A Preliminary Genomic Analysis of the Omicron Variants of SARS-CoV-2 in Central India During the third wave of the COVID-19 Pandemic

• Published in: Archives of medical research Vol. 53; no. 6; pp. 574 - 584
• Main Authors: Singh, Priyanka, Negi, Sanjay Singh, Bhargava, Anudita, Kolla, Vara Prasad, Arora, Ripu Daman
• Format: Journal Article
• Language: English
• Published: Elsevier Inc 01.09.2022; Instituto Mexicano del Seguro Social (IMSS). Published by Elsevier Inc
• Subjects: Lineage; Non-structural Protein; Original; Phylogenetic; Spike; Spike; Phylogenetic; Lineage; Non-structural Protein
• ISSN: 0188-4409; 1873-5487
• DOI: 10.1016/j.arcmed.2022.08.006

Omicron was detected in South Africa for the first time at the month of November 2021, from then it expanded swiftly over the world, outcompeting other SARS-CoV-2 variants such as Delta. The toxicity, resistance to antiviral medicines, transmissibility, and vaccine-induced immunity of newly developed SARS-CoV-2 variants are major worldwide health concerns. This study investigates the comprehensive explanation of all mutations and their evolutionary linkages between the Omicron variant and recently discovered SARS‐CoV‐2 variants. On Illumina MiniSeq Machine, 31 RNA isolates from clinical specimens were sequenced utilizing next-generation sequencing technique. Different bioinformatics tools have been used to analyze the mutations in omicron variant. A phylogenetic tree was constructed to determine Omicron's evolutionary relationships with other variants. In our investigation, we discovered 79 distinct types of mutations in 31 fully vaccinated COVID-19 positive samples. Mostly mutations were found in non-spike region. According to the NJ approach of phylogenetic tree revels, the nearest variants were in the order listed, based on sequence identity: Omicron, Gamma, Alpha, Delta, Mu and Beta. On the other hand as per UPGMA approach, the Omicron variation creates a novel monophyletic clade that is distinct from previous SARS-CoV-2 variants. Despite the fact that some of the mutations are prevalent in Omicron and other VOCs, there are several unique mutations that have been connected to the virus's transmissibility and immune evasion, indicating a substantial shift in SARS-CoV-2 evolution.