Modelling

Viral evolution was modelled over the time using an individual-based model. The model tracked the proportion of free virions of the wild-type virus Eng195, the resistant virus K229R + P653L and viruses containing a single mutation, K229R or P653L. The model was initialised with 10⁶ virions, a mix of K229R + P653L virus and Eng195 in the ratio 95:5, as in the inoculum, and assumes a well-mixed population with virions infecting cells randomly. Evolution of the virus was tracked over 20 generations of replication, with 10⁶ cells available for infection during each generation giving an average MOI of 1. Both the number of virions and the population of cells stayed constant between generations. We allowed for varying amounts of reassortment by adjusting the ratio of viruses to cells. During each replication cycle, each virion enters a random cell. The burst size from each cell was Poisson distributed, with mean proportional to the summed fitnesses of the virion(s) infecting that cell. As default, the mean burst size for a cell infected by 1 virion was 10 [39]. In the baseline model, Eng195, K229R, P653L and K229R + P653L were assigned a relative fitness, with default values equal to 1, 0.01, 1.25 and 1 respectively. Within a cell, new segments were produced with a probability equal to the proportion of founding virions in that cell. These segments were randomly combined into virions, allowing reassortment, assuming each virus RNA segment in the cell had an equal chance, unrelated to genotype, of being incorporated into progeny virus. Newly produced virions mutated either PB1 or PA with probability μ = 2 ×10⁻⁴ [1]. Excess virions were discarded randomly to maintain the viral population size.

For the model with mutation only, each cell produced whole virions for each strain, proportional to the founding virions for each strain in that cell. The newly produced virions were mutated as per above.

Code to reproduce model results can be found at https://github.com/ada-w-yan/reassortment/.