Hepatitis C Virus: Hepatitis C virus (HCV) genotyping is reported to be the primary tool for assessing the course of infection and determining treatment duration. Several molecular methods targeting different HCV genomic regions have been described for determining genotype. Most commercial methods target the 5′ untranslated region (5′UTR), which is the region of choice for qualitative and quantitative HCV RNA detection because of its high degree of conservation among different subtypes In addition, accurate subtyping may be important for future studies aiming to develop new drugs and to increase our understanding of how HCV becomes resistant to therapies. The determination of the infecting genotype is however important for the prediction of response to antiviral treatment: genotype 1 is generally associated with a poor response to interferon alone, whereas genotypes 2 and 3 are associated with more favorable responses. The current gold standard of therapy – pegylated interferon- in combination with ribavirin – significantly improves response for all genotypes


Methodology: Taqman Real time PCR assay

Clinical Use:

  • Identify HCV genotype (1-4) for epidemiologic and prognostic purposes
  • Determine whether to begin antiviral therapy in patients with chronic hepatitis C virus (HCV) infection
  • Assess need for liver biopsy
  • Determine duration and dosage of treatment
  • Predict and monitor response to therapy


  • Injection-drug abusers
  • All pregnant women
  • Men who have sex with men
  • Persons who are sources for exposures (needle-stick, sexual assault)
  • Persons with elevated ALT/AST of unknown etiology
  • Persons needing immunosuppressive therapy (transplant, rheumatology and gastroenterology)
  • HIV-positive persons


HCV RNA PCR quantitative test – monitor effectiveness of treatment and perform when treatment is complete

  • Monthly until week 12 of treatment
  • Negative result confirms treatment success
Performed:  Every day
Reported: 2-3 days

Specimen Required: Blood, serum, plasma, Collect in: Lavender (EDTA), pink (K2EDTA), or serum separator tube. Stability collection to initiation of testing On Cells: Ambient: 4 hours; after separation from cells: Refrigerated: 48 hours; Frozen at -20°C: 72 hours; Frozen at -70°C: 4 months. Do not thaw avoid repeated freezing and thawing

Specimen Preparation: Separate serum or plasma from cells within 24 hours.


Storage/Transport Temperature: Frozen-20 0C. Refrigerate specimens at 2°C-4°C.

Unacceptable Conditions
:  Heparinized specimens, Hemolysis sample, Quantity not sufficient for analysis, specimen grossly contaminated, specimen too old, frozen whole blood specimen, specimen leaky or tube broken.


Interpretation: This test can detect 4 genotypes of HCV based on genetic differences in the HCV genome the genotype are 1,2,3,4. With new therapies, length of treatment varies based on genotyping. Hepatitis C Virus RNA genotyping can detect over the linear range 40-107 IU/mL. However this does not mean that lower copies or higher copies cannot be detected. The lower copies can be detected in some cases. This is a limitation of the currently available extraction systems. The test is intended for use in conjunction with clinical presentation and other markers as an aid in assessing viral response to antiviral treatment as measured by change in HCV RNA genotyping levels. The determination of the infecting genotype is however important for the prediction of response to antiviral treatment. Hepatitis C virus type 1 and type 4 infections may be associated with more severe disease and decreased responsiveness to therapy. In addition, types 2 and 3 may be treated with shorter durations of therapy. A negative result does not preclude the presence of HCV infection because results depend on adequate/proper patient sample storage and transportation as RNA is fragile and thermo labile, absence of inhibitors and sufficient RNA to be detected.

The result of this test must always be correlated with clinical status and history of the patient and other relevant data and   should not be used alone for the interpretation.                           

Note: The test is intended for use in conjunction with clinical presentation and other laboratory markers as an indicator of disease prognosis.  This test is also used as an aid in assessing viral response to antiretroviral treatment as measured by changes in HCV RNA levels in genotyping.

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