Direct in situ reverse transcriptase-linked polymerase chain reaction with biotinylated primers for the detection of hepatitis C virus RNA in liver biopsies

To assess the presence and the cellular distribution of hepatitis C virus (HCV) RNA in the liver of 11 patients with confirmed HCV infection, a direct in situ reverse transcriptase-linked polymerase chain reaction (RT-PCR) method was performed on formalin-fixed and paraffin-embedded biopsies. The oligonucleotide primers used were specific to the 5′ non coding region. An unlabelled downstream oligonucleotide served as a primer for reverse transcription as well as PCR. The upstream oligonucleotide serving as a primer for PCR was biotinylated, allowing a direct enzymatic detection of PCR products. HCV infected cells revealed cytoplasmic staining mainly concentrated towards the interface of the nucleus and cytoplasm. Most of the stained cells were hepatocytes and sometimes Kupffer cells. The results were compared with those obtained by RT-PCR of RNA extracted from the corresponding tissue block. Extracted HCV RNA could be detected in liver tissues of nine out of 11 (82%) infected patients. The detection rate using in situ RT-PCR was 7/11 (63%). The use of labelled primers improved specificity of direct in situ methods, by preventing non-specific incorporation of labelled dNTPs into fragmented DNA. Further studies are however required in order to increase detection sensitivity of HCV infection by in situ molecular methods.