Analysis of the conserved and mutated amino acid sequences in the spike protein enhances the understanding of phylognetic relationship among coronavirus variants from the wild type.

Abstract

In the light of the COVID-19 pandemic, an elaborative computational analysis was conducted regarding coronaviruses, their phylogeny, and the different strains of the pathogen responsible for the disease, SARS-CoV-2. In the front, this disease looks like the common cold. However, it can lead to acute respiratory failure, septic shock, and organ failure. Like the Spanish flu pandemic in 1918, the COVID-19 pandemic also became the cause of millions of lives lost across the globe. Coronaviruses consist of four basic proteins - spike, nucleocapsid, membrane, and envelope proteins. Spike proteins (S) are structures protruding from the surface of the virus and facilitate its entry into the the host cells via interaction with the ACE-2 receptors who are also found on the surface of the host cells. For this research work, the entire sequence of the spike protein was considered, and a table was created carrying out the comparison between the spike protein sequences of the WT and 13 different variants (Alpha, Beta, Gamma, Kappa, Delta, Mu, Epsilon, Lambda, Omicron, Mu, Eta, Zeta, and Theta). This table helped detect the conserved parts of spike protein sequence across all variants, conserved mutations as well as mutations unique to certain variants. Findings from the table are then used to study phylogenetic trees which explain the emergence of new coronavirus variants and their genetic distances from the WT.