Figure 6

Estimation of days since infection based on Hamming distance distribution. The Hamming distance (HD₀) distribution (multiplied by the number of sampled sequences) from the founder nef strain, SIVmac239, is shown for each sequence sample from each animal (black boxes) with the best fitting Poisson distribution (red lines). The goodness-of-fit p value of each fit is listed in Table 1. The bottom right corner panel shows a comparison between actual days post infection and the estimated days since infection based on HD₀ distribution for animals r00065 (black) and r00098 (blue). The correlation coefficient between the actual and estimated dates post-infection for r00065 is -0.91 and for r98018 is 0.47.