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

Gusti Ngurah Mahardika; Nyoman B Mahendra; Bayu K Mahardika; Ida B K Suardana; Made Pharmawati

doi:10.1155/2022/2164749

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

Biochem Res Int. 2022 Apr 11:2022:2164749. doi: 10.1155/2022/2164749. eCollection 2022.

Authors

Gusti Ngurah Mahardika¹, Nyoman B Mahendra², Bayu K Mahardika¹, Ida B K Suardana³, Made Pharmawati⁴

Affiliations

¹ The Animal Biomedical and Molecular Biology Laboratory, Udayana University, Jl. Sesetan-Markisa 6A, Denpasar 80223, Bali, Indonesia.
² The Department of Obstetrics and Genecology, The Faculty of Medicine, Udayana University, Denpasar, Bali, Indonesia.
³ Virology Laboratory, The Faculty of Veterinary Medicine, Udayana University, Denpasar, Bali, Indonesia.
⁴ The Biology Study Program, The Faculty of Mathematic and Natural Science, Udayana University, Kampus Bukit Jimbaran, Badung, Bali, Indonesia.

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.