The immunodominant and neutralization linear epitopes for SARS-CoV-2

Abstract

Although vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are under development, the antigen epitopes on the virus and their immunogenicity are poorly understood. Here, we simulate the 3D structures and predict the B cell epitopes on the spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins of SARS-CoV-2 using structure-based approaches and validate epitope immunogenicity by immunizing mice. Almost all 33 predicted epitopes effectively induce antibody production, six of these are immunodominant epitopes in individuals, and 23 are conserved within SARS-CoV-2, SARS-CoV, and bat coronavirus RaTG13. We find that the immunodominant epitopes of individuals with domestic (China) SARS-CoV-2 are different from those of individuals with imported (Europe) SARS-CoV-2, which may be caused by mutations on the S (G614D) and N proteins. Importantly, we find several epitopes on the S protein that elicit neutralizing antibodies against D614 and G614 SARS-CoV-2, which can contribute to vaccine design against coronaviruses.

Keywords: COVID-19; SARS-CoV-2; immunodominant epitope; neutralizing epitope; vaccine.

Graphical abstract

Figure 1

Predication and validation of epitopes on SARS-CoV-2 (A–D) Molecular simulated structures and predicted epitopes of major proteins of SARS-CoV-2. Shown are top and side views of 3D structures (gray) and the predicted epitopes (colored) of the spike (S) protein (A), envelope (E) protein (B), membrane (M) protein (C), and nucleocapsid (N) protein (D). (E–H) Epitope-conjugated HBc-S VLPs induce high antibody titers against epitope peptides and SARS-CoV-2 proteins. (E) Schematic of the immunization design. (F–H) 96-well plates were coated with peptides (F) and S (G) and N (H) proteins. Data are shown as mean ± SEM (compared with the HBc-S control; ^∗∗∗p < 0.001; ^∗∗∗∗p < 0.0001; one-way ANOVA followed by Dunnett’s test; compared with non-glycosylated epitope; #p < 0.05; Student’s t test).

Figure 2

Imported and domestic COVID-19 have different immunodominant epitopes (A) The landscape of adjusted epitope-specific antibody levels in early convalescent sera of individuals with imported and domestic COVID-19. Gray indicates not tested. (B–G) Immunodominant epitopes binding with the antibodies in early convalescent sera from individuals with imported and domestic COVID-19. Data are shown as mean ± SEM. The cutoff lines were based on the mean value plus 3 SD in 4–5 healthy persons.

Figure 3

Antibodies induced by epitopes of the S protein inhibit SARS-CoV-2 pseudovirus infection (A and B) Neutralizing potency of mice sera after the third immunization with each vaccine was measured with D614 (A) or G614 (B) SARS-CoV-2 pseudoviruses (PsVs). Data are shown as mean ± SEM (compared with the HBc-S control;^∗p < 0.05; ^∗∗p < 0.01; ^∗∗∗p < 0.001; ^∗∗∗∗p < 0.0001; compared with non-glycosylated epitope; #p < 0.05; ##p < 0.01; ####p < 0.0001). (C) 2-Fold serial dilution neutralizing assay against G614 SARS-CoV-2 pseudoviruses. Data are shown as mean ± SEM. (D–I) Spatial positions of D614 (D–F) and G614 pseudovirus (G–I) neutralizing epitopes (colored), respectively, in or near the N-terminal domain (NTD; D and G), receptor-binding domain (RBD; E and H), and S2′ cleavage site (F and I) of the S protein (gray).