SARS-CoV-2 in Egypt: epidemiology, clinical characterization and bioinformatics analysis

• Published in: Heliyon Vol. 8; no. 2; p. e08864
• Main Authors: Alotaibi, Badriyah, El-Masry, Thanaa A., Seadawy, Mohamed G., Farghali, Mahmoud H., El-Harty, Bassem E., Saleh, Asmaa, Mahran, Yasmen F., Fahim, Jackline S., Desoky, Mohamed S., Abd El-Monsef, Mohamed M.E., El-Bouseary, Maisra M.
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01-02-2022; Elsevier
• Subjects: Clinical data; COVID-19; Haplotypes; rRT-PCR; Whole genome sequencing; COVID-19; Clinical data; Haplotypes; Whole genome sequencing; rRT-PCR
• ISSN: 2405-8440; 2405-8440
• DOI: 10.1016/j.heliyon.2022.e08864

COVID-19 is an infectious disease caused by SARS-CoV-2 and has spread globally, resulting in the ongoing coronavirus pandemic. The current study aimed to analyze the clinical and epidemiological features of COVID-19 in Egypt. Oropharyngeal swabs were collected from 197 suspected patients who were admitted to the Army Hospital and confirmation of the positivity was performed by rRT-PCR assay. Whole genomic sequencing was conducted using Illumina iSeq 100® System. The average age of the participants was 48 years, of which 132 (67%) were male. The main clinical symptoms were pneumonia (98%), fever (92%), and dry cough (66%). The results of the laboratory showed that lymphocytopenia (79.2%), decreased levels of haemoglobin (77.7%), increased levels of interleukin 6, C-reactive protein, serum ferritin, and D-dimer (77.2%, 55.3%, 55.3%, and 25.9%, respectively), and leukocytopenia (25.9%) were more common. The CT findings showed that scattered opacities (55.8%) and ground-glass appearance (27.9%) were frequently reported. The recovered validated sequences (n = 144) were submitted to NCBI Virus GenBank. All sequenced viruses have at least 99% identity to Wuhan-Hu-1. All variants were GH clade, B.1 PANGO lineage, and L.GP.YP.HT haplotype. The most predominant subclade was D614G/Q57H/V5F/G823S. Our findings have aided in a deep understanding of COVID-19 evolution and identifying strains with unique mutational patterns in Egypt.
•Isolation and clinical characterization of SARS-CoV-2 from Egyptian patients.•Whole Genome Sequencing of recovered isolates revealed unique sequences.•Egyptian SARS-CoV-2 variants in 2020 with at least 99% identity to Wuhan-Hu-1.•Egyptian SARS-CoV-2 variants were GH clade and L.GP.YP.HT haplotype.•A unique mutation (D614G/Q57H/V5F/G823S) pattern was predominant among SARS-CoV-2.
COVID-19; rRT-PCR; Clinical data; Whole genome sequencing; Haplotypes.