In silico mutation analysis of the SARS-CoV-2 Spike glycoprotein in the Omicron (B.1.1.529) variant isolated from the Iraqi patients

Abstract

Since its first breakout in December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has impacted the lives of millions of people worldwide. The virus has been rapidly mutating, and the accumulation of various mutations has precipitated the emergence of several new variants. The Omicron variant (B.1.1.529 lineage) was first identified in Botswana and South Africa back in November 2021. Since then, several Omicron sub-lineages have emerged as a result of hypermutations. In this study, a computational analysis of the 381 spike glycoprotein (S protein) of the SARS-CoV-2 Omicron variants isolated from Iraqi patients was performed. The full-length S protein sequences (1273 amino acids) were obtained from the publicly accessible Global Initiative on Sharing All Influenza Data database. A total of 60 mutation sites were recognized: 49 substitution sites, ten deletions, and one insertion. K417N and N440K were the most prevalent mutations (n = 379, 99.4%), followed by G339D (n = 377, 98.9%) and S373P and S375F (both n = 367, 96.3%). Both BA.1.1 (n = 198, 52%) and BA.1 (n = 91, 14%) were the predominant variant types encountered throughout this study. The current work offers the data of SARS-CoV-2 Omicron variants derived from the Iraqi patients. The data from this study could assist in the molecular design of more potent vaccines and/or antiviral drugs against the virus and also provide a fundamental understanding of SARS-CoV-2 evolution with concerns about their pathogenicity.