Fig. 5.

High viral load is also associated with elevated recombination rate in Participant 1. A) Viral load trajectory over the number of days since estimated date of infection (EDI) for Participant 1. The background shading indicates the two groups (above the horizontal median line in orange and below the line in blue) that pairs of time points were divided into based on their average viral load. Each group contains approximately $\mathrm{6,000}$ LDMs. B) Curve fits representing the median estimates from each group’s corresponding bootstrap distribution (1,000 bootstraps) are overlaid on the binned average of the LDMs in the in vivo data for Participant 1 (moving average used for display purposes only, window size = 1,000 bp × generations). C) Recombination rate estimates for times with average viral load measurements above or below the median using only data from Participant 1. Each box indicates the interquartile range of the bootstrapped distribution of $\hat{\rho }$ for the given viral load group (1,000 Bootstraps). The median estimate is indicated via the central line. Identical analyses for Participants 3, 4, and 7 are shown in supplementary Fig. S15, Supplementary Material online.