Comirnaty-Elicited and Convalescent Sera Recognize Different Spike Epitopes

Abstract

Many of the approved SARS-CoV-2 vaccines are based on a stabilized variant of the spike protein. This raises the question of whether the immune response against the stabilized spike is identical to the immune response that is elicited by the native spike in the case of a SARS-CoV-2 infection. Using a peptide array-based approach, we analysed the binding of antibodies from Comirnaty-elicited, convalescent, and control sera to the peptides covering the spike protein. A total of 37 linear epitopes were identified. A total of 26 of these epitopes were almost exclusively recognized by the convalescent sera. Mapping these epitopes to the spike structures revealed that most of these 26 epitopes are masked in the pre-fusion structure. In particular, in the conserved central helix, three epitopes that are only exposed in the post-fusion conformation were identified. This indicates a higher spike-specific antibody diversity in convalescent sera. These differences could be relevant for the breadth of spike-specific immune response.

Keywords: SARS-CoV-2 spike; convalescent; linear epitopes; peptide array; stabilized spike protein.

Figure 1

Mapping of linear S protein epitopes. (A) Heatmap of IgG antibody immune response of 31 sera from COVID-19 convalescent patients, 25 BNT162b2 vaccinated patients, and 4 healthy donors. FI: fluorescence intensity. (B) Schematic structure of the S protein and condensed heatmap of all 56 sera grouped in vaccinated and convalescent patients. RBD: Receptor binding domain; FC: furin cleavage site; FP: fusion peptide; KV: amino acid positions K986 and V987, which are mutated to proline in the pre-fusion stabilized S protein; CH: central helix; TM: transmembrane domain; CT: cytoplasmic tail.

Figure 2

Validation of the peptide array results. (A) FI means of the 50 highest peptides from the different sera groups. (B) Anti-RBD ELISA of the different sera groups. Vacc.: vaccine-elicited sera; Conval.: convalescent; Ctrl.: Neg. sera. (non-vaccinated and non-infected) * p-value ≤ 0.05; ** p-value ≤ 0.01; **** p-value ≤ 0.0001.

Figure 3

Location of the linear epitopes in the pre-fusion stabilized S protein and post-fusion S protein structure. (A–C) Pre-fusion stabilized S Protein (PDB: 6VYB). Gray: pre-fusion dimer in closed-state; green: pre-fusion monomer in open-state (RBD-UP); blue: linear epitopes present only in vaccinated sera; orange: linear epitopes present in both groups; red: linear epitopes exclusive in convalescent sera. (D) Post-fusion S protein (PDB: 6M3W) exposed the CH helices of all three monomers. Gray: Post-fusion trimer; red/blue/orange: CH of the three monomers; beige: linker region.