Profiling of linear B-cell epitopes against human coronaviruses in pooled sera sampled early in the COVID-19 pandemic

Abstract

Background Antibodies play a key role in the immune defence against infectious pathogens. Understanding the underlying process of B cell recognition is not only of fundamental interest; it supports important applications within diagnostics and therapeutics. Whereas conformational B cell epitope recognition is complicated to decipher, linear B cell epitopes offer a straightforward approach that can be reduced to peptide recognition. Methods We utilised an overlapping peptide approach encompassing the proteomes of the seven human-infecting coronaviruses. Pooled sera from eight PCR-confirmed COVID-19 convalescents and eight pre-pandemic controls were analysed. 13-mer peptides overlapping by 11 amino acids were synthesised and incubated with the pooled sera. Fluorochrome-labelled anti-IgG and -IgA antibodies were applied to detect antibody-peptide interactions. Strong antibody interactions spanning consecutive peptides were identified as 'high-fidelity regions' (HFRs) and mapped to coronavirus proteomes using a 60% homology threshold for clustering. Results We found 333 HFRs derived from human coronaviruses. Among these, 98 (29%) mapped to SARS-CoV-2, 144 (44%) to one or more common cold coronaviruses (CCC), and 54 (16%) cross-mapped to both SARS-CoV-2 and CCCs. The remaining 37 (11%) mapped to either SARS-CoV or MERS-CoV. Notably, COVID-19 serum favoured SARS-CoV-2-mapped HFRs, while pre-pandemic serum favoured CCC-mapped HFRs. The primary targets for linear B cell epitopes were the ORF1ab protein (60%), spike protein (21%), and nucleoprotein (15%) in absolute numbers; however, the order was reversed in terms of epitope density. Conclusion We identified linear B cell epitopes across coronaviruses, highlighting pan-, alpha-, beta-, or SARS-CoV-2-corona-specific B cell recognition patterns. These insights could aid in understanding past and present coronavirus exposures. Additionally, our results indicate potential cross-reactivity of pre-pandemic anti-CCC antibodies with SARS-CoV-2, possibly influencing COVID-19 outcomes. Lastly, our methodology offers a rapid and thorough approach to high-resolution linear B-cell epitope mapping, which is crucial for future studies of emerging infectious diseases.