I want to amlify HIV-1 partial pol gene(1036bp) for further sequencing.I extract RNA from plasma of positive patient using Favorgen total viral nucleic acid extraction kit and further converted to cDNA using Thermoscientic Kit.I run GAPDH as a control for cDNA synthesis.The problem is that am getting a proper band for GAPDH but smears for viral gene.The same problem happen even amplifying Proviral DNA.

I would appreciate if any research fellow researcher share their experience of working with HIV-1?