Kasr Al-Aini School of Medicine, Cairo University, Cairo, Egypt., El Khateeb SM; Department of Clinical and Chemical Pathology, Kasr Al-Aini School of Medicine, Cairo University, Cairo, Egypt., Soliman LH; Department of Clinical and Chemical Pathology, Kasr Al-Aini School of Medicine, Cairo University, Cairo, Egypt., Haddad SE; Department of Clinical and Chemical Pathology, Kasr Al-Aini School of Medicine, Cairo University, Cairo, Egypt., Hatem A; Department of Pulmonary Medicine, Kasr Al-Aini School of Medicine, Cairo University, Cairo, Egypt., Ismail MS; Department of Pulmonary Medicine, Kasr Al-Aini School of Medicine, Cairo University, Cairo, Egypt., Hossam M; Department of Internal Medicine, Kasr Al-Aini School of Medicine, Cairo University, Cairo, Egypt., Mansour T; Virology and Immunology Department, National Cancer Institute, Cairo University, Cairo, Egypt.; Department of Clinical Pathology, Children's Cancer Hospital Egypt 57357, Cairo, Egypt., Shalaby L; Infectious Disease Unit, Children's Cancer Hospital Egypt 57357, Cairo, Egypt.; Department of Pediatric Oncology, National Cancer Institute, Cairo University, Cairo, Egypt., Soliman S; Department of Clinical Pathology, Children's Cancer Hospital Egypt 57357, Cairo, Egypt.; Department of Clinical Pathology, National Cancer Institute, Cairo University, Cairo, Egypt., Hassan R; Department of Clinical and Chemical Pathology, Kasr Al-Aini School of Medicine, Cairo University, Cairo, Egypt.; Molecular Microbiology Unit, Children's Cancer Hospital Egypt 57357, Cairo, Egypt., Hammad M; Department of Pediatric Oncology, National Cancer Institute, Cairo University, Cairo, Egypt.; Department of Pediatric Oncology, Children's Cancer Hospital Egypt 57357, Cairo, Egypt., Abdo I; Department of Clinical Pharmacy, Children's Cancer Hospital Egypt 57357, Cairo, Egypt., Magdeldin S; Proteomics and Metabolomics Unit, Department of Basic Research, Children's Cancer Hospital Egypt 57357, Cairo, Egypt.; Department of Physiology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt., ElHaddad A; Department of Pediatric Oncology, National Cancer Institute, Cairo University, Cairo, Egypt.; Department of Pediatric Oncology, Children's Cancer Hospital Egypt 57357, Cairo, Egypt., Abouelnaga S; Department of Pediatric Oncology, National Cancer Institute, Cairo University, Cairo, Egypt.; Department of Pediatric Oncology, Children's Cancer Hospital Egypt 57357, Cairo, Egypt., Sayed AA; Genomics Program, Department of Basic Research, Children's Cancer Hospital Egypt 57357, Cairo, Egypt. ahmad.sayed@57357.org.; Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt. ahmad.sayed@57357.org.
Jazyk: angličtina
Zdroj: Scientific reports [Sci Rep] 2022 Aug 25; Vol. 12 (1), pp. 14511. Date of Electronic Publication: 2022 Aug 25.
DOI: 10.1038/s41598-022-18644-4
Abstrakt: 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.
(© 2022. The Author(s).)
Databáze: MEDLINE
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