Broadly recognized, cross-reactive SARS-CoV-2 CD4 T cell epitopes are highly conserved across human coronaviruses and presented by common HLA alleles. Becerra-Artiles et al.
Sequence homology between SARS-CoV-2 and common-cold human coronaviruses (HCoVs) raises the possibility that memory T cells elicited to prior HCoV infection can impact response in COVID-19. We studied T cell cross-reactivity between SARS-CoV-2 and HCoVs by measuring responses to SARS-CoV-2 S protein in convalescent COVID-19 donors, mRNA COVID-19 vaccine recipients, and individuals not exposed to SARS-CoV-2. We expanded T cell lines from SARS-CoV-2 donors in vitro by stimulation with HCoV S peptides, which enriches for cross-reactive T cells. We found that SARS-CoV-2 spike sequence S811-831 dominated the cross-reactive response. S811-831 is highly conserved across SARS-CoV-2 variants, and human and animal coronaviruses. Most donors tested recognized S811-831, including severe and mild COVID-19 donors, individuals receiving mRNA vaccines, and previously unexposed donors, although most unexposed donors required in vitro expansion to detect these cross-reactive cells. We defined minimal epitopes within S811-831 as well as the presenting HLA alleles. We identified two major reactivity patterns, with an N-terminal epitope RSFIEDLLF S815-823 presented by DQ5 (DQA1*01:01/DQB1*05:01), and a partially overlapping C-terminal epitope IEDLLFNKV S818-826 presented by DP2 (DPA1*01:03 DPB1*02:01) and DP4 (DPA1*01:03/DPB1*04:01). The broad recognition of these epitopes is driven in part by the prevalence of the presenting HLA alleles, particularly DP4, which is the most common allele worldwide. T cells recognizing S811-831 were cross-reactive for HCoV homologous sequences. The key to this cross-reactive recognition seems to be the remarkable conservation across coronaviruses of amino acids at expected T cell contact positions for both the DQ5 and DP4 binding frames. The selection for DP4 and DQ5 as preferred presenting elements for cross-reactive recognition may be related to their binding motifs, which accommodate peptide sequence variability while still presenting identical residues for TCR recognition. T cells cross-reactive for both SARS-CoV-2 and HCoVs comprise a small fraction of the overall response in both pre-pandemic and COVID-19 donors. The responses were characterized by a highly diverse TCR repertoire, mainly specific to individual donors with a few public clonotypes. Table S1 shows the demographic, clinical, serological, and HLA typing of the donors used in the study. Table S2 shows a summary of immunological assays performed on T cell clones. Table S3 summarizes the MHC binding prediction on 3 candidate cross-reactive epitopes. Table S4 lists the selected coronaviruses used for the conservation analysis. Table S5 provides information on the TCR clonotypes identified in different samples and the analysis of sequence sharing among samples. Table S6 provides the results from the GLIPH algorithm applied to our data. Table S7 lists sequences of synthetic peptides used throughout the study.