Quantification of genomic RNA and reverse transcription intermediates in cells infected with NL4.3, PKI-NL4.3 or H89-NL4.3 viruses. MAGIC-5B cells were infected with normalized amounts of NL4.3, PKI-NL4.3 or H89-NL4.3. Levels of genomic RNA (A) or (-)ssDNA or second strand transfer cDNA (B) in the infected cells were monitored by qRT-PCR or qPCR respectively. Control experiments consisted of mock infected cells (-) or NL4.3 infected cells maintained in the presence of 10 μM AZT. Values are expressed as percentage of NL4.3 conditions ± SD. Specificity of qRT-PCR detection of genomic RNA was controlled by preincubation of the cells for 30 min at 37°C in the presence of 1 μg/ml T20 fusion inhibitor before virus exposure.