Viruses Selectively Hide CD8 T Cell Epitopes. (132.7)

Abstract

Abstract Viruses employ various means to evade immune detection. One common evasion strategy is the removal of CD8 cytotoxic T-lymphocyte (CTL) epitopes. We here use a combination of multiple bioinformatic tools and large amount of genomic data to compute the epitope repertoire presented by over 1,300 viruses in multiple HLA alleles. We define the "Size of Immune Repertoire (SIR) score," which represents the ratio between the epitope density within a protein and the expected density. We show that virusal proteins in general have a higher epitope density than human proteins. This difference is due to a good fit to the human MHC system to the typical amino acid usage of viruses. Among different viruses, viruses infecting humans present less epitopes than non-human viruses. This selection is not at the amino acid usage level, but through the removal of specific epitopes. Within a single virus, not all the proteins express the same epitopes density. Proteins expressed early in the viral life cycle have a lower epitope density than late proteins. Such a difference is not observed in non-human viruses, The targeting of the CTL immune response to viral late structural and enzyme proteins, allow the virus time interval to propagate before its host cells are destroyed by CTLs.