Evolution of provirus environment of clones with increasing abundance in long term infected animals.

<p><b>A.</b> Proviral load in long-term infected animals (i.e. infected for more than 2 years). Median is indicated by the horizontal black line. <b>B.</b> Oligoclonality index in the long-term infected animals. Median is indicated by the horizontal black line. <b>C.</b> The pie-charts depict the distribution of clone abundance for each animal. The size of each slice in the pie-charts represents the relative abundance of each BLV-infected clone. Note that although the gray tones are identical between different animals, the clones are different. <b>D.</b> Genomic heat map of integration preferences compared to the distribution observed in the lowest abundance clones (clone abundance less than 1 cell per 1000 PBMCs). Genomic features analyzed are shown to the left of the heat map. Gene and CpG proximity was calculated with a genomic interval of 50 kb. An interval of 5 kb was used for interspersed repeats. For each genomic feature, the integration frequency was examined for clones having a given abundance as shown at the top of the heat map. A colored scale is shown along the right hand side of the panel with increasing shades of blue indicating depletion compared to the distribution of the lowest abundance clones and increasing shades of red indicating enrichment. In the column at the highest clone abundance (clone abundance more than 50 cells per 1000 PBMCs), p-values are calculated by Chi-squared test for trend and show significance of the increasing or decreasing trend from the smallest clones. Data are representative for all 7 animals.