Hyper-Variable Spike Protein of Omicron Corona Virus and Its Differences with Alpha and Delta Variants: Prospects of RT-PCR and New Vaccine

NCBI SARS-CoV-2 Database was analyzed between November-December, 2021 to decipher the spread of Delta corona virus variants in USA and compared with highly transmissible new omicron variant recently originated South Africa. Presently, B.1.617.2 AY.103 lineages spike protein L452R, T478K, P681R mutations F157/R158 two amino acids deletions were predominant superseded deadly outbreaks B.1.1.7 Alpha H69, V70 Y145 as well N501Y, D614G mutations. Interestingly, has six V70, V143, Y144, Y145, L212 immune-escape 29 including most N501Y (Y498 omicron) (G611 omicron). This indicated that by combination among B.1.1.7, AY.X lineages. A unique three (EPE) insertion at 215 position detected compensate suggesting further recombination events. Three Serine residues mutated 371 (S=L, L368 omicron), 373 (S=P, P370 Omicron), 375 (S=F, F372 but compensated 446 (G=S, S443 496 S493 RBD domain virus. The (ERS) deletion 30 N-protein acts another signature Omicron less mutation 2/3 5’-end genome codes for ORF1ab poly-protein dominant P4715L RNA-dependent RNA polymerase. However, overall acid composition, alipathic index, instability index found fairly constant although hydrophobic plot gave some difference Wuhan viruses. BLAST search 20nt 19nt perfect match hyper-variable 22957-22977nt region comprising 488-493 (NH2-PLRSYS-CO2H) ch-2 Seladonia tumulorum or ch-16 Steromphala cineraria respectively. primer set designed from gene did not primers regions worked well. Such hyper-variation suggested DNA vaccine mRNA using may efficiently protect infection attenuated whole will be safer vaccine.