Page 54 - GPD-2-3

Gene & Protein in Disease

ORIGINAL RESEARCH ARTICLE
In silico mutation analysis of the SARS-CoV-2

Spike glycoprotein in the Omicron (B.1.1.529)
variant isolated from the Iraqi patients

Dana Khdr Sabir*

Charmo Center for Research, Training, and Consultancy, Charmo University, Chamchamal,
Sulaymaniyah, Kurdistan Region, Iraq

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
*Corresponding author:
Dana Khdr Sabir BA.1.1 (n = 198, 52%) and BA.1 (n = 91, 14%) were the predominant variant types
(dana.sabir@charmouniversity.org) encountered throughout this study. The current work offers the data of SARS-CoV-2
Citation: Sabir DK, 2023, Omicron variants derived from the Iraqi patients. The data from this study could
In silico mutation analysis of the assist in the molecular design of more potent vaccines and/or antiviral drugs against
SARS-CoV-2 Spike glycoprotein the virus and also provide a fundamental understanding of SARS-CoV-2 evolution
in the Omicron (B.1.1.529) variant
isolated from the Iraqi patients. with concerns about their pathogenicity.
Gene Protein Dis, 2(3): 1646.
https://doi.org/10.36922/gpd.1646
Keywords: Severe acute respiratory syndrome coronavirus 2; Omicron; Iraq; Mutations;
Received: August 21, 2023
Accepted: September 20, 2023 Variant; Spike glycoprotein
Published Online: September 29,
2023
Copyright: © 2023 Author(s).
This is an Open-Access article 1. Introduction
distributed under the terms of the
Creative Commons Attribution The coronavirus disease (COVID-19) is a highly contagious infectious disease caused by
License, permitting distribution, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which was first reported
reproduction in any medium, which in late December 2019 in China [1,2] . The disease has impacted almost all sectors of life [3,4] ,
provided that the original work is
[5]
properly cited. infecting more than 750 million cases and causing 7 million deaths worldwide . In Iraq
alone, 2.5 million COVID-19 cases and more than 25000 COVID-19-related deaths have
Publisher’s Note: AccScience
Publishing remains neutral with been reported [6,7] .
regard to jurisdictional claims in
published maps and institutional SARS-CoV-2 virus belongs to the beta-coronavirus genus, consisting of non-
affiliations. segmented, positive-sense, single-stranded RNA [8-10] . This virus has a genome size of ~30

Volume 2 Issue 3 (2023) 1 https://doi.org/10.36922/gpd.1646