Bhattacharya Manojit, Sharma Ashish Ranjan, Mallick Bidyut, Lee Sang-Soo, Seo Eun-Min, Chakraborty Chiranjib
Department of Zoology, Fakir Mohan University, Balasore, Odisha, India.
Institute for Skeletal Aging and Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-do, South Korea.
Front Microbiol. 2022 Aug 12;13:895695. doi: 10.3389/fmicb.2022.895695. eCollection 2022.
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 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.
严重急性呼吸综合征冠状病毒2（SARS-CoV-2）病毒及其变体的迅速传播在全球造成了灾难性影响。已经出现了几种变体，包括B.1.351（贝塔）、B.1.1.28/三重突变体（P.1）、B.1.1.7（阿尔法）和B.1.429（伊普西龙）。我们使用武汉毒株和其他变体对全长刺突糖蛋白进行了比较性和综合性抗原性图谱分析，并通过分析确定了9肽、15肽和20肽细胞毒性T淋巴细胞（CTL）表位。研究发现，B.1.1.7变体中的9肽CTL表位区域具有最高的抗原性，且在三种表位类型中平均水平最高。对9肽CTL表位的聚类分析在70%水平描绘出一个有两个节点（KGFNCYFPL和EGFNCYFPL）的显著聚类。噬菌体展示肽显示出具有三个聚类的模拟9肽CTL表位。圆二色光谱分析显示，武汉毒株和除B.1.429之外的所有变体的刺突糖蛋白具有相同的条带模式。所构建的超抗原（SAg）样区域的三维模型发现了与人类T细胞受体（TCR）的相互作用模式，表明SAg样成分可能与TCRβ链相互作用。本研究从刺突糖蛋白中鉴定出了另一个部分SAg样区域（ANQFNSAIGKI）。未来的研究应考察CD8 T细胞抗原加工的分子机制，尤其是刺突糖蛋白所有变体的抗原。
