Prevalent and immunodominant CD8 T cell epitopes are conserved in SARS-CoV-2 variants
Saskia Meyer,
Isaac Blaas,
Ravi Chand Bollineni,
Marina Delic-Sarac,
Trung T. Tran,
Cathrine Knetter,
Ke-Zheng Dai,
Torfinn Støve Madssen,
John T. Vaage,
Alice Gustavsen,
Weiwen Yang,
Lise Sofie Haug Nissen-Meyer,
Karolos Douvlataniotis,
Maarja Laos,
Morten Milek Nielsen,
Bernd Thiede,
Arne Søraas,
Fridtjof Lund-Johansen,
Even H. Rustad,
Johanna Olweus
Affiliations
Saskia Meyer
Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway; Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
Isaac Blaas
Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway; Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
Ravi Chand Bollineni
Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway; Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
Marina Delic-Sarac
Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway; Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
Trung T. Tran
Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway
Cathrine Knetter
Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway; Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
Ke-Zheng Dai
Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway
Torfinn Støve Madssen
Department of Circulation and Medical Imaging, NTNU, 7030 Trondheim, Norway
John T. Vaage
Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway; Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway
Alice Gustavsen
Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway
Weiwen Yang
Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway; Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
Lise Sofie Haug Nissen-Meyer
Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway
Karolos Douvlataniotis
Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway; Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
Maarja Laos
Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway; Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway; Institute of Biomedicine and Translational Medicine, Faculty of Medicine, University of Tartu, 50411 Tartu, Estonia
Morten Milek Nielsen
Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway; Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
Bernd Thiede
Department of Biosciences, University of Oslo, 0371 Oslo, Norway
Arne Søraas
Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
Fridtjof Lund-Johansen
Department of Immunology, Oslo University Hospital, 0424 Oslo, Norway; ImmunoLingo Convergence Center, University of Oslo, 0372 Oslo, Norway
Even H. Rustad
Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway; Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway; Corresponding author
Johanna Olweus
Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0379 Oslo, Norway; Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway; Corresponding author
Summary: The emergence of SARS-CoV-2 variants of concern (VOC) is driven by mutations that mediate escape from neutralizing antibodies. There is also evidence that mutations can cause loss of T cell epitopes. However, studies on viral escape from T cell immunity have been hampered by uncertain estimates of epitope prevalence. Here, we map and quantify CD8 T cell responses to SARS-CoV-2-specific minimal epitopes in blood drawn from April to June 2020 from 83 COVID-19 convalescents. Among 37 HLA ligands eluted from five prevalent alleles and an additional 86 predicted binders, we identify 29 epitopes with an immunoprevalence ranging from 3% to 100% among individuals expressing the relevant HLA allele. Mutations in VOC are reported in 10.3% of the epitopes, while 20.6% of the non-immunogenic peptides are mutated in VOC. The nine most prevalent epitopes are conserved in VOC. Thus, comprehensive mapping of epitope prevalence does not provide evidence that mutations in VOC are driven by escape of T cell immunity.
