title: Comparison of different HCV viral load and genotyping assays.
abstract: BACKGROUND
  We report an interlaboratory comparison of methods for the determination of hepatitis C virus (HCV) serum load and genotype between a recently, established molecular laboratory at the Alaska Native Medical Center (ANMC) and two independent laboratories using different assays. At ANMC, a Real-time quantitative RT-PCR amplification methodology (QPCR) has been developed in which HCV viral loads are determined by interpolation of QPCR results to those of standards calibrated to the World Health Organization (WHO) First International Standard for HCV. HCV genotype is subsequently determined by direct sequencing of the DNA fragment generated from the QPCR assay.
  
  
  OBJECTIVE
  The above methods were statistically compared to results obtained for the same patient sera by two independent laboratories using different commercially available viral load assays; Quantiplex HCV RNA (Bayer Diagnostics) and Amplicor HCV Monitor (v 2.0) (Roche Molecular Systems), as well as two different genotyping assays; restriction fragment length polymorphism (RFLP) and INNO-LiPA HCV II (Innogenetics).
  
  
  RESULTS
  ANMC's Real-time QPCR HCV viral load results compared moderately well with those obtained by the Quantiplex HCV RNA method (R2=0.3813), and compared quite well with recent lot numbers of Amplicor HCV Monitor in which viral loads are derived in IU/ml (R2=0.6408), but compared poorly with earlier lot numbers of Amplicor HCV Monitor in which viral loads were derived in copies/ml (R2=0.0913). The ANMC direct sequencing method for genotype determination compared moderately to very well with both the RFLP (84-86%) and INNO-LiPA (85-97.5%) methods.
  
  
  CONCLUSIONS
  These viral load comparisons highlight the discrepancies that may occur when patient HCV viral loads are monitored using different types of assays. Comparison of HCV genotype by different methods is more reliable statistically and important clinically for predicting probability of response to antiviral therapy. However, viral loads are important for monitoring response once therapy has begun.
authors.affiliation: Biomedical Program, University of Alaska Anchorage, Anchorage, AK, USA.
authors.forename: Jonathan C
authors.initials: JC
authors.lastname: Anderson
authors.forename: Josephine
authors.initials: J
authors.lastname: Simonetti
authors.forename: Dennis G
authors.initials: DG
authors.lastname: Fisher
authors.forename: James
authors.initials: J
authors.lastname: Williams
authors.forename: Yasuhiro
authors.initials: Y
authors.lastname: Yamamura
authors.forename: Nayra
authors.initials: N
authors.lastname: Rodriguez
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Sullivan
authors.forename: David R
authors.initials: DR
authors.lastname: Gretch
authors.forename: Brian
authors.initials: B
authors.lastname: McMahon
authors.forename: Kandace J
authors.initials: KJ
authors.lastname: Williams
mesh_terms: D005069:Evaluation Studies as Topic; D005838:Genotype; D016174:Hepacivirus / Q000302:isolation & purification / Q000502:physiology*; D006526:Hepatitis C / Q000097:blood / Q000821:virology*; D006801:Humans; D021141:Nucleic Acid Amplification Techniques; D016133:Polymerase Chain Reaction; D012367:RNA, Viral / Q000032:analysis / Q000097:blood*; D011933:Reagent Kits, Diagnostic; D012680:Sensitivity and Specificity; D019562:Viral Load
chemical_list: D012367:RNA, Viral; D011933:Reagent Kits, Diagnostic