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

Abstract

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spike protein L452R, T478K, P681R mutations and F157/R158 two amino acids deletions were predominant in the USA and superseded the deadly outbreaks of B.1.1.7 Alpha variant with deletions of H69, V70 and Y145 amino acids as well as N501Y, and D614G highly transmissible mutations.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

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“…We recently reported the variations (Deletions, Insertions and Point Mutations) in the ORF1ab, ORF7a and ORF8 proteins [32][33][34]. Similarly, Spike protein deletions and huge mutations in omicron variants were well documented [25]. As for example, 24LPP deletion was found in most omicron corona viruses and 69HV spike deletion was found in omicron BA.1, BA.…”

“…The Nsp1 protein is 180aa (regulatory factor), nsp2 is 638aa (RNA topoisomerase), nsp3 is ~1945aa (C3 protease), nsp4 is 500aa (membrane factor), nsp5 is ~305aa (C5 protease), nsp6 is 290aa (membrane factor), nsp7 is 183aa (accessory protein to replication), nsp8 is 198aa (accessory protein to replication), nsp9 is 113aa (RNA binding factor), nsp10 is 139aa (RNA binding factor), nsp11 is only 13aa (unknown function), nsp12 is 918aa (RNA-dependent RNA polymerase), nsp13 is 601aa (RNA helicase-capping methyltransferase), nsp14 is 527aa (exoribonuclease-methyltransferase) , nsp15 is 346aa (endoribonuclease-recombinase), nsp16 is 298aa (2'-O Uridine rRNA methyltransferase) [9][10][11][12][13][14][15][16][17][18][19][20][21][22]. On the country, structural spike protein is 1273aa long and other structural proteins (M, N, E) of corona virus are relatively very small [24][25][26][27][28][29]. The regulatory proteins like orf3a, orf7a, orf7b, orf8 and orf10 were also characterized having interacted with many cellular proteins [30][31][32][33][34][35].…”

The G36S, M147I, G265S, T568I, N852S new mutations in the Spike of Omicron JN.1 subvariants: New subvariants JN.1.1 to JN.1.5 nomenclature and oligonucleotides design for JN.1 subvariants detection

“…We clearly demonstrated through multi-alignment approach that nsp2 was an RNA topoisomerase that was a target for vaccine and drug development (4) and nsp13 was a mRNA Capping Methyltranaferase (5) and nsp16 was a Uridine 2'-OH RlmE methyltransferase (6). Due to mutation, deletion and insertion coronavirus spread and its death potential was changed time to time generating many Variant Of Concern (VOC) (7,8). In USA, Wuhan D614G rst peak occurred between March-August, 2020, Alpha (B.…”

Highly infectious, less pathogenic and antibody resistant Omicron XBB.1, XBB.1.5 and XBB.1.5.1-XBB.1.5.39 subvariant Coronaviruses do not produce ORF8 protein due to 8th codon GGA=TGA Termination Codon Mutation

“…SARS-CoV-2 is a large positivestranded RNA virus with round 30000 nucleotides genome ( gure-1). It has structural proteins Membrane (M), Envelope (E), Nucleocapsid (N), Spike (S) coded from 3'-1/3 part of the virus independently but RNAdependent RNA polymerase was coded from nsp12 domain of ORF1ab polyprotein coded from 2/3 of the 5'-part of the genome and such polyprotein was degraded into sixteen polypeptides (nsp1-nsp16) (Chakraborty, 2022a). The nsp2 protein is RNA topoisomerase with new therapeutic target (Chakraborty, 2020a) whereas Nsp3 and nsp5 are proteases that cleave polyprotein into sixteen polypeptides with diverse functions.…”