This figure mimics the format of the second figure of Poon et al (2016) and shows that our re-analysis recapitulates the main reported results of high-frequency shared genetic diversity between epidemiologically unrelated individuals. (A) Viral genetic diversity at hemagglutinin codon 335 in H3N2 human influenza infections. At this codon, both variants encode the same amino acid. This plot shows within-host variants that were present at a frequency of at least 1% in both sequencing replicates at sites with minimum sequencing coverage of 200 reads. Shaded regions indicate individuals from the same household. (B) Viral genetic diversity in the HA1 domain of hemagglutinin in H3N2 human influenza infections in our re-analysis. Each panel represents a separate site in the genome and is labeled by the codon it represents. Sites shown harbored within-host variation at a frequency of at least 3% in both sequencing replicates for at least two samples in the study.