Figure 2

Probe sequence detection during reverse transcription. Coloured bars spatially represent the nucleic acid sequence detected by each O-FISH probe. The pol probe (light green) detects positive sense viral genomic RNA until its degradation during minus strand DNA elongation and it also detects very late stage plus strand DNA synthesis (plus strand DNA elongation). The U5/PBS probe (light blue) detects the positive sense 5’ LTR section of the viral RNA genome and it also detects the plus strand strong stop (+sss) DNA that occurs immediately before the second strand transfer. The strong stop probe (purple) detects minus strand strong stop DNA, which is the first segment of DNA produced during reverse transcription and therefore detects all cDNA from early reverse transcription onwards. The gag probe (dark green) detects all cDNA from an intermediate point in reverse transcription (after minus strand DNA elongation) onwards. Figure adapted from Telesnitsky & Goff ²⁹.