Experimental and mathematical insights on the competition between poliovirus and a defective interfering genome

During replication, RNA virus populations accumulate genome alterations, such as mutations and deletions. The interactions between individual variants within the population can determine the fitness of the virus and, thus, the outcome of infection. We developed an ordinary differential equation model to infer the effect of the interaction between defective interfering (DI) replicons and wild-type (WT) poliovirus. We measure production of RNA and viral particles during a single infection cycle, and use these data to infer model parameters. We find that DI replicates faster than WT, but an equilibrium is established when both WT and DI compete for resources needed for RNA replication and genome encapsidation. In the presence of DI, the concentration of WT virions at cell lysis is suppressed by the factor of 5. Multiple generations within a single cell infection provide opportunities for significant inhibition of WT replication by competition with the faster replicating DI genomes.