Most viral peptides displayed by class I MHC on infected cells are immunogenic

Significance CD8+ T cells are key to the defense of animals against virus infection. These immune cells recognize peptides derived from viral proteins that are displayed on the surface of infected cells in a complex with host proteins known as MHC I. Many viral peptides are displayed by MHC I on infected cells, but it has never been shown what fraction of these can induce an immune response. We answered this long-standing question, finding that more than 80% of vaccinia virus peptides presented by MHC I on infected mouse cells were immunogenic across a population of mice. CD8+ T cells are essential effectors in antiviral immunity, recognizing short virus-derived peptides presented by MHC class I (pMHCI) on the surface of infected cells. However, the fraction of viral pMHCI on infected cells that are immunogenic has not been shown for any virus. To approach this fundamental question, we used peptide sequencing by high-resolution mass spectrometry to identify more than 170 vaccinia virus pMHCI presented on infected mouse cells. Next, we screened each peptide for immunogenicity in multiple virus-infected mice, revealing a wide range of immunogenicities. A surprisingly high fraction (>80%) of pMHCI were immunogenic in at least one infected mouse, and nearly 40% were immunogenic across more than half of the mice screened. The high number of peptides found to be immunogenic and the distribution of responses across mice give us insight into the specificity of antiviral CD8+ T cell responses.