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

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...

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Autores principales:	Abdel-Rahman N. Zekri, Abeer A. Bahnasy, Mohamed M. Hafez, Zeinab K. Hassan, Ola S. Ahmed, Hany K. Soliman, Enas R. El-Sisi, Mona H. Salah El Dine, May S. Solimane, Lamyaa S. Abdel Latife, Mohamed G. Seadawy, Ahmed S. Elsafty, Mohamed Abouelhoda
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/a410ffaa918946a9bf6f8ab8e24af909
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spelling	oai:doaj.org-article:a410ffaa918946a9bf6f8ab8e24af9092021-11-08T10:55:40ZCharacterization of the SARS-CoV-2 genomes in Egypt in first and second waves of infection10.1038/s41598-021-99014-42045-2322https://doaj.org/article/a410ffaa918946a9bf6f8ab8e24af9092021-11-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-99014-4https://doaj.org/toc/2045-2322Abstract 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.Abdel-Rahman N. ZekriAbeer A. BahnasyMohamed M. HafezZeinab K. HassanOla S. AhmedHany K. SolimanEnas R. El-SisiMona H. Salah El DineMay S. SolimaneLamyaa S. Abdel LatifeMohamed G. SeadawyAhmed S. ElsaftyMohamed AbouelhodaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Abdel-Rahman N. Zekri Abeer A. Bahnasy Mohamed M. Hafez Zeinab K. Hassan Ola S. Ahmed Hany K. Soliman Enas R. El-Sisi Mona H. Salah El Dine May S. Solimane Lamyaa S. Abdel Latife Mohamed G. Seadawy Ahmed S. Elsafty Mohamed Abouelhoda Characterization of the SARS-CoV-2 genomes in Egypt in first and second waves of infection
description	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.
format	article
author	Abdel-Rahman N. Zekri Abeer A. Bahnasy Mohamed M. Hafez Zeinab K. Hassan Ola S. Ahmed Hany K. Soliman Enas R. El-Sisi Mona H. Salah El Dine May S. Solimane Lamyaa S. Abdel Latife Mohamed G. Seadawy Ahmed S. Elsafty Mohamed Abouelhoda
author_facet	Abdel-Rahman N. Zekri Abeer A. Bahnasy Mohamed M. Hafez Zeinab K. Hassan Ola S. Ahmed Hany K. Soliman Enas R. El-Sisi Mona H. Salah El Dine May S. Solimane Lamyaa S. Abdel Latife Mohamed G. Seadawy Ahmed S. Elsafty Mohamed Abouelhoda
author_sort	Abdel-Rahman N. Zekri
title	Characterization of the SARS-CoV-2 genomes in Egypt in first and second waves of infection
title_short	Characterization of the SARS-CoV-2 genomes in Egypt in first and second waves of infection
title_full	Characterization of the SARS-CoV-2 genomes in Egypt in first and second waves of infection
title_fullStr	Characterization of the SARS-CoV-2 genomes in Egypt in first and second waves of infection
title_full_unstemmed	Characterization of the SARS-CoV-2 genomes in Egypt in first and second waves of infection
title_sort	characterization of the sars-cov-2 genomes in egypt in first and second waves of infection
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/a410ffaa918946a9bf6f8ab8e24af909
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Characterization of the SARS-CoV-2 genomes in Egypt in first and second waves of infection

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