Identification of mouse CD4+ T cell epitopes in SARS-CoV-2 BA.1 spike and nucleocapsid for use in peptide:MHCII tetramers

Bricio Moreno, L.; Barreto de Albuquerque, J.; Neary, J. M.; Nguyen, T.; Hastie, K. M.; Landeras-Bueno, S.; Hariharan, C.; Nathan, A.; Getz, M. A.; Gayton, A. C.; Khatri, A.; Gaiha, G. D.; Saphire, E. O.; Luster, A. D.; Moon, J. J.

doi:10.1101/2023.11.16.566918

bioRxiv · 10.1101/2023.11.16.566918

Identification of mouse CD4+ T cell epitopes in SARS-CoV-2 BA.1 spike and nucleocapsid for use in peptide:MHCII tetramers

Bricio Moreno, L.·Barreto de Albuquerque, J.·Neary, J. M.·Nguyen, T.·Hastie, K. M.·Landeras-Bueno, S.·Hariharan, C.·Nathan, A.·Getz, M. A.·Gayton, A. C.·Khatri, A.·Gaiha, G. D.·Saphire, E. O.·Luster, A. D.·Moon, J. J.

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Abstract

Understanding adaptive immunity against SARS-CoV-2 is a major requisite for the development of effective vaccines and treatments for COVID-19. CD4+ T cells play an integral role in this process primarily by generating antiviral cytokines and providing help to antibody-producing B cells. To empower detailed studies of SARS-CoV-2-specific CD4+ T cell responses in mouse models, we comprehensively mapped I-Ab-restricted epitopes for the spike and nucleocapsid proteins of the BA.1 variant of concern via IFN{gamma} ELISpot assay. This was followed by the generation of corresponding peptide:MHCII tetramer reagents to directly stain epitope-specific T cells. Using this rigorous validation strategy, we identified 6 reliably immunogenic epitopes in spike and 3 in nucleocapsid, all of which are conserved in the ancestral Wuhan strain. We also validated a previously identified epitope from Wuhan that is absent in BA.1. These epitopes and tetramers will be invaluable tools for SARS-CoV-2 antigen-specific CD4+ T cell studies in mice.

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Bricio Moreno, L., Barreto de Albuquerque, J., Neary, J. M., Nguyen, T., Hastie, K. M., Landeras-Bueno, S., Hariharan, C., Nathan, A., Getz, M. A., Gayton, A. C., Khatri, A., Gaiha, G. D., Saphire, E. O., Luster, A. D., Moon, J. J.. 2023-11-17. Identification of mouse CD4+ T cell epitopes in SARS-CoV-2 BA.1 spike and nucleocapsid for use in peptide:MHCII tetramers. https://doi.org/10.1101/2023.11.16.566918

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