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Bioinformatics 2009 25(12):i39-i44; doi:10.1093/bioinformatics/btp221
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Viruses selectively mutate their CD8+ T-cell epitopes—a large-scale immunomic analysis

Tal Vider-Shalit 1, Ronit Sarid 2, Kobi Maman 1, Lea Tsaban 1, Ran Levi and Yoram Louzoun 1,2,*

1Department of Mathematics and Gonda Brain Research Center, Bar Ilan University, Ramat Gan 52900, Israel and 2The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan 52900, Israel

*To whom correspondence should be addressed.


  Abstract

Motivation: Viruses employ various means to evade immune detection. One common evasion strategy is the removal of CD8+cytotoxic T-lymphocyte epitopes. We here use a combination of multiple bioinformatic tools and large amount of genomic data to compute the epitope repertoire presented by over 1300 viruses in many HLA alleles. We define the ‘Size of Immune Repertoire score’, which represents the ratio between the epitope density within a protein and the expected density. This score is used to study viral immune evasion.

Results: We show that viral proteins in general have a higher epitope density than human proteins. This difference is due to a good fit of the human MHC molecules 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 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 removal of early epitopes and the targeting of the cellular immune response to late viral proteins, allow the virus a time interval to propagate before its host cells are destroyed by T cells.

Contact: louzouy{at}math.biu.ac.il


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