Genomic characterization of SARS-CoV-2 in Egypt: insights into spike protein thermodynamic stability

Deena Jalal; Omar Samir; Mariam G Elzayat; Hend E El-Shqanqery; Aya A Diab; Lamiaa ElKaialy; Aya M Mohammed; Donia Hamdy; Islam K Matar; Khaled Amer; Mostafa Elnakib; Wael Hassan; Tarek Mansour; Sonia Soliman; Reem Hassan; Ghada M Al-Toukhy; Mahmoud Hammad; Ibrahim Abdo; Ahmed A Sayed

doi:10.3389/fmicb.2023.1190133

Genomic characterization of SARS-CoV-2 in Egypt: insights into spike protein thermodynamic stability

Front Microbiol. 2023 Jun 2:14:1190133. doi: 10.3389/fmicb.2023.1190133. eCollection 2023.

Authors

Deena Jalal¹, Omar Samir¹, Mariam G Elzayat¹, Hend E El-Shqanqery¹, Aya A Diab¹, Lamiaa ElKaialy¹, Aya M Mohammed¹, Donia Hamdy¹, Islam K Matar^{1

2}, Khaled Amer³, Mostafa Elnakib³, Wael Hassan³, Tarek Mansour^{4

5}, Sonia Soliman^{5

6}, Reem Hassan^{7

8}, Ghada M Al-Toukhy⁹, Mahmoud Hammad^{10

11}, Ibrahim Abdo¹², Ahmed A Sayed^{1

13}

Affiliations

¹ Department of Basic Research, Genomics and Epigenomics Program, Children's Cancer Hospital Egypt 57357, Cairo, Egypt.
² Department of Chemistry, Saint Mary's University, Halifax, NS, Canada.
³ Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt.
⁴ Department of Virology and Immunology, National Cancer Institute, Cairo University, Cairo, Egypt.
⁵ Department of Clinical Pathology, Children's Cancer Hospital Egypt 57357, Cairo, Egypt.
⁶ Department of Clinical Pathology, National Cancer Institute, Cairo University, Cairo, Egypt.
⁷ Department of Clinical and Chemical Pathology, Kasr Al-Aini School of Medicine, Cairo University, Cairo, Egypt.
⁸ Molecular Microbiology Unit, Children's Cancer Hospital Egypt 57357, Cairo, Egypt.
⁹ Department of Virology and Immunology, Children's Cancer Hospital Egypt 57357, Cairo, Egypt.
¹⁰ Department of Pediatric Oncology, National Cancer Institute, Cairo University, Cairo, Egypt.
¹¹ Department of Pediatric Oncology, Children's Cancer Hospital Egypt 57357, Cairo, Egypt.
¹² Department of Clinical Pharmacy, Children's Cancer Hospital Egypt 57357, Cairo, Egypt.
¹³ Faculty of Science, Department of Biochemistry, Ain Shams University, Cairo, Egypt.

Abstract

The overall pattern of the SARS-CoV-2 pandemic so far has been a series of waves; surges in new cases followed by declines. The appearance of novel mutations and variants underlie the rises in infections, making surveillance of SARS-CoV-2 mutations and prediction of variant evolution of utmost importance. In this study, we sequenced 320 SARS-CoV-2 viral genomes isolated from patients from the outpatient COVID-19 clinic in the Children's Cancer Hospital Egypt 57357 (CCHE 57357) and the Egypt Center for Research and Regenerative Medicine (ECRRM). The samples were collected between March and December 2021, covering the third and fourth waves of the pandemic. The third wave was found to be dominated by Nextclade 20D in our samples, with a small number of alpha variants. The delta variant was found to dominate the fourth wave samples, with the appearance of omicron variants late in 2021. Phylogenetic analysis reveals that the omicron variants are closest genetically to early pandemic variants. Mutation analysis shows SNPs, stop codon mutation gain, and deletion/insertion mutations, with distinct patterns of mutations governed by Nextclade or WHO variant. Finally, we observed a large number of highly correlated mutations, and some negatively correlated mutations, and identified a general inclination toward mutations that lead to enhanced thermodynamic stability of the spike protein. Overall, this study contributes genetic and phylogenetic data, as well as provides insights into SARS-CoV-2 viral evolution that may eventually help in the prediction of evolving mutations for better vaccine development and drug targets.

Keywords: Egypt; SARS-CoV-2; genome sequencing; mutations; phylogenetic analysis; protein stability; spike.