A poxvirus model reveals general correlates of antigen presentation and immunogenicity for viral CD8 ⁺ T cell epitopes

CD8⁺ T cells are essential effectors in antiviral immunity that kill infected cells displaying viral peptide epitopes on major histocompatibility complex class I (MHC I). The pathways underpinning antigen presentation on MHC I are well known, but we lack a quantitative understanding of the relationships between source proteins and presented epitopes and how these relate to immunogenicity. We used mass spectrometry to interrogate vaccinia virus infection to reveal that up to 90% of epitopes were presented as fast as their source proteins were translated, but that protein amounts failed to correlate with epitope levels. Unexpectedly, epitope levels on infected cells also failed to correlate with immunogenicity. However, by extending our analysis to produce the first measurements of viral epitope levels from infected mice, we found a significant but moderate correlation with immunogenicity. These data provide empirical evidence for and against several associations that to date have been assumed or are not well resolved.