Epitope Profiling Reveals the Antibody Immune Response Difference Between COVID-19 Infected and Vaccinated

Antibodies play an important part in combating SARS-CoV-2 infection whether generated by the infection or vaccination. However, the many epitopes generated by infection have not been fully investigated with only a few epitopes known and these being mostly limited to the S protein's receptor binding domain (RBD) and the N-terminal domain which limits vaccine and drug design 1-4. The difference between epitopes generated by infection and vaccination has also not been studied. To address this, we employed a SARS-CoV-2 proteome microarray to screen for linear epitopes recognized by antibodies present in COVID-19 patients and individuals vaccinated with the Pfizer-BioNTech mRNA COVID-19 Vaccine. The proteome microarray consisted of S, N, and E proteins, as well as spotting peptides that were 15 amino acids in length with overlaps of 5-amino acids, covering the entire SARS-CoV-2 proteome (MN908947.3) (Figure 1). Blood samples were incubated onto the arrays followed by an incubation of fluorescent secondary anti-human antibodies. Fluorescent intensity data generated and normalized using the Z-score method and then further analyzed for significance by parametric one-way ANOVA with Dunnett's post hoc test (COVID-19 cohort) and repeated measure ANOVAs with Dunnett's post hoc tests (vaccinated cohort). The full-length S protein showed a significant increase in COVID-19 patients at around 20-23 days after symptom onset and vaccinated individuals over all time points in both IgM and IgG antibodies (Figure 2A). Linear mapping of the IgM epitopes revealed a degree of overlap between infected and vaccinated individuals (22.2%; 6/27 total) with both having epitopes in the RBD and fusion peptide (FP) (Figure 2B). Structural mapping on 3D models of the S protein showed that all epitopes where on the surface of the protein and that COVID-19 generated epitopes have a different pattern than those generated by vaccination (Figure 2C). An Epitope identified in this study with future prospects is epitope S481-495 from COIVD-19 patients that partially overlapped the binding site of two neutralizing antibodies previously isolated from COVID-19 patients, S2H135 and F2B-2F61, and contacted amino acids that interact with ACE2 receptor6,7. One epitope of note from the vaccinated individuals is epitope S811-825 which mapped adjacent to the fusion-peptide proximal region. These epitopes may be helpful in future vaccine and antibody therapy development. 1 Ju, B. et al. Nature 584, 115-119. 2 Robbiani, D. F. et al. Nature 584, 437-442. 3 Seydoux, E. et al. bioRxiv. 4 Wu, Y. et al. Science 368, 1274-1278. 5 Piccoli, L. et al. Cell 183, 1024-1042 e1021. 6 Casalino, L. et al. ACS Cent Sci 6, 1722-1734. 7 Wang, Q. et al. Cell 181, 894-904 e899. © FASEB.