Submission history

Received: 20 January 2022

Accepted: 31 January 2022

Acknowledgments

Chris Groen, Willemijn van der Kleij, Eveline de Haan, Roos Robert, virorunners and colleagues of the Erasmus MC HCW study team are acknowledged for their excellent study support. Faye de Wilt, Djenolan van Mourik, Suzanne van Efferen, Suzanne Hendrickx, Felicity Chandler are thanked for their technical support and Chantal Reusken for providing the clinical specimen for SARS-CoV-2 Omicron culture. We acknowledge QIAGEN for supporting the study by providing the QuantiFERON SARS-CoV-2 RUO Starter Packs and Extended Packs. QIAGEN had no role in study design, data acquisition and analysis. Assay overview images were created with biorender.com. SARS-CoV-2 CD4 and CD8 peptide mega pools are subject to an MTA agreement with La Jolla Institute for Immunology.

Funding: This work was financially supported by the Netherlands Organization for Health Research and Development (ZONMW) grant agreement 10150062010008 to B.L.H. and grant agreement 10430072110001 to R.D.d.V., C.G.v.K., H.v.d.K and R.S., the Health~Holland grants EMCLHS20017 to D.G., L.G., and R.D.d.V. and grant LSHM19136 to B.L.H co-funced by the PPP Allowance made available by the Health~Holland, Top Sector Life Sciences & Health, to stimulate public –private partnerships, and the European Union’s Horizon 2020 research and innovation program under grant no. 101003589 (RECoVER: M.P.G.K.). BJAR received a research grant from the Erasmus foundation. B.L.H is supported by the NIH/NIAID Centers of Excellence for Influenza Research and Response (CEIRR) under contract 75N93021C00014-Icahn School of Medicine at Mt. Sinai. This project has been funded in whole or in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. 75N93021C00016 to A.S. and Contract No. 75N9301900065 to A.S, D.W.

Author contributions: Conceptualization: C.H.G.v.K., B.J.A.R., P.H.M.v.d.K., A.S., M.P.G.K., B.L.H., R.D.d.V. Formal analysis: C.H.G.v.K., D.G., K.S.S., A.Z.M., M.M.L., D.W., R.D.d.V. Funding acquisition: C.H.G.v.K., B.J.A.R., D.W., P.H.M.v.d.K., A.S., M.P.G.K., A.G., B.L.H., R.D.d.V Investigation: C.H.G.v.K., D.G., K.S.S., A.Z.M., M.M.L., S.B., S.S., L.G., R.S.G.S., N.N.N., L.C.R., L.L.A.v.D, J.d.W., K.A., T.I.B., H.d.J., D.W., A.G., B.J.H., R.D.d.V. Project administration: C.H.G.v.K., S.B., L.G., R.S.G., B.J.A.R., R.D.d.V. Resources: C.H.G.v.K., M.M.L., B.J.A.R., D.W., P.H.M.v.d.K., A.S., M.P.G.K., A.G., B.L.H., R.D.d.V. Supervision: C.H.G.v.K., M.M.L., B.J.A.R., P.H.M.v.d.K., A.S., M.P.G.K., B.L.H., R.D.d.V. Visualization: C.H.G.v.K., D.G., R.D.d.V. Writing—original draft: C.H.G.v.K., B.L.H., R.D.d.V. Writing—review and editing: all authors reviewed and edited the final version.

Conflict of interest: A.S. is a consultant for Gritstone Bio, Flow Pharma, Arcturus Therapeutics, ImmunoScape, CellCarta, Avalia, Moderna, Fortress and Repertoire. L.J.I. has filed for patent protection for various aspects of T cell epitope and vaccine design work. The other authors declare that they have no competing interests.

Data and materials availability: The sequences generated in this study have been deposited in GenBank under accession numbers OM286905, OM287123, and OM287553. All data needed to evaluate the conclusions in the paper are present in the paper or the Supplementary Materials.

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