Epitope Profiling Reveals the Critical Antigenic Determinants in SARS-CoV-2 RBD-Based Antigen

Abstract

The ongoing COVID-19 pandemic caused by SARS-CoV-2 is a huge public health crisis for the globe. The receptor-binding domain (RBD) of SARS-CoV-2 spike (S) protein plays a vital role in viral infection and serves as a major target for developing neutralizing antibodies. In this study, the antibody response to the RBD of SARS-CoV-2 S protein was analyzed by a panel of sera from animals immunized with RBD-based antigens and four linear B-cell epitope peptides (R345, R405, R450 and R465) were revealed. The immunogenicity of three immunodominant peptides (R345, R405, R465) was further accessed by peptide immunization in mice, and all of them could induced potent antibody response to SARS-CoV-2 S protein, indicating that the three determinants in the RBD were immunogenic. We further generated and characterized monoclonal antibodies (15G9, 12C10 and 10D2) binding to these epitope peptides, and finely mapped the three immunodominant epitopes using the corresponding antibodies. Neutralization assays showed that all three monoclonal antibodies had neutralization activity. Results from IFA and western blotting showed that 12C10 was a cross-reactive antibody against both of SARS-CoV-2 and SARS-CoV. Results from conservative and structural analysis showed that 350VYAWN354 was a highly conserved epitope and exposed on the surface of SARS-CoV-2 S trimer, whereas 473YQAGSTP479 located in the receptor binding motif (RBM) was variable among different SARS-CoV-2 strains. 407VRQIAP412 was a highly conserved, but cryptic epitope shared between SARS-CoV-2 and SARS-CoV. These findings provide important information for understanding the humoral antibody response to the RBD of SARS-CoV-2 S protein and may facilitate further efforts to design SARS-CoV-2 vaccines and the target of COVID-19 diagnostic.

The SARS-CoV-2 spike residues 616/644 and 1138/1169 delineate two antibody epitopes in COVID-19 mRNA COMIRNATY vaccine (Pfizer/BioNTech)

“…To our knowledge, it is not yet known whether the SARS-CoV-2 spike residues 616/644 and 1138/1169 contribute to the protective efficacy of Pfizer-BioNTech COVID-19 vaccine comirnaty 23 , 31 – 34 , 37 , 38 . There is some evidence that potent neutralization of SARS-CoV-2 requires both spike conformational changes and receptor blockade elicited by antibody binding 10 , 13 – 18 , 38 .…”

“…Despite the lack of information on the protection conferred by the S2P6 peptide-reactive antibodies against SARS-CoV-2 infection, the data obtained with the B-cell epitope S2P6 peptide broadens our understanding on the efficacy of COVID-19 mRNA comirnaty vaccine. Finally, our study raises the question on the medical applicability of a vaccine formulation based on linear B-cell epitope peptides, e.g., the S2P6 peptide containing the residues 1138/1169 located in the C-terminal region of S2 subunit from SARS-CoV-2 spike protein 37 – 39 .…”

SARS-CoV-2–Specific Vaccine Candidates; the Contribution of Structural Vaccinology

“…For SARS-CoV-2, Jiang et al analysed the RBD-specific Ab response from a panel of sera from animals immunised with RBD-based antigens and identified four linear B cell epitope peptides: 350VYAWN345, 407VRQIAP412, S450-469 and 473YQAGSTP479 [66]. Three immunodominant peptides, 350VYAWN345, 407VRQIAP412 and 473YQAGSTP479, were revealed to induce a potent Ab response to the SARS-CoV-2 S protein in the mouse model.…”

“…The M proteins and nucleoproteins of influenza were revealed to be more conserved than the proteins exposed on the viral surface, such as haemagglutinin and neuraminidase. Moreover, Patel et al reported that the T cell immune response elicited by the conserved influenza epitopes may enhance the broad-spectrum efficacy of the pan-influenza vaccine [66]. Although further investigations are required to examine if these discoveries are applicable in designing a pan-coronavirus vaccine, these studies suggest that the non-S proteins of SARS-CoV-2 may be suitable in stimulating robust anti-viral T cell immune responses and are less susceptible to genetic drift.…”

“…If the memory of lymphocytes is lost before the emergence of a novel coronavirus, a broad-spectrum vaccine is ineffectual. Additionally, several studies reported that the pan-influenza vaccine confers better protective efficacy against seasonal influenza, rather than pandemic influenza [65,66]. This knowledge implies that a broad-spectrum vaccine may not be suitable against pandemic coronaviruses.…”