Shared Antigen-specific CD8+ T cell Responses Against the SARS-COV-2 Spike Protein in HLA A*02:01 COVID-19 Participants

Chour, W.; Xu, A. M.; Ng, A. H. C.; Choi, J.; Xie, J.; Yuan, D.; Lee, J. K.; Delucia, D. C.; Edmark, R.; Jones, L.; Schmitt, T. M.; Chaffee, M. E.; Duvvuri, V.; Greenberg, P. D.; Murray, K.; Wallick, J.; Algren, H. A.; Berrington, W. R.; O'Mahoney, D. S.; Goldman, J. D.; Heath, J. R.

We report here on antigens from the SARS-CoV-2 virus spike protein, that when presented by Class I MHC, can lead to cytotoxic CD8+ T cell anti-viral responses in COVID-19 patients. We present a method in which the SARS-CoV-2 spike protein is converted into a library of peptide antigen-Major Histocompatibility Complexes (pMHCs) as single chain trimers that contain the peptide antigen, the MHC HLA allele, and the {beta}-2 microglobulin sub-unit. That library is used to detect the evolution of virus-specific T cell populations from two COVID-19 patients, at two time points over the course of infection. Both patients exhibit similar virus-specific T cell populations, but very different time-trajectories of those populations. These results can be used to track those virus-specific T cell populations over the course of an infection, thus providing deep insight into the variations in immune system trajectories observed in different COVID-19 patients.