Fig. 3. Population dynamics across the EV-A71 genotype network.

(A) The distribution of genotypes across the mutational network of EV-A71 across passages. The color indicates the relative frequency of genotypes within the population at each passage. The size represents the number of cells infected with that genotype. The “modal genotype,” or the most common genotype, is labeled. By P5, the modal sequence has shifted five mutations from the original modal sequence. (B) Plot showing the genetic distance of genotypes in the population relative to the modal sequence. (C) Violin plot and boxplot showing the distribution, mean, and median mutations per genome relative to the P1 modal genotype. Point indicates mean mutations per genome, and box shows the median and interquartile range of the population. (D) A genotype frequency plot showing the distribution and dynamics of specific genotypes in the population over passage. Major genotypes in the network are highlighted, and their relationship is shown in the subway map representation of the major genotypes in the network.