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-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.
['Zekri|Abdel-Rahman N|AN|', 'Easa Amer|Khaled|K|', 'Hafez|Mohammed M|MM|', 'Hassan|Zeinab K|ZK|', 'Ahmed|Ola S|OS|', 'Soliman|Hany K|HK|', 'Bahnasy|Abeer A|AA|', 'Abdel Hamid|Wael|W|', 'Gad|Ahmad|A|', 'Ali|Mahmoud|M|', 'Ali Hassan|Wael|W|', 'Samir Madboly|Mahmoud|M|', 'Abdel Raouf|Ahmad|A|', 'Khattab|Ayman A|AA|', 'Salah El Din Hamdy|Mona|M|', 'Sherif Soliman|May|M|', 'Hamdi El Sissy|Maha|M|', 'Mohamed El Khateeb|Sara|S|', 'Hosny Ezzelarab|Moushira|M|', 'Fathalla|Lamiaa A|LA|', 'Abouelhoda|Mohamed|M|']
D000328:Adult D000086382:COVID-19 D000087123:COVID-19 Nucleic Acid Testing D004534:Egypt D005260:Female D016679:Genome, Viral D059014:High-Throughput Nucleotide Sequencing D006801:Humans D008297:Male D008875:Middle Aged D012367:RNA, Viral D000086402:SARS-CoV-2 D000073336:Whole Genome Sequencing
Nasopharyngeal swab Next generation sequencing Sars-CoV2 Real time PCR