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SARS-CoV-2 genome variations and evolution patterns in Egypt: a multi-center study
Deena Jalal1, Mariam G Elzayat1, Hend E El-Shqanqery1
1Genomics Program, Department of Basic Research, Children's Cancer Hospital Egypt 57357, Cairo, Egypt.
Scientific Reports
|August 25, 2022
Summary
This study tracked the spread of SARS-CoV-2 variants in Egypt, identifying mutations linked to increased COVID-19 severity. Genetic analysis revealed specific viral clades and spike protein variants circulating in the region.
Area of Science:
- Virology
- Genomics
- Epidemiology
Background:
- The COVID-19 pandemic, caused by SARS-CoV-2, emerged in late 2019.
- Tracking viral evolution and variants is crucial for understanding transmission dynamics.
Purpose of the Study:
- To analyze the genetic diversity and phylogenetic patterns of SARS-CoV-2 in Egypt.
- To identify mutations associated with clinical severity of COVID-19.
Main Methods:
- Whole-genome sequencing of 110 SARS-CoV-2 samples collected between May 2020 and January 2021.
- Phylogenetic analysis using Nextstrain clades.
- Correlation of genetic variants with clinical severity data.
Main Results:
- Sequenced samples predominantly belonged to Nextstrain clades 20A and 20D, with clade 20B present early on.
- The D614G spike protein variant showed high prevalence.
- Four specific mutations (spike H49Y, ORF3a H78Y, ORF8 E64stop, nucleocapsid E378V) were associated with increased disease severity.
Conclusions:
- The study provides crucial genetic and phylogenetic data on SARS-CoV-2 spread in Egypt.
- Identified mutations offer potential biomarkers for predicting COVID-19 severity.
- Findings contribute to understanding the pandemic's evolution in the region.
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