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

• DOI: 10.3389/fmolb.2022.817735
• Publication Date: 2022-03-08T10:07:58Z
• Authors: Sara H. A. Agwa; Hesham Elghazaly; Mahmoud Shawky El...; Yahia A. Yahia; Radwa Khaled; Aya M. Abd Elsamee; Reham M. Darwish; Shaimaa M. Elsayed; Hala Hafez; Basma S. Mahmoud; Fouda EM; Marwa Matboli
• Keywords: 0301 basic medicine; QH301-705.5; Evolutionary biology; Infectious disease (medical specialty); Coronavirus Disease 2019 Research; FOS: Health sciences; Biochemistry, Genetics and Molecular Biology (miscellaneous); Biochemistry; Gene; Coronavirus Disease 2019; 03 medical and health sciences; Virology; Health Sciences; Genetics; Pathology; Molecular Biosciences; Disease; Biology (General); Molecular Biology; Biology; Lineage (genetic); Pandemic; SARS-CoV-2; Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); Ebola Virus Research and Outbreaks; 3. Good health; Coronavirus disease 2019 (COVID-19); Coronavirus; Infectious Diseases; NGS; FOS: Biological sciences; Mutation; Medicine; Egypt; C36 lineage; mutation

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.