Deciphering the receptor binding domain (RBD) structure of SARS-CoV-2 variants to reveal the similarity of T-cell and B-cell epitopes for antibody recognition

The major outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused considerable issues worldwide. To date, the pandemic SARS-CoV-2 strain has now subsequently mutated from the Wuhan original variant which enhances invasion and transmission as well as evades host immune response efficacy. The receptor binding domain (RBD) is a receptor protein found on the viral membrane that is essential for interacting with angiotensin converting enzyme type 2 (ACE2). The interaction between viral RBD and host ACE2 is the initial step for SARS-CoV-2 invasion. The wild-type SARS-CoV-2 and a few variations of concern (VOCs), including Alpha, Beta, Delta, and Gamma, were utilized in this study to identify functional sites as well as B-cell and T-cell epitopes that may have an impact on the RBD immunogenicity of various SARS-CoV-2 variants. The B-cell and T-cell epitope analysis for S1-RBD demonstrated all of the variants contained comparable epitopes, suggesting that the host immune system may be able to recognize the RBD variants after the initial infection. To verify this assumption, using Western blot analysis, we expressed soluble S1-RBD variants in E. coli BL21(DE3) and showed that an anti-S1-RBD polyclonal antibody could recognize all the variants investigated in this study.