Models of RNA virus evolution and their roles in vaccine design

Ojosnegros, Samuel; Beerenwinkel, Niko

Viral evolution and the genetic diversity it produces are fundamental factors for the success of vaccine candidates, because immune responses need to be stimulated against a potentially very broad spectrum of existing viruses and new viral immune escape variants are likely to be generated. Mathematical modeling of viral evolutionary dynamics will therefore play an increasingly important role in vaccine design. It can identify genomic regions that are under selective pressure, support the selection or construction of vaccine strains, predict evolutionary escape from immune pressure, guide vaccination campaigns, estimate the effect of therapeutic vaccines, and support the design of new attenuation strategies. Most of our discussion has been in the context of RNA viruses and many issues are most pronounced for this class of viruses. Nevertheless, we expect most statistical models and computational methods to be applicable to other viruses and different pathogens, too. On the other hand, the distinct evolutionary dynamics of influenza A and HIV-1, two of the most widely studied RNA viruses, have highlighted the need for careful analysis of viral infection dynamics within and among individuals.