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Direct detection of hepatitis C virus (HCV) RNA in serum or plasma is useful for validating the performance of anti-HCV assays and for the discrimination of persons with persistent HCV infections from those with resolved infections. Quantitation of HCV RNA may also be useful for disease prognosis and therapeutic monitoring. Previous studies have reported detection of HCV RNA in 50 to 70 percent of blood donors who were positive on anti-HCV supplemental tests. There is concern that specimen processing and storage conditions might influence the stability, and hence the detectability, of HCV RNA. To address this concern, the rate of detection of HCV RNA by the polymerase chain reaction (PCR) using donor pilot tube sera (PTS) previously subjected to routine donor screening and supplemental testing was compared with HCV PCR results obtained with fresh-frozen plasma (FFP) derived from the same donations. All 16 anti-HCV supplemental test-positive donations evaluated were HCV RNA positive with FFP, whereas only 10 (62.5%) were positive with PTS (p = 0.024). None of 11 FFP or PTS samples from HCV enzyme immunoassay-reactive donations not confirmed by supplemental anti-HCV assays tested positive for HCV RNA. Direct comparison of sample type (serum vs. plasma) and various storage conditions using specimens from two seropositive donors showed that room-temperature storage results in marked reduction in HCV RNA signal, while replicate freezing and thawing caused a moderate reduction. These data indicate that well-controlled sample processing and storage conditions are critical to the sensitive and potentially quantitative analysis of HCV RNA.