@article {235272,
	title = {SARS-CoV-2 genome variations and evolution patterns in Egypt: a multi-center study.},
	journal = {Scientific reports},
	volume = {12},
	year = {2022},
	pages = {14511},
	abstract = {<p>A serious global public health emergency emerged late November 2019 in Wuhan City, China, by a new highly pathogenic virus, SARS-CoV-2. The virus evolution spread has been tracked by three developing databases: GISAID, Nextstrain and PANGO to understand its circulating variants. In this study, 110 diagnosed positive COVID-19 patient{\textquoteright}s samples, were collected from Kasr Al-Aini Hospital and the Children Cancer Hospital Egypt 57357 between May 2020 and January 2021, with clinical severity ranging from mild to severe. The viral genomes were sequenced by next generation sequencing, and phylogenetic analysis was performed to understand viral transmission dynamics. According to Nextstrain clades, most of our sequenced samples belonged to clades 20A and 20D, which in addition to clade 20B were present from the beginning of sample collection in May 2020. Clades 19A and 19B, on the other hand, appeared in the mid and late 2020 respectively, followed by the disappearance of clade 20B at the end of 2020. We identified a relatively high prevalence of the D614G spike protein variant and novel patterns of mutations associated together and with different clades. We also identified four mutations, spike H49Y, ORF3a H78Y, ORF8 E64stop and nucleocapsid E378V, associated with higher disease severity. Altogether, our study contributes genetic, phylogenetic, and clinical correlation data about the spread of the SARS-CoV-2 pandemic in Egypt.</p>
},
	author = {Jalal, Deena and Elzayat, Mariam G and El-Shqanqery, Hend E and Diab, Aya A and Yahia, Abdelrahman and Samir, Omar and Usama Bakry and Khaled Amer and ElNaqeeb, Mostafa and Wael Hassan and Talat, Hala S and Hala M Farawela and Hamdy, Mona S and Soliman, May S and Maha H. Elsissy and Ezzelarab, Moushira H and El Khateeb, Sara M and Soliman, Lamyaa H and Haddad, Sara E and Hatem, Ashraf and Mohamed S. Ismail and Hossam, Maha and Mansour, Tarek and Lobna Shalaby and Soliman, Sonia and Hassan, Reem and Mahmoud Hammad and Abdo, Ibrahim and Magdeldin, Sameh and Alaa Elhaddad and Abouelnaga, Sherif and Sayed, Ahmed A}
}
