ABSTRACT
Background: A large global effort is ongoing to develop vaccines against SARS-CoV-2, the causative agent of COVID-19. While there is accumulating information on the antibody response against SARS-CoV-2, less is known about the SARS-CoV-2 antigens that are targeted by CD8 T cells. Such knowledge will be of high value to gain fundamental insights into the antigenic landscape of SARS-CoV-2 recognized by CD8 T cells, to develop tool allowing focused analysis of the SARS-CoV-2 specific T cell responses directly ex vivo, and to understand whether current vaccine designs are covering the CD8 T cell recognized antigens. Methods: To address this issue, we have analyzed samples from 18 COVID-19 patients for CD8 T cell recognition of 500 predicted SARS-CoV-2-derived epitopes restricted to 10 common HLA-A and HLA-B alleles. For each HLA allele, the top 50 epitopes were selected based on predicted binding affinity and likelihood of successful proteasomal processing. To probe for CD8 T cell recognition of the selected epitope-HLA complexes, we made use of our in-house technology based on multiplexing of peptide HLA (pHLA) multimers conjugated to fluorescent dyes. Results: In addition to previous studies showing CD8 T cell reactivity towards epitopes derived from the spike protein of SARS-CoV-2, we have identified several CD8 T cell recognized epitopes derived from the ORF1ab, including one epitope displaying clear immunodominant properties across patients positive for HLA-A*01:01. Investigation of the functional status of part of the identified responses (including 4 responses specific for the immunodominant epitope) revealed that the T cell responses were highly dysfunctional. In addition the SARS-CoV-2 specific CD8 T cell responses displayed an increased expression of NKG2A in comparison with bulk CD8 T cells, which may explain their dysfunctional state. Conclusions: Our data suggest that part of the ORF1ab encodes multiple CD8 T cell antigens including one immunodominant epitope. Noteworthy these epitopes were derived from a part of the viral genome that is not included in the majority of vaccine candidates in development, and this may potentially influence their clinical activity and safety profile. Legal entity responsible for the study: The authors. Funding: Has not received any funding. Disclosure: All authors have declared no conflicts of interest.
ABSTRACT
While there is accumulating evidence on the antibody response against SARS-CoV-2, we are only beginning toacquire knowledge regarding the SARS-CoV-2 specific CD8 T-cell response. Therefore, it is an urgent matter to gaina deeper insight into the virus specific CD8 T-cell response to both assist vaccine design and provide tools toevaluate the vaccine-induced T-cell responses. To address this issue, we have analyzed samples from 20 COVID-19 patients for CD8 T-cell recognition of 500 predicted SARS-CoV-2-derived epitopes restricted to 10 of the mostcommon HLA-A and HLA-B alleles. For each HLA allele, the top 50 epitopes were selected based on predictedbinding affinity and likelihood of successful proteasomal processing. In addition, SARS-CoV-2 epitope predictionsshared by the science community were considered. To probe for CD8 T-cell recognition of the selected epitopes, wemade use of our in-house technology based on multiplexing of peptide HLA (pHLA) multimers conjugated tofluorescent dyes. Our data demonstrated that CD8 T-cell reactivity against SARS-CoV-2 was common. Remarkably, a substantial fraction of the observed CD8 T-cell responses were directed towards the ORF1ab polyprotein 1ab.These CD8 T-cell responses were frequently of a profound magnitude. In particular, a CD8 T-cell response towardsa potentially immunodominant epitope (TTDPSFLGRY) restricted to the HLA-A∗01:01 allele was found in all patientspositive for this allele. Interestingly, the fraction of SARS-CoV-2 specific CD8 T cells expressing the inhibitoryreceptor NKG2A was higher as compared to bulk CD8 T cells. In conclusion, the fact that a major part of theidentified SARS-CoV-2 specific CD8 T-cell response is directed against a part of the viral genome that is notincluded in the majority of vaccine candidates currently in development may potentially influence their clinical activityand toxicity profile.