MD Study of New Variant of Omicron Viruses Lineages of BA.n (n=1-5)

A large number of mutations have been identified in the Omicron variant, including multiple mutations to the receptor binding domain of the spike protein, which has been associated with reduced antibody response. BA.n (n=1-5) are omicron viruses with a combination of mutations containing critical spike protein, which is a concern for humans. Regarding their mutations, BA.4 and BA.5 share mutations across their genomes with both BA.1 and BA.2 but are most similar to BA.2. The Delta variant consists of several mutations in the spike protein, where four of them are most important. One of these is known as L452R, which was first reported in March 2020 in Denmark. This mutation has been shown to be more transmissible than wild-type strains and has also been related to reduced antibody influence and decreased neutralization during vaccination. The first dominant of Omicron-Covid- 19 (BA.1) produced around thirty mutations in its Spike protein in 2019. Quickly, BA.1 became the dominant variant worldwide. Omicron is dangerous for public health concerns due to its high infectivity and antibody evasion. Omicron has three lineages or sub-variants: BA.1, BA.2, and BA.3. Among them, BA.1 is the currently prevailing sub-variant. Omicron BA.1 has around 65 mutations such as N440K, N501Y, S477N on non-structure protein (NSP3), NSP4, NSP5, NSP6, NSP12, NSP14, S protein, envelope protein, membrane protein, and nucleus capsid proteins. Through this work, we simulated several spike protein structures and peptide-like inhibitor structures, including small-molecule inhibitors, via molecular dynamic and docking methods.