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.

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.