MULTIPLE SEQUENCE ALIGNMENT TO DETERMINE MUTATION IN SPIKE PROTEIN OF DIFFERENT COVID-19 VARIANTS

Abstract

The outbreak of the coronavirus disease in 2019 (COVID-19) was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The disease has been rapidly spread around the globe affecting more than 180 countries. During the COVID-19 pandemic, SARS-CoV-2 has accumulated mutations throughout viral genes encoding the spike (S) glycoprotein D614G mutation became the predominant globally. The potential threats are that SARS-CoV-2 is gradually mutating during incessant transmission among humans. Although most mutations in the SARS-CoV-2 genome are expected to be either deleterious and swiftly purged or relatively neutral, a small proportion will affect functional properties and may alter infectivity, disease severity, or interactions with host immunity. Therefore, this research work is aimed to determine the different mutational changes and phylogenetic relationship among different SARS-CoV-2 variants of the covid-19 virus using a relevant bioinformatics software BioEdit and MEGA 6.0 (Molecular Evolutionary Genetics Analysis version 6.0). The result shows mutation in the positions 491, 621, and 688 in the SARS-CoV-2 spike protein. Such mutations in the S-protein are very critical and might be an associated risk factor of virus transmission. The phylogenetic study has classified the SARS-CoV-2 variants into different countries. This information might provide insight on the impacts on antigenicity and contextualizing them in the S protein structure and observed mutation frequencies in global sequences datasets.

Keywords

• SARS-CoV-2
• Phylogenetic
• Amino acids
• Covid-19
• mutation