Figure 5.

H1N1 and H7N9 transmission bottlenecks in ferret donor–recipient pairs. (A) ‘TV plots’ showing intersection iSNV frequencies in all eleven donor–recipient pairs. The inset box highlights low-frequency iSNVs (1–10 per cent). Colors denote virus groups. The plot uses the first time point at which the virus became detectable in the recipient (y axis) and the time point preceding such detection for the donor (x axis). (B) Maximum likelihood estimates for mean transmission bottleneck size with 95 per cent CI in individual donor–recipient pairs. Bottleneck sizes could not be estimated for two pairs (rGD/3 pair 9 and pair 11) because there were no polymorphic sites detected in the donor. The mean H1N1 estimate was calculated using Pairs 3, 4, 5, and 6. The mean H7N9 estimate was calculated using Pairs 1, 2, 7, 8, and 10.