J Adv Res
. 2020 Nov 26.
doi: 10.1016/j.jare.2020.11.012. Online ahead of print.
Genomic characterization of SARS-CoV-2 in Egypt
Abdel-Rahman N Zekri 1 , Khaled Easa Amer 2 , Mohammed M Hafez 1 , Zeinab K Hassan 1 , Ola S Ahmed 1 , Hany K Soliman 1 , Abeer A Bahnasy 3 , Wael Abdel Hamid 4 , Ahmad Gad 4 , Mahmoud Ali 2 , Wael Hassan 2 , Mahmoud Samir 2 , Ahmad Raouf 2 , Ayman A Khattab 2 , Mona Salah El Din Hamdy 5 , May Sherif Soliman 5 , Maha Hamdi El Sissy 5 , Sara Mohamed El Khateeb 5 , Moushira Hosny Ezzelarab 5 , Lamiaa A Fathalla 6 , Mohamed Abouelhoda 7
Affiliations
- PMID: 33262895
- PMCID: PMC7688418
- DOI: 10.1016/j.jare.2020.11.012
Abstract
Introduction: The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread throughout the globe, causing a pandemic. In Egypt over 96,108 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.
Keywords: Next generation sequencing; Sars-CoV2; real time PCR.