Genetic drift and purifying selection shape within-host influenza A virus populations during natural swine infections
Fig 5
Longitudinal dynamics of iSNVs in singly infected pigs.
(A) The number of iSNVs detected in each sample, plotted according to the number of days since that animal had its first PCR positive sample. Results are stratified by IAV lineage. (B) Changes in the frequency of synonymous (left) and non-synonymous (right) iSNVs, plotted according to the number of days between samples. iSNVs that were detected at both time points are shown in blue. iSNVs that were detected only in the first sample are shown in red. iSNVs that were detected only in the second sample are shown in yellow. (C) Cumulative distribution showing the proportion of iSNVs that persist between one day and the next with a frequency change that is less than or equal to the frequency change shown on the x-axis. Red line shows results from the swine data; the blue line shows results from humans IAV infections, as calculated from the data provided in [19]. For both datasets, we called iSNVs as present if found at frequencies of ≥3% and ≤97%.