Polymerase chain reaction assay for hepatitis C virus RNA using a single tube for reverse transcription and serial rounds of amplification with nested primer pairs.

A procedure is described for the detection of hepatitis C virus (HCV) RNA in blood by means of the polymerase chain reaction (PCR) in which the reverse transcription step and two rounds of amplification are carried out in a single tube. This results in fewer manipulations, reduced risk of contamination, and economy of time. The procedures are generally applicable to other assays based on the PCR. We describe the preparation (from 100 microL serum) of test samples that remain stable for at least 6 days under specified conditions and an assay that employs nested primer pairs homologous to conserved sequences in the 5' noncoding region. The method was tested on 107 sera from the United States and Japan. Correlation with first-generation anti-HCV was 77%. Two sets of nested primer pairs homologous to sequences in the 5' noncoding region and one set based on structural region sequences showed differences in their reactivities with serum HCV RNA. The recommended single tube procedure specified a primer for reverse transcription that was conserved in all reported HCV genomes but absent from pestivirus genomic sequences. The effects of preanalytical factors on the detection of HCV RNA were studied. Qualitatively, there was no change in the HCV RNA-positivity of sera that were exposed to room temperature for 24 hours. Quantitative studies showed a decrease in titer in some specimens. Three cycles of freeze-thawing had no detectable effects on the titers of HCV RNA.