tetano
Editor, Senior Moderator
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[SUP] 1 [/SUP], Khaled Easa Amer[SUP] 2 [/SUP], Mohammed M Hafez[SUP] 1 [/SUP], Zeinab K Hassan[SUP] 1 [/SUP], Ola S Ahmed[SUP] 1 [/SUP], Hany K Soliman[SUP] 1 [/SUP], Abeer A Bahnasy[SUP] 3 [/SUP], Wael Abdel Hamid[SUP] 4 [/SUP], Ahmad Gad[SUP] 4 [/SUP], Mahmoud Ali[SUP] 2 [/SUP], Wael Hassan[SUP] 2 [/SUP], Mahmoud Samir[SUP] 2 [/SUP], Ahmad Raouf[SUP] 2 [/SUP], Ayman A Khattab[SUP] 2 [/SUP], Mona Salah El Din Hamdy[SUP] 5 [/SUP], May Sherif Soliman[SUP] 5 [/SUP], Maha Hamdi El Sissy[SUP] 5 [/SUP], Sara Mohamed El Khateeb[SUP] 5 [/SUP], Moushira Hosny Ezzelarab[SUP] 5 [/SUP], Lamiaa A Fathalla[SUP] 6 [/SUP], Mohamed Abouelhoda[SUP] 7 [/SUP]
Affiliations
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.
. 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[SUP] 1 [/SUP], Khaled Easa Amer[SUP] 2 [/SUP], Mohammed M Hafez[SUP] 1 [/SUP], Zeinab K Hassan[SUP] 1 [/SUP], Ola S Ahmed[SUP] 1 [/SUP], Hany K Soliman[SUP] 1 [/SUP], Abeer A Bahnasy[SUP] 3 [/SUP], Wael Abdel Hamid[SUP] 4 [/SUP], Ahmad Gad[SUP] 4 [/SUP], Mahmoud Ali[SUP] 2 [/SUP], Wael Hassan[SUP] 2 [/SUP], Mahmoud Samir[SUP] 2 [/SUP], Ahmad Raouf[SUP] 2 [/SUP], Ayman A Khattab[SUP] 2 [/SUP], Mona Salah El Din Hamdy[SUP] 5 [/SUP], May Sherif Soliman[SUP] 5 [/SUP], Maha Hamdi El Sissy[SUP] 5 [/SUP], Sara Mohamed El Khateeb[SUP] 5 [/SUP], Moushira Hosny Ezzelarab[SUP] 5 [/SUP], Lamiaa A Fathalla[SUP] 6 [/SUP], Mohamed Abouelhoda[SUP] 7 [/SUP]
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.