FIG 5.

Overall influenza A virus bottleneck size estimates and probabilities of variant transfer under these estimates. (A) The negative binomial probability density function (pdf) describing overall transmission bottleneck sizes across H1N1p and H3N2 viral subtypes, parameterized with MLE values of an r value of 4 and a p value of 0.980. Vertical black lines show the 95% range of this distribution. The MLE bottleneck size estimates for the H3N2 (orange) and H1N1 (green) transmission pairs are shown above the pdf. (B) Probability of a donor-identified variant being either transferred or identified (called) in the recipient host as a function of donor variant frequency. Probabilities of a donor variant being present in a recipient host are shown in purple, given bottleneck size estimates provided by the negative binomial distribution shown in panel A. Probabilities of donor-identified variants being called present in a recipient host, given these same bottleneck size estimates and the assumptions of the beta-binomial sampling models, are shown in gray. The empirical probabilities of donor-identified variants being called in a recipient, as calculated from the combined H1N1p and H3N2 data sets over 3% frequency bins, are shown in black.