Models of RNA virus evolution and their roles in vaccine design

Ojosnegros, Samuel; Beerenwinkel, Niko

Molecular profiling techniques, including DNA sequencing, have produced an enormous amount of data on viral spread, genetic diversity, and infection dynamics. The integration and analysis of these data can provide valuable information on the evolution of viral pathogens. Mathematical, statistical, and computational methods are necessary to deal with those large data sets and to predict phenotypes form genetic data that ultimately can be used in vaccine development. In this review, we summarize some computational and mathematical techniques that play a critical role in understanding viral evolution and vaccine design. Specifically, we discuss phylogenetic methods for vaccine strain selection, statistical models of evolutionary escape from selective immune pressure, and virus dynamics models for therapeutic vaccines and attenuation strategies. Our major examples are Influenza, human immunodeficiency virus (HIV), and foot-and-mouth disease virus (FMDV). They are all RNA viruses of great medical or veterinary importance and have been studied extensively.