Table 1.
Influenza samples over four seasons within two household transmission studies.
Fig 1.
Genetic diversity of specimens.
(A) histogram of iSNV frequency. (B) histogram of number of iSNVs per specimen. (C) scatter plot of iSNV frequency between sample replicates. (D) density plot of iSNV frequency of synonymous and non-synonymous mutations.
Table 2.
Transmission pair characteristics.
Fig 2.
Shared iSNV and clonal distribution.
(A) Shared genetic diversity between transmission pairs. Each point is an iSNV within a transmission pair. iSNVs are based on within host consensus sequence (≥ 50% frequency) and numerical corrections account for differences in between-pair consensus base at a particular locus. Details of numerical corrections applied can be found in Methods. (B) Distribution of number of clonal differences between transmission pair members for the overall study population.
Fig 3.
Bottleneck size with sample size overall and by metadata factors.
Bottleneck estimates for overall population and by host/viral factors (year, subtype, age, sex, and vaccination status). Overall population and subgroup analysis bottleneck estimates were calculated with independent distributions (clonal method) or a weighted averaging method (iSNV method). Additional details on bottleneck estimation method can be found in Methods. Purple bars represent estimates found using clonal model and blue bars represent estimates found using beta-binomial model (in all cases, 1). Host factors are listed in format of X/Y with X representing donor factor and Y representing recipient factor. “A” stands for adult. “C” stands for child. “M” stands for male. “F” stands for female. “V” stands for vaccinated. “U” stands for unvaccinated or unknown vaccination status. 95% confidence intervals are shown by black error bars.