Targets and cross-reactivity of human T cell recognition of Common Cold Coronaviruses. Tarke et al.
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Table S3. List of CD4+ T cell epitopes identified in this study, related to Figure 2. NL63 and OC43 epitopes information pertaining protein composition and location are included togther with the sequence identity values related to each of the representative sequence for Sarbecoviruses (n=10), Betacoronaviruses excluding Sarbecoviruses (n=15) and Alphacoronaviruses (n=15).
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88 healthy adult PBMC donors were screened for T cell reactivity to NL63 and OC43 antigens encompassing the entire proteome. Specific donor-antigen combinations associated with good reactivity for CD4+ T cells, were then deconvoluted based on the availability of donor cells. To identify specific CD4+ T cell epitopes, we deconvoluted peptide pools corresponding to the six immunodominant antigens (S, M, N, nsp2, nsp3 and nsp12) identified as accounting for 80% or more of the NL63 and OC43 CD4+ T cell activity (see Fig. 1, Targets and cross-reactivity of human T cell recognition of Common Cold Coronaviruses. Tarke et al.). Epitope deconvolution was performed in at least 8 independent donors per antigen. CD4+ T cell epitopes were defined using an HLA-unbiased approach. First, overlapping peptides spanning the entire sequence of the antigen in question were pooled in intermediate pools of about 10 peptides each, and tested for reactivity in the AIM assay. The intermediate pools found to be positive in the AIM assays, were then deconvoluted to identify the specific peptides associated with the positive response in a second round of experiments 52. The positivity threshold was defined as >100 net AIM+ cell counts (background subtracted by the average of triplicate negative controls) and a Stimulation Index (SI) >2, as previously described (Tarke et al., Cell Rep Med 2021; da Silva Antunes et al., Journal of immunology research 2020). Table S3 provides a summary of the 165 epitopes identified, fairly evenly distributed between NL63 (n=87) and OC43 (n=78). Overall, these results provide an unbiased genome-wide CD4+ T cell epitope identification screen to two CCC.