For each animal, the sequenced clones for all samples (A), plasma only (B), or CSF only (C) were aligned (BioEdit) and a distance matrix was calculated (Mega, 3.0). The means of these distances for each time is plotted versus time for Group A: 1/04L, 1/28Q, 1/42N, Group B: 1/02N, 1/52N, 1/56L, and Group C: 2/02P, 2/31P, 2/AC42 to show the overall diversity of clones within each macaque including all times. Standard errors are indicated for each animal. Statistical differences in diversity between Groups were calculated by student’s T-test(Noel, Jr. et al, 2006;Noel, Jr. & Kumar, 2006). A value of 0.05 was set as the level of significance.