Identifying SARS-CoV-2 Lineage Mutation Hallmarks and Correlating Them With Clinical Outcomes in Egypt: A Pilot Study

Sara H A Agwa; Hesham Elghazaly; Mahmoud Shawky El Meteini; Yahia A Yahia; Radwa Khaled; Aya M Abd Elsamee; Reham M Darwish; Shaimaa M Elsayed; Hala Hafez; Basma S Mahmoud; Fouda Em; Marwa Matboli

doi:10.3389/fmolb.2022.817735

Identifying SARS-CoV-2 Lineage Mutation Hallmarks and Correlating Them With Clinical Outcomes in Egypt: A Pilot Study

Front Mol Biosci. 2022 Mar 8:9:817735. doi: 10.3389/fmolb.2022.817735. eCollection 2022.

Authors

Sara H A Agwa¹, Hesham Elghazaly², Mahmoud Shawky El Meteini³, Yahia A Yahia⁴, Radwa Khaled^{5

6}, Aya M Abd Elsamee⁷, Reham M Darwish⁷, Shaimaa M Elsayed⁷, Hala Hafez⁸, Basma S Mahmoud⁸, Fouda Em⁹, Marwa Matboli¹⁰

Affiliations

¹ Clinical Pathology and Molecular Genomics Unit of Medical Ain Shams Research Institute (MASRI), Faculty of Medicine, Ain Shams University, Cairo, Egypt.
² Oncology Department, Medical Ain Shams Research Institute (MASRI), Cairo, Egypt.
³ Department of General Surgery, The School of Medicine, University of Ain Shams, Abbassia, Cairo, Egypt.
⁴ Biochemistry Department, Faculty of Pharmacy, Misr University for Science and Technology, Giza, Egypt.
⁵ Biotechnology/Biomolecular Chemistry Program, Faculty of Science, Cairo University, Cairo, Egypt.
⁶ Biochemistry Department, Faculty of Medicine, Modern University for Technology and Information, Cairo, Egypt.
⁷ Biochemistry and Molecular Genomics Unit of Medical Ain Shams Research Institute (MASRI), Ain Shams University, Cairo, Egypt.
⁸ Clinical Pathology Department, Infection Control Unit, University of Ain Shams, Cairo, Egypt.
⁹ Pediatric Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
¹⁰ Medicinal Biochemistry and Molecular Biology Department, Faculty of Medicine, University of Ain Shams, Cairo, Egypt.

Abstract

The SARS-CoV-2 pandemic has led to over 4.9 million deaths as of October 2021. One of the main challenges of creating vaccines, treatment, or diagnostic tools for the virus is its mutations and emerging variants. A couple of variants were declared as more virulent and infectious than others. Some approaches were used as nomenclature for SARS-CoV-2 variants and lineages. One of the most used is the Pangolin nomenclature. In our study, we enrolled 35 confirmed SARS-CoV-2 patients and sequenced the viral RNA in their samples. We also aimed to highlight the hallmark mutations in the most frequent lineage. We identified a seven-mutation signature for the SARS-CoV-2 C36 lineage, detected in 56 countries and an emerging lineage in Egypt. In addition, we identified one mutation which was highly negatively correlated with the lineage. On the other hand, we found no significant correlation between our clinical outcomes and the C36 lineage. In conclusion, the C36 lineage is an emerging SARS-CoV-2 variant that needs more investigation regarding its clinical outcomes compared to other strains. Our study paves the way for easier diagnosis of variants of concern using mutation signatures.

Keywords: C36 lineage; Egypt; NGS; SARS-CoV-2; mutation.