I need to distinguish HIV integrated DNA, from HIV unintegrated and HIV-mRNA. For the first 2 ALU-LTR PCR works well and shouldn't be a problem because mRNA can't be detected without RT reaction, so basically doing 2 independent reactions the problem is solved.

The problem is that for my experiment flowchart, I can't take the sample before cDNA reaction (RT) is done... so I had already the mRNA transformed into cDNA...

My only doubt is if HIV-mRNA had ALU elements within or not, if not, theres no problem to use ALU, but in case the ALU elements are present in HIV-mRNA, I will not be able to distinguish from mRNA and integrated DNA.

Greetings

Gibran Horemheb