title: HCV RNA measurement in samples with diverse genotypes using versions 1 and 2 of the Roche COBAS® AmpliPrep/COBAS® TaqMan® HCV test.
abstract: BACKGROUND
  Accurate HCV RNA measurement is required for monitoring treatment. Underquantification has been reported with some genotypes, particularly genotype 4, using version 1 of the Roche COBAS(®) AmpliPrep/COBAS(®) TaqMan(®) HCV Test.
  
  
  OBJECTIVE
  Compare the viral loads of clinical specimens representing diverse genotypes from across the United States using versions 1 (V1) and 2 (V2) of the Roche COBAS(®) AmpliPrep/COBAS(®) TaqMan(®) HCV Test. Assess the frequency of nt145 and nt165 variants in the 5' UTR associated with detection failures and underquantification in a large clinical sample database.
  
  
  METHODS
  Three hundred archived clinical samples were measured using V1 and V2. Bland-Altman analysis was performed on log-transformed results and compared by genotype. The frequencies of nt145 and nt165 variants from 15,817 sequences were calculated.
  
  
  RESULTS
  On average, V2 results were 0.16 logIU/mL lower than V1 results. The average genotype 4 sample was 0.08 logIU/mL higher in V1 than V2. The largest individual sample differences were -2.10 (genotype 2b) and 1.57 (genotype 2a) logIU/mL. For genotype 4 samples, the greatest underquantification by V1 was 1.46 logIU/mL. There were 13 (0.082%) variants at nt145 and 24 variants at nt165 (0.152%), including one sequence with variants at both positions (0.0063%).
  
  
  CONCLUSIONS
  Genotype 4 samples from the U.S. are rarely underquantified and not disproportionately so compared to other genotypes using the COBAS(®) AmpliPrep/COBAS(®) TaqMan(®) HCV Tests. Variants at the nt145 and nt165 positions are uncommon in the U.S. and double variants are exceedingly rare. Underquantification of HCV samples with the V1 assay is likely a very rare occurrence in U.S.
authors.affiliation: ARUP Institute for Clinical and Experimental Pathology(®), 500 Chipeta Way, Salt Lake City, UT 84108, USA. Electronic address: michael.pyne@aruplab.com.
authors.forename: Michael T
authors.initials: MT
authors.lastname: Pyne
authors.affiliation: ARUP Institute for Clinical and Experimental Pathology(®), 500 Chipeta Way, Salt Lake City, UT 84108, USA.
authors.forename: Melanie
authors.initials: M
authors.lastname: Mallory
authors.affiliation: ARUP Institute for Clinical and Experimental Pathology(®), 500 Chipeta Way, Salt Lake City, UT 84108, USA; University of Utah Department of Pathology, 15 N Medical Drive East, Salt Lake City, UT 84112, USA.
authors.forename: David R
authors.initials: DR
authors.lastname: Hillyard
mesh_terms: D020121:5' Untranslated Regions; D005838:Genotype; D016174:Hepacivirus / Q000235:genetics / Q000302:isolation & purification*; D006526:Hepatitis C / Q000821:virology*; D006801:Humans; D007159:Immunologic Tests / Q000379:methods; D025202:Molecular Diagnostic Techniques; D021141:Nucleic Acid Amplification Techniques; D012367:RNA, Viral / Q000097:blood* / Q000235:genetics; D012680:Sensitivity and Specificity; D014481:United States; D019562:Viral Load
chemical_list: D020121:5' Untranslated Regions; D012367:RNA, Viral
keywords: Genotype; Hepatitis C virus; RNA; Viral load