Figure 1.

Individual phylogenetic tree of HIV-1 V3 amino acid sequences from Pt.1. Proviral quasispecies harboured by monocytes (red circle = CD36-provirus) and T lymphocytes (green circle = CD26-provirus) of Pt.1 were analyzed after long term suppression of viremia. Nucleotide sequences obtained by ultra-deep pyrosequencing were translated in amino acid sequences and filtered through the correction algorithm described in the Material and Methods section. Unique sequences for each sample type were used to build phylogenetic trees with the neighbour-joining method. Bootstrap values ≥ 80% are shown. The cellular sources of proviral and viral sequences are indicated by coloured bullets. Sample type-specific cluster with bootstrap values ≥ 80% are encircled with the corresponding colours. PSSM score was calculated for each of these clusters, and the corresponding values are included in the insert, together with their relative abundance in the corresponding sample type. Bars indicate p distance scale.