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Proffered Paper - SARS-CoV-2 and cancer 2

LBA73 - The ORF1ab of SARS-CoV-2 encodes an immunodominant epitope restricted by HLA-A*01:01


20 Sep 2020


Proffered Paper - SARS-CoV-2 and cancer 2


COVID-19 and Cancer

Tumour Site


Pia Kvistborg


Annals of Oncology (2020) 31 (suppl_4): S1142-S1215. 10.1016/annonc/annonc325


P. Kvistborg1, A. Gangaev1, S. Ketelaars1, S. Patiweal1, A. Dopler1, O. Isaeva1, K. Hoefakker1, S. De Biasi2, C. Mussini2, G. Guaraldi2, M. Girardis2, C. Talavera Ormeno3, P. Hekking3, N. Lardy4, M. Toebes1, R. Balderas5, T.N. Schumacher6, H. Ovaa3, A. Cossarizza2

Author affiliations

  • 1 Immunology, NKI-AVL - Netherlands Cancer Institute/Antoni van Leeuwenhoek Hospital, 1066CX - Amsterdam/NL
  • 2 Department Of Medical And Surgical Sciences For Children And Adults, University of Modena, Modena/IT
  • 3 Department Of Cell And Chemical Biology, Leiden University Medical Center, Leiden/NL
  • 4 Department Of Immunogenetics, Sanquin Diagnostics, Amsterdam/NL
  • 5 Department Of Biological Sciences, BD Bioscience, San Jose/US
  • 6 Immunology, Netherlands Cancer Institute/Antoni van Leeuwenhoek hospital (NKI-AVL), 1066CX - Amsterdam/NL


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Abstract LBA73


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.


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.


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.


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.

Clinical trial identification

Editorial acknowledgement

Legal entity responsible for the study

The authors.


Has not received any funding.


All authors have declared no conflicts of interest.

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