Molecular evolutionary analysis of the SARS-CoV-2 through the mutation analysis of Spike, Envelope and RdRp proteins

Abstract

COVID-19 pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), was declared in 2020 by the World Health Organization. New mutations have been identified, leading to various variants of this virus, including Alpha, Beta, Gamma, Delta, and Omicron, which are classified as variants of concern (VOCs) and have raised considerable concerns for global public health. Such constant spread and changes in the genome of the virus require continuous monitoring. This research focuses on the evolution of SARS-CoV-2 through a detailed presentation of the viral genome, protein structure and interpretation, with the presentation of phylogenetic characteristics and patterns. We obtained the sequence data from the European region focusing on the S, E, and RdRp proteins from the publicly available NCBI database. We next used the MEGA11 package to generate the multiple sequence alignments and create phylogenetic trees. The SWISS-MODEL server was connected to the Protein Data Bank to obtained tertiary structure images of all the proteins presented in the paper. Stability studies of obtained mutations were performed via MUpro online tool. The results indicate a substantial impact of the Omicron variant relative to others, particularly concerning the alterations and mutations observed in the spike (S) protein, which is crucial in the infection process.