Annotating Spike Protein Polymorphic Amino Acids of Variants of SARS-CoV-2, Including Omicron

Abstract

The prolonged global spread and community transmission of severe acute respiratory syndrome virus 2 (SARS-CoV-2) has led to the emergence of variants and brought questions regarding disease severity and vaccine effectiveness. We conducted simple bioinformatics on the spike gene of a representative of each variant. The data show that a number of polymorphic amino acids are located mostly on the amino-terminal side of the S1/S2 cleavage site. The Omicron variant diverges from the others, with the highest number of amino acid substitutions, including the receptor-binding site (RBS), epitopes, S1/S2 cleavage site, fusion peptide, and heptad repeat 1. The current sharp global increase in the frequency of the Omicron genome constitutes evidence of its high community transmissibility. In conclusion, the proposed guideline could give an immediate insight of the probable biological nature of any variant of SARS-Cov-2. As the Omicron diverged the farthest from the original pandemic strain, Wuhan-Hu-1, we expect different epidemiological and clinical patterns of Omicron cases. On vaccine efficacy, slight changes in some epitopes while others are conserved should not lead to a significant reduction in the effectiveness of an approved vaccine.

Consensus insertion/deletions and amino acid variations of all coding and noncoding regions of the SARS-CoV-2 Omicron clades, including the XBB and BQ.1 lineages

“…Scienti c explanation is paramount to understand the potential threat of subvariants or lineages. Most papers on SARS-CoV-2 variants covered the spike of the virus [3,4]. For this objective, the examination of the whole genome is important to predict the overall impact of subvariants [14].…”

“…Since many dominant amino acid residues in Spike are uniformly divergent from Wuhan-Hu-1, those who survived the Omicron wave should have protective immunity to all Omicron clades/lineages. Applying the template of Spike residues and their possible functions as published previously [4], the consensus amino acid changes in Omicron clades/lineages from Wuhan-Hu-1 are located in the Receptor Binding Domain/Receptor Binding Site (RBD/RBS) (S376P, S378F, K420N, N443K, S480N, T481K, E487A, Q501R, N504Y, Y508H), linear epitopes (S378F, K420N, E487A, Q501R, D617G, N767K), possible conformationdependent epitopes (N682K, P684H), the S1/S2 cleavage site ((N682K, P684H), the fusion peptide (D799Y), and Heptad Repeat 1 (Q957H and N972K). With this pattern, it is expected that the Omicron variant has different biological characteristics than the original SARS-CoV-2 strain.…”

“…It is believed to occur due to rapid evolution of SARS-CoV-2 which has led to the generation of many variants. The most recent and dominant variant is Omicron [1,4,5]. This variant has swiftly diverged into at least eight clades based on the data available in GISAID (https://nextstrain.org).…”

“…Stop codon in the position 62 of ORF7A in one sequence 3. Stop codon in the position 8 in one 21K sequence 4. Stop codon in the position 8 in one sequence data 5.…”

Consensus insertion/deletions and amino acid variations of all coding and noncoding regions of the SARS-CoV-2 Omicron clades, including the XBB and BQ.1 lineages

“…It is believed to occur due to the rapid evolution of SARS-CoV-2, which has led to the generation of many variants. The most recent and dominant variant is Omicron [ 1 , 4 , 5 ]. This variant has swiftly diverged into at least eight clades based on the data available in GISAID ( https://nextstrain.org ).…”