Binding signatures and cross-reactivity in the SARS-CoV-2 immune response

ABSTRACT

Background: Mounting evidence indicates that antibodies generated during SARS-CoV-2 infection are correlates of protection. Antibodies targeting Spike (S) on the viral surface have been shown to neutralize the virus. However, the full repertoire of neutralizing and non-neutralizing antibodies against SARSCoV-2, as well as cross-reactivity between SARS-CoV-2 and other circulating (CoVs), remains unclear. We sought to profile the complete repertoire of linear CoV epitopes targeted by the humoral immune response in patients with and without COVID-19 from Seattle, WA. Methods: To map the linear epitope profiles in patients, we developed a comprehensive pan-CoV phage display library composed of 39 amino acid peptides covering the complete genomes of SARS-CoV-2 and the six other CoVs known to infect humans. Using samples from patients with confirmed COVID-19 and with no known SARS-CoV-2 exposure, we immunoprecipitated antibodies against CoV peptides, deep sequenced the co-immunoprecipitated phage, and applied a customized computational pipeline to define SARS-CoV-2 and crossreactive epitopes. Results: The dominant immune responses to SARS-CoV-2 were targeted to regions spanning S, Nucleocapsid (N), and ORF1ab. We identified 17 epitopes within S that were present in two or more individuals, spanning both the S1 and S2 subunits, with some detected in > 75% of individuals. The most commonly mapped S epitope (S- residues 1121-1159) was a region just upstream of the second heptad repeat. We identified nine epitopes within N that were reactive in at least two individuals, four of which were present in at least 35% of patients. The two most prominent N epitopes were derived from the RNA binding domain (N residues 141-179 and 161-199). Epitopes isolated from ORF1ab were the most variable across patients. Of the 46 unique ORF1ab epitopes we identified, only five were present in two or more individuals, suggesting that ORF1ab responses are individual-specific. We also found a high degree of variation in the total number of epitopes targeted by individuals (ranging from 2 to 25). Finally, we identified four unique cross-reactive sequences that were bound by antibodies in SARS-CoV-2 unexposed individuals. Conclusion: Our study comprehensively defined the linear epitope profiles of a population of COVID-19 and SARS-CoV-2 unexposed patients. Epitope maps and functional characterization of SARS-CoV-2 antibodies will be critical for the development of a broad repertoire of COVID-19 treatments and vaccine strategies.