Master of Science
A deterministic model is developed of the within-host dynamics of a budding virus, and coupled with a detailed life-history model using a branching process approach to follow the fate of de novo beneficial mutations affecting five life-history traits: clearance, attachment, eclipse, budding, and cell death. Although the model can be generalized for any given budding virus, our work was done with a major emphasis on the early stages of infection with influenza A virus in human populations. The branching process was then interleaved with a stochastic process describing the disease transmission of this virus. These techniques allowed us to predict that mutations affecting clearance and cell death rate, two adaptive changes in influenza A's life-history traits, are most likely to persist for small selective advantage (s<0.08) when rare. These results also show that the overall adaptability of the virus is much higher than classically predicted, and that the period of growth between bottlenecks has a greater impact on increasing survival probability relative to the impact of bottlenecks, which is consistent with previous work.
Reid, Jennifer NS, "The survival probability of beneficial de novo mutations in budding viruses, with an emphasis on influenza A viral dynamics" (2016). Electronic Thesis and Dissertation Repository. 3901.