Proteomic Approach for Comparative Analysis of the Spike Protein of SARS-CoV-2 Omicron (B.1.1.529) Variant and Other Pango Lineages

Abstract

The novel SARS-CoV-2 variant, Omicron (B.1.1.529), is being testified, and the WHO has characterized Omicron as a variant of concern due to its higher transmissibility and very contagious behavior, immunization breakthrough cases. Here, the comparative proteomic study has been conducted on spike-protein, hACE2 of five lineages (α, β, δ, γ and Omicron. The docking was performed on spike protein- hACE-2 protein using HADDOCK, and PRODIGY was used to analyze the binding energy affinity using a reduced Haddock score. Followed by superimposition in different variant-based protein structures and calculated the esteem root mean square deviation (RMSD). This study reveals that Omicron was seen generating a monophyletic clade. Further, as α variant is the principal advanced strain after Wuhan SARS-CoV-2, and that is the reason it was showing the least likeness rate with the Omicron and connoting Omicron has developed of late with the extreme number of mutations. α variant has shown the highest binding affinity with hACE2, followed by β strain, and followed with γ. Omicron showed a penultimate binding relationship, while the δ variant was seen as having the least binding affinity. This proteomic basis in silico analysis of variable spike proteins of variants will impart light on the development of vaccines and the identification of mutations occurring in the upcoming variants.

Monitoring SARS-CoV-2 genetic variability: A post-market surveillance workflow for combined bioinformatic and laboratory evaluation of commercial RT-PCR assay performance

“…These are a subset of the previously analyzed sequences. Classification of VOCs and VOIs was obtained from official sources from the World Health Organization, the US Centers for Disease Control and Prevention, the European Centre for Disease Prevention and Control, and the UK Medicines and Healthcare products Regulatory Agency [12][13][14][15][16] and the global report on the Phylogenetic Assignment of Named Global Outbreak (PANGO) lineage website [17]; The list of variants analyzed during the implementation of the PMS workflow are provided in S1 In-vitro testing. In-vitro testing was performed using synthetic dsDNA sequences (gBlocks™ Gene Fragments, Integrated DNA Technologies, Coralville, IA, USA) to assess the impact of the flagged sequences on the assay sensitivity.…”

Correction: Jain et al. Proteomic Approach for Comparative Analysis of the Spike Protein of SARS-CoV-2 Omicron (B.1.1.529) Variant and Other Pango Lineages. Proteomes 2022, 10, 34

“…In the publication [ 1 ], there was an error regarding the affiliation for “Prashant Kaushik”. The updated affiliation should be: “Independent Researcher, 46022 Valencia, Spain”.…”

Exploring Factors Influencing Changes in Incidence and Severity of Multisystem Inflammatory Syndrome in Children

“…In addition, the Omicron spike showed the greatest number of strong binders of T cells compared to Delta and other pre-Delta variants. This means that Omicron retains the predicted highest ability to generate antibodies by MHC II presentation and trigger adaptive immunity [ 62 ]. Moreover, except from the Alpha variant, the difference in the tertiary structure of spike between Omicron and Delta has shown to be greatest among other pre-Delta variants, and that may change host–pathogen interactions significantly.…”

“…The N-terminal domain (NTD) of the spike protein accounts for about 35% of the antibody response to SARS-CoV-2. However, in the case of Omicron, only about one-third of these antibodies are neutralizing [ 62 ]. SARS-CoV-2 is a neutralization-sensitive virus.…”

“…Clearly, antibodies that target the RBD of spike are able to prevent the interaction though ACE-2 on the cell wall, reaching neutralization, but other sites of spike have gained interest. In particular, different antibodies are able to recognize similar spatial (tertiary) epitopes, in a region of spike identified as a supersite, that prevent interaction and invasion of the cell [ 62 ]. Few other antibodies have shown the interesting ability to bind specifically to different epitopes than the supersite.…”