How SARS-CoV-2 Omicron Variant Affects Immunity?

Without a question, SARS-CoV has had a significant impact on human life. From children’s schooling to people’s occupations (businessmen or servicemen), from housewives to working women, everyone faded up as a result of the pandemic. It appeared in our lives as if by magic and caused a profound change in everything. As a zoonotic virus, we must recognise the severity of this infection. It is easily spread from animals to people. SARS-CoV-2, also known as B.1.1.529, was discovered in South Africa for the first time. The crucial thing to remember is that the SARS-CoV-2 source is still unknown. Although its genome is discovered using an RNA metagenomic method. The genome has a length of 29,881 bp. It also contains 9860 encoded amino acids, as well as structural and non-structural proteins. The presence of glycoprotein gives it a crown-like appearance that makes it visible under a microscope. 

It is essential to understand the impact of the recently modified SARS-CoV-2 Omicron Variant on human immunity. Understanding the impact of this coronavirus variety will assist doctors in reducing its risk to the human body. According to research, the SARS-CoV-2 Omicron Variant spreads quicker than other variations. Several investigations on the influence of the Omicron Variant on antibody binding and its interaction with CD8+ T-cells are critical to limiting the variant’s transmission and harmful consequences. 

The scientists examined the influence of mutations in the SARS-CoV-2 Omicron virus on the Major Histocompatibility Complex (MHC-binding) and the variant’s subsequent escape of the CD8+ T-cell immune response in one of the investigations. The researchers gathered the SARS-CoV-2 reference genome, protein family domains, and mutations from various links. The top five Human Leukocyte Antigen (HLA) alleles were picked from sub-Saharan Africa, Black South Africa, Zulu South Africa, Europe, and White South Africa. Net MHC pan-4.1 was utilised by the researchers to execute MHC binding for each epitope with 8, 9, 10, or 11 amino acids. The amplitude of the quotient between the best-ranked epitope in the Immune Epitope Database (IEDB) and the best-ranked homologous epitope from either Omicron or Delta virus was determined. As a baseline, SARS-CoV-2 epitopes that tested positive for MHC ligands or T-cell tests were used. The mutant epitopes and their homologous counterparts were found. The researchers used Fisher’s exact test on different populations and lineages to assess the improvement in protein Major Histocompatibility Complex (pMHC) binding. The top five HLA alleles in the populations were tested for mutations. Mutations with fewer decreased binding epitopes had an odds ratio less than 1 and a significant p-value, whereas mutations with more reduced binding epitopes had an odds ratio greater than 1 and a significant p-value. 

This study discovered that the SARS-CoV-2 Omicron viral spike protein contained 34 mutations. Omicron and the reference genome shared 80% of IEDB epitopes. There were no exact matches for 13 epitopes in the reference genome. One of these 13 epitopes was found in the Omicron sequence and coincided with a mutation found in the Beta lineage.

In the spike protein, there was no homogeneity in epitope coverage. One mutation in the Omicron version affected nine epitopes, while two mutations had no effect on any epitopes. Three mutations were also found to be shared by Delta and Omicron Variants. In addition, one mutation was found to affect the same amino acid in both Variants. The number of mutations and the total number of mutant epitopes were associated in an increasing non-linear association. 

The IEDB epitope, HLA allele, and similar epitopes, which had a lower anticipated MHC binding affinity, increased the wild-type expected MHC binding.

The study looked at 35 HLA alleles from the HLA-A, HLA-B, and HLA-C genes and discovered that one amino acid substitution in Delta VOC increased the VOC’s binding affinity. Three amino acid changes observed in the Omicron VOC improved the VOC’s HMC binding affinity.

The pHMC SARS-CoV-2 Omicron Variant mutations lowered MHC binding capacity. The altered epitopes lowered the HLA response, indicating that the Variants evaded CD8+ T-cells in particular HLA alleles. This research also demonstrated that the Omicron Variant does not completely elude the human immune response. Omicron mutations introducing amino acids associated with enhanced immunogenicity, on the other hand, were also found. Although the Omicron VOC did not demonstrate a robust immune escape mechanism in this investigation, it is critical to monitor the mutations’ potential for facilitating immune evasion and their impact on disease severity. 

For more interesting facts, download the best medical coaching app eGurukul 3.0

FAQs 

Q1: What do we know about SARS-CoV-2 Omicron variant mutations?

A1: As the WHO has stated, Omicron has numerous mutations, which is the primary source of worry. This variety has been determined to have a higher risk of reinfection than other viruses of concern (VOC). Because there is little information on the variant, WHO has directed member countries to boost genome sequencing efforts and submit the metadata to medical databases for further research.

Q2: What precautions should we take to avoid becoming infected with the Omicron variant?

A2: The precautions and actions to be followed remain unchanged. It is critical to adequately mask yourself, take both doses of immunizations (if not already vaccinated), keep social distance, and maintain good ventilation to the greatest extent possible.

Q3: What distinguishes SARS-CoV-2 as a variation of concern (VoC)? A3: This variant features a considerable number of mutations, particularly more than 30 on the virus spike protein, which is the primary target of the immune response. From the mutations in Omicron that have previously been linked to increased infectivity and immune escape, as well as the abrupt spike in the number of positive cases in South Africa, the WHO has designated Omicron as a Variant of Concern (VOC).