Fig. 3.

The persistence of barcode lineages indicates immune escape. (A) The number of observed barcodes at each time of sampling is shown for animals 25611 (cyan) and 7811 (pink). (B) The fraction of barcode lineages harboring Tat-SL8 escape mutations (at frequencies exceeding the limit of detection for linkage of our assay) at each time point is shown for each animal. (C and D) The number of barcode lineages harboring any escape mutations (black lines) and specific escape mutations (colored lines, with protein sequences shown in the key) at each time point is shown for animal 25611 (C) and animal 7811 (D). Barcode lineages with escape mutations at frequencies below the limit of detection for linkage of our assay are excluded.