Omicron, delta, and beta, deadliest among SARS-CoV-2 variants: an in silico analysis

Abstract

SARS-CoV-2 has a higher mutation rate since it is emerging in Wuhan, China, and has a high propensity for mutation as it contains RNA as its genome. Because of its high transmissibility and new variants constantly mutating, global health and populations worldwide are under severe threat. There are many mutations that cause structural changes and their transmission power and risk severity, but the spike protein mutation was mainly responsible for the higher transmission and risk severity of SARS-CoV-2. From several geographic locations, including Africa, Asia, Europe, Oceania, and North and South America, fifty sequences of SARS-CoV-2 structural and nonstructural proteins (NSPs) from five variants were retrieved. BioEdit is used to perform multiple sequence alignments and protein homology modeling were performed using the Swiss model. Then, using Pymol, the proteins' 3D structures were seen, and their structural analysis was performed by superimposing them against the Wuhan sequence. Their RMSD values were also noted. Sequence alignment showed several common mutations and a few uncommon regional mutations in each of the five variants, but only the Beta, Delta, and Omicron variants had a few unique mutations. Structural analysis of such unique mutations revealed that they caused structural deviations in Beta, Delta, and Omicron spike proteins. Those findings provide insight into the functional and structural changes and its effects in SARS-CoV-2 spike protein mutations in Beta, Delta, and Omicron and a spike protein vulnerability that could be utilized to obtain comprehensive protection against those variants. Additionally, these variants had higher death rates, higher hospitalization rates, and more illnesses, all of which had a significant correlation with the structural deviations caused by those particular mutations. This study can help with regional vaccine strain selection, virus pathogenicity testing, diagnosis, and treatment.