Optimal viral immune surveillance evasion strategies

Following cell entry, viruses can be detected by cytotoxic T lymphocytes. These cytotoxic T lymphocytes can induce host cell apoptosis and prevent the propagation of the virus. Viruses with fewer epitopes have a higher survival probability, and are selected through evolution. However, mutations have a fitness cost and on evolutionary periods viruses maintain some epitopes. The number of epitopes in each viral protein is a balance between the selective advantage of having fewer epitopes and the reduced fitness following the epitope removing mutations. We discuss a bioinformatic analysis of the number of epitopes in various viral proteins and propose an optimization framework to explain these numbers. We show, using a genomic analysis and a theoretical optimization framework, that a critical factor affecting the number of presented epitopes is the expression stage in the viral life cycle of the gene coding for the protein. The early expression of epitopes can lead to the destruction of the host cell before budding can take place. We show that a lower number of epitopes is expected in early proteins even if late proteins have a much higher copy number.