SARS-CoV-2 vaccine-breakthrough infections (VBIs) by Omicron (B.1.1.529) variant and consequences in structural and functional impact

This study investigated the efficacy of existing vaccinations against hospitalization and infection due to the Omicron variant of COVID-19, particularly for those who received two doses of Moderna or Pfizer vaccines and one dose of a vaccine by Johnson & Johnson or who were vaccinated more than five months previously. A total of 36 variants in Omicron’s spike protein, targeted by all three vaccinations, have made antibodies less effective at neutralizing the virus. Genotyping of SARS-CoV-2 viral sequencing revealed clinically significant variants such as E484K in three genetic mutations (T95I, D614G, and del142-144). One woman displayed two of these mutations, indicating a potential risk of infection following successful immunization, as recently reported by Hacisuleyman (2021). We examined the effects of mutations on domains (NID, RBM, and SD2) found at the interfaces of spike domains Omicron B.1.1529, Delta/B.1.1529, Alpha/B.1.1.7, VUM B.1.526, B.1.575.2, and B.1.1214 (formerly VOI Iota). We tested the affinity of Omicron for hACE2 and found that the wild and mutant spike proteins were using atomistic molecular dynamics simulations. According to binding free energies calculated during mutagenesis, hACE2 bound Omicron spike more strongly than SARS-CoV-2 wild strain. T95I, D614G, and E484K are three substitutions that significantly contribute to the RBD, corresponding to hACE2 binding energies and a doubling of Omicron spike proteins’ electrostatic potential. Omicron appears to bind hACE2 with greater affinity, increasing its infectivity and transmissibility. The spike virus was designed to strengthen antibody immune evasion through binding while boosting receptor binding by enhancing IgG and IgM antibodies that stimulate human β -cell, as opposed to the wild strain, which has more vital stimulation of both antibodies. * VBIs : Vaccine-breakthrough infections COVID-19 : Coronavirus ACE2 : Angiotensin-Converting Enzyme 2 RBD : Receptor-binding domain NTD : N-terminal domain RBM : Receptor binding motif SD2 : Subdomain AAS : Amino acid substitutions WHO : World Health Organization MD : Molecular dynamics WT : Wild type MT : Mutant dbSNP : Single nucleotide polymorphism database PDB : Protein data bank NVT : Equilibrate the system FASTA : Fast Alignment Search Tool SIFT : Sorting intolerant from tolerant SNAP : Screening for non-acceptable polymorphisms PROVEAN : Protein variation effect analyzer S1-CTD : Predictor of human deleterious single nucleotide polymorphisms (PhD-SNP) Subunits C-terminal domain RMSD : Root-mean-square deviation RMSF : Root mean square fluctuation TGF-b : Transforming growth factor IFN-g : Interferon-gamma SODA : Protein solubility based on disorder and aggregation PASTA : Prediction of amyloid structural aggregation VOC : Variant of concern SASA : Solvent-accessible surface area PLP : Proteolipid protein HR1 & 2 : Heptad repeat 1 heptad repeat 2 TA : Transmembrane anchor IT : Intracellular tail MOE : Molecular operating environment RSA : Relative solvent accessibility DC : Dendritic cells EP : Electroporation NID : Immunomodulatory drugs Rg : Radius of gyration VSV : Vesicular stomatitis virus EPI : Enhancer Promoter Interactions