Efforts are being made worldwide to understand the immune response to SARS-CoV-2, the virus responsible for the COVID-19 pandemic, including the impact of T cell immunity and cross-recognition with seasonal coronaviruses. Screening SARS-CoV-2 peptide pools revealed that the nucleocapsid (N) protein induced an immunodominant response in HLA-B7 + COVID-19-recovered individuals that was also detectable in unexposed donors. A single N-encoded epitope that was highly conserved across circulating coronaviruses drove this immunodominant response. In vitro peptide stimulation and crystal structure analyses revealed T cell-mediated cross-reactivity towards circulating OC43 and HKU-1 beta coronaviruses, but not 229E or NL63 alpha coronaviruses, due to different peptide conformations. TCR sequencing indicated cross-reactivity was driven by private T cell receptor repertoires with a bias for TRBV27 and a long CDR3β loop. Together, our findings demonstrate the basis of selective T cell cross-reactivity towards an immunodominant SARS-CoV-2 epitope and its homologues from seasonal coronaviruses, suggesting long-lived protective immunity.

Role of the funding source:The funders of the study had no role in the study design, data collection, data analysis, data interpretation, or the writing of the manuscript. The corresponding authors had full access to all the data in the study and had final responsibility for the decision to submit for publication. Conflict of interest: MPP has received consulting fees and research funding from Atara Biotherapeutics and is a member of the Neurology Clinical Advisory Panel of Atara Biotherapeutics. CS has received consulting fees from Atara Biotherapeutics. SB is a member of the advisory boards of Roche, Sanofi Genzyme, Merck, and Teva. KAG has received personal fees from Roche and travel support from Sanofi Aventis. AS has received educational and travel support from Merck Serono Australia. KDH is a member of the advisory boards of Merck Serono Australia, Biogen Australia, and Roche Australia. BTA is an employee of, and owns equity shares in, Atara Biotherapeutics. SRB has received a license fee payment from Atara Biotherapeutics. AC has received a consulting fee from Sanofi Genzyme. RK is a consultant and member of the scientific advisory board of Atara Biotherapeutics and has received a license fee payment and research funding from Atara Biotherapeutics.

No abstract

Fluorochrome-conjugated peptide–major histocompatibility complex (pMHC) multimers are widely used for flow cytometric visualization of antigen-specific T cells. The most common multimers, streptavidin–biotin-based ‘tetramers’, can be manufactured readily in the laboratory. Unfortunately, there are large differences between the threshold of T cell receptor (TCR) affinity required to capture pMHC tetramers from solution and that which is required for T cell activation. This disparity means that tetramers sometimes fail to stain antigen-specific T cells within a sample, an issue that is particularly problematic when staining tumour-specific, autoimmune or MHC class II-restricted T cells, which often display TCRs of low affinity for pMHC. Here, we compared optimized staining with tetramers and dextramers (dextran-based multimers), with the latter carrying greater numbers of both pMHC and fluorochrome per molecule. Most notably, we find that: (i) dextramers stain more brightly than tetramers; (ii) dextramers outperform tetramers when TCR–pMHC affinity is low; (iii) dextramers outperform tetramers with pMHC class II reagents where there is an absence of co-receptor stabilization; and (iv) dextramer sensitivity is enhanced further by specific protein kinase inhibition. Dextramers are compatible with current state-of-the-art flow cytometry platforms and will probably find particular utility in the fields of autoimmunity and cancer immunology.