B.1.1.7 (Alpha) variant is the most antigenic compared to Wuhan strain, B.1.351, B.1.1.28/triple mutant and B.1.429 variants

Manojit Bhattacharya; Ashish Ranjan Sharma; Bidyut Mallick; Sang-Soo Lee; Eun-Min Seo; Chiranjib Chakraborty

doi:10.3389/fmicb.2022.895695

B.1.1.7 (Alpha) variant is the most antigenic compared to Wuhan strain, B.1.351, B.1.1.28/triple mutant and B.1.429 variants

Front Microbiol. 2022 Aug 12:13:895695. doi: 10.3389/fmicb.2022.895695. eCollection 2022.

Authors

Manojit Bhattacharya¹, Ashish Ranjan Sharma², Bidyut Mallick³, Sang-Soo Lee², Eun-Min Seo², Chiranjib Chakraborty⁴

Affiliations

¹ Department of Zoology, Fakir Mohan University, Balasore, Odisha, India.
² Institute for Skeletal Aging and Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-do, South Korea.
³ Department of Applied Science, Galgotias College of Engineering and Technology, Greater Noida, Uttar Pradesh, India.
⁴ Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, India.

Abstract

The rapid spread of the SARS-CoV-2 virus and its variants has created a catastrophic impact worldwide. Several variants have emerged, including B.1.351 (Beta), B.1.1.28/triple mutant (P.1), B.1.1.7 (Alpha), and B.1.429 (Epsilon). We performed comparative and comprehensive antigenicity mapping of the total S-glycoprotein using the Wuhan strain and the other variants and identified 9-mer, 15-mer, and 20-mer CTL epitopes through in silico analysis. The study found that 9-mer CTL epitope regions in the B.1.1.7 variant had the highest antigenicity and an average of the three epitope types. Cluster analysis of the 9-mer CTL epitopes depicted one significant cluster at the 70% level with two nodes (KGFNCYFPL and EGFNCYFPL). The phage-displayed peptides showed mimic 9-mer CTL epitopes with three clusters. CD spectra analysis showed the same band pattern of S-glycoprotein of Wuhan strain and all variants other than B.1.429. The developed 3D model of the superantigen (SAg)-like regions found an interaction pattern with the human TCR, indicating that the SAg-like component might interact with the TCR beta chain. The present study identified another partial SAg-like region (ANQFNSAIGKI) from the S-glycoprotein. Future research should examine the molecular mechanism of antigen processing for CD8⁺ T cells, especially all the variants' antigens of S-glycoprotein.

Keywords: B.1.1.7; CD spectra; CTL epitopes; SAg-like region; antigenicity; cluster; emerging variants; phage-displayed peptides.