UCSF

In this dissertation, we aim to explore the mechanisms that drive virus evolution and how the dynamics of that evolutionary process reveal the underlying molecular basis for adaptation. In Part I, we present an experimental and computational approach that enables the use of next-generation sequencing technology to describe the genetic composition of virus populations with unprecedented accuracy. Using this approach, we define the mutation rates of poliovirus and uncover the mutation landscape of the population. Further, by monitoring changes in variant frequencies on serially passaged populations, we determined fitness values for thousands of mutations across the viral genome. Mapping of these fitness values onto three-dimensional structures of viral proteins offers a powerful approach for exploring structure-function relationships and potentially uncovering novel functions. Our study provides the first single-nucleotide fitness landscape of an evolving RNA virus and establishes a general experimental platform for studying the genetic changes underlying the evolution of virus populations. In Part II, we examine the effects of recombination on viral fitness and pathogenesis. We isolate a recombination-deficient poliovirus variant and find that, while recombination is detrimental for virus replication in tissue culture, it plays a critical role in the outcome of infection in animals. Notably, recombination defective virus exhibits severe attenuation following intravenous inoculation, which is associated with a significant reduction in population size resulting from bottlenecking during intra-host spread. Because the impact of high mutational loads manifests most strongly at small population sizes, our data suggests that the repair of mutagenized genomes is an essential function of recombination, reducing the burden of high mutational loads in virus populations, and may drive the long-term maintenance of recombination in viral species despite its associated fitness costs.