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Hepatitis C Quantitative PCR

Hepatitis C virus is a single stranded RNA virus. Hepatitis C virus (HCV) is a major cause of chronic liver disease in the United States. Approximately 4 million people in the United States are currently infected. Of those known to be infected, 2.7 million have chronic liver disease. An estimated 40,000 new infections are suspected each year. Of the six different HCV genotypes, genotype 1 is most common, followed by 2 and 3.

The initial test for hepatitis C (HCV) infection is an immunoassay that detects antibodies to multiple HCV proteins. Supplemental or confirmatory testing is recommended for all reactive HCV antibody tests to determine the presence of active infection. Detection of HCV RNA in the blood by polymerase chain reaction (PCR) is indicative of active infection. PCR testing has been available since September 1995. In this assay, a DNA copy of viral RNA is synthesized by reverse transcription. This DNA molecule is amplified millions of times by PCR.  Because of its high sensitivity, PCR can detect HCV infection much sooner than antibody tests. Most patients have detectable levels of HCV RNA in plasma within 1 to 2 weeks of exposure.  HCV RNA detection precedes ALT elevation by 10 to 12 weeks and seroconversion by 10 to 24 weeks. The highest levels of circulating viral RNA are found during the early course of infection, suggesting that patients are most infectious during this time. Variation among HCV genotypes is less likely to affect PCR test performance than antibody tests, because PCR primers are based on the highly conserved untranslated region of the HCV genome. 

Once HCV infection has been established, quantitative HCV PCR (viral load) can provide prognostic information. Predictors of response to antiviral therapy include viral load of less than 2,000,000 IU/mL, genotype other than 1, shorter duration of infection, female gender, and low body weight. The HCV positive patient with negative viral load should have the test repeated in 3 to 4 months, because some patients with active infection have intermittently undetectable viral loads.

Direct-acting antivirals (DAAs) are oral drugs that are used in combination to target multiple phases of the HCV life cycle. DAAs include inhibitors of the nonstructural 5B RNA polymerase, nonstructural 5A protein, and serine nonstructural 3/4A protease. Because of their high rates of viral eradication and excellent safety profile, current guidelines recommend treatment of all persons infected with HCV unless their life expectancy is less than 1 year due to non–HCV-comorbidities.The goal of therapy is to cure HCV infection to prevent cirrhosis, liver decompensation, hepatocellular carcinoma and death. Recommended duration of treatment is 8 to 12 weeks.

Cure is defined as a sustained viral response, which means undetectable HCV RNA using a sensitive PCR assay with a lower limit of detection (LOD) and lower limit of quantitation (LOQ) of 15 IU/mL. Up to date guidelines can be found at

If detectable HCV RNA returns within 12 weeks of treatment discontinuation it is considered a relapse, and treatment-emergent resistance to some or all of the drugs in the failed treatment regimen is likely. Although relapse after SVR at 12 weeks is rare (<2  in 1000 patients), guidelines recommend confirming SVR 24 to 48 weeks after therapy. More often, viremia after SVR at 12 weeks represents reinfection due to new exposure.

Samples having no HCV target detected are reported as ‘not detected.’ Samples having detectable and quantifiable HCV target are reported as the numeric value up to 200 million IU/mL. The unit of measurement for the Hepatitis C Virus RNA changed from copies/mL to IU/mL in March 2001.

Specimen requirement for HCV Quantitative PCR is 2 to 4mL of serum or EDTA plasma. Tubes containing heparin cannot be used. Specimen must be centrifuged for 18 to 20 minutes and separated from the cells within 6 hours of draw.


Marks K and Naggie S. Management of Hepatitis C in 2019. JAMA 2019;322:355-56.

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