Latency detection in HIV-1 phylogenies. To avoid effects of selection, only 3rd codon DNA positions were used for phylogenetic reconstruction and latency detection. Latency was detected in an untreated patient (K-G), an elite suppressor (O-9), a successfully treated patient (B-139), and in a patient with failed treatment (M-105). These are representative patients of each group in Table 1. All 26 patient trees are shown in the online supplementary materials (Additional file 1: Figure S1). Taxa are labeled P for plasma-derived virus and R for resting CD4+ T cell pro-virus. Filled symbols indicate significant reduction in genetic distance (circles p < 0.05; squares p < 0.01; triangles p < 0.001). Crossed circles indicate potential recombinants, omitted from latency detection. Unlabelled ingroup taxa indicate additional sequences from neither plasma nor resting cells. Color indicates time since 1st sample of patient. Patient K-G was rooted at 1st sample close to PHI (unlabeled taxa), and the other patients were rooted by an outgroup (HIV-1 HXB2, unlabelled). The circled numbers are observations of interest discussed in the text.