Distributions of pairwise sequence distance for sequence pairs drawn from the same patient (intrapatient) or from different patients (interpatients), and for sequence pairs of polyphyletic origin from putative superinfected patients. The distribution of the distances for 80.000 randomly chosen sequence pairs of different patients is shown in red. Intrapatient sequence distances are shown in blue (truncated above 200 to optimize the scale for comparison). The green overlaid histogram depicts polyphyletic sequence pairs from potentially superinfected patients (identified from the initial phylogenetic analysis). There is no clear cutoff for the distribution of intrapatient distances.