Characterization of the SARS-CoV-2 genomes in Egypt in first and second waves of infection

Abdel-Rahman N Zekri,Hany K Soliman,Abeer A Bahnasy,Ahmed S Elsafty,Mona H Salah El Dine,May S Solimane,Mohamed G Seadawy,Lamyaa S Abdel Latife,Ola S Ahmed,Mohamed Abouelhoda,Enas R El-Sisi,Mohamed M Hafez,Zeinab K Hassan

doi:10.1038/s41598-021-99014-4

Abdel-Rahman N Zekri, Hany K Soliman + Show 11 more

Open Access

https://doi.org/10.1038/s41598-021-99014-4

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Journal: Scientific Reports	Publication Date: Nov 3, 2021
Citations: 11	License type: open-access

Affiliation: Cairo University

Abstract

At Wuhan, in December 2019, the SRAS-CoV-2 outbreak was detected and it has been the pandemic worldwide. This study aims to investigate the mutations in sequence of the SARS-CoV-2 genome and characterize the mutation patterns in Egyptian COVID-19 patients during different waves of infection. The samples were collected from 250 COVID-19 patients and the whole genome sequencing was conducted using Next Generation Sequencing. The viral sequence analysis showed 1115 different genome from all Egyptian samples in the second wave mutations including 613 missense mutations, 431 synonymous mutations, 25 upstream gene mutations, 24 downstream gene mutations, 10 frame-shift deletions, and 6 stop gained mutation. The Egyptian genomic strains sequenced in second wave of infection are different to that of the first wave. We observe a shift of lineage prevalence from the strain B.1 to B.1.1.1. Only one case was of the new English B.1.1.7. Few samples have one or two mutations of interest from the Brazil and South Africa isolates. New clade 20B appear by March 2020 and 20D appear by May 2020 till January 2021.

Highlights

At Wuhan, in December 2019, the SRAS-CoV-2 outbreak was detected and it has been the pandemic worldwide
The disease caused by the infection of this new pathogen is called Coronavirus 2019 disease (COVID-19) and has spread rapidly
This study reveals molecular features and patterns of mutation of SARS-CoV-2 strains circulating from January 2020 to the end of January 2021 in COVID-19 Egyptian patients

Summary

Introduction

At Wuhan, in December 2019, the SRAS-CoV-2 outbreak was detected and it has been the pandemic worldwide. This study aims to investigate the mutations in sequence of the SARS-CoV-2 genome and characterize the mutation patterns in Egyptian COVID-19 patients during different waves of infection. The viral sequence analysis showed 1115 different genome from all Egyptian samples in the second wave mutations including 613 missense mutations, 431 synonymous mutations, 25 upstream gene mutations, 24 downstream gene mutations, 10 frame-shift deletions, and 6 stop gained mutation. The Egyptian genomic strains sequenced in second wave of infection are different to that of the first wave. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was first detected in late December 2019 as an etiological agent for pneumonia cluster cases in Wuhan City, Hubei Province, C. SARS-CoV2 infections are common with a wide variety of healthcare procedures, including asymptomatic and fatal, and are often undiagnosed with low to moderate symptoms including sore throat, dry cough, and f ever[5,6]

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