Fig. 5.

Origin of Identical P6–PR–RT sequences. Identical subgenomic P6–PR–RT sequences observed during ART can be originate from multiple mechanisms including (Top) genetic bottleneck of multiple viruses during selection of drug resistance, (Middle) immune pressure (i.e., CTL/antibody) driving persistence of select proviruses, and (Bottom) clonal expansion of cells containing a provirus with identical integration site and sequence. Hypothetical integration sites and proviral deletions are shown. Reconstruction of the replication-competent ancestor resulting in sequences in red triangles is also shown.