Performance of TRUGENE hepatitis C virus 5' noncoding genotyping kit, a new CLIP sequencing-based assay for hepatitis C virus genotype determination.
The performance of the recently developed, standardized direct sequencing assay for hepatitis C virus (HCV) genotyping [TRUGENE HCV 5'-NC (noncoding)] was assessed in comparison with the reverse hybridization-based assay INNO-LIPA HCV II. Both assays allow HCV genotyping starting from amplification products generated by the diagnostic Roche AMPLICOR HCV test. HCV amplicons from 205 patients were used for this study: 34 were tested prospectively by both methods, while 171 had been stored at -20 degrees C for up to 2 years after LiPA genotyping. The TRUGENE procedure failed to determine a genotype in six low-titered samples (3.5 +/- 0.3 log UI/mL vs. 5.2 +/- 0.5 UI/mL for typable samples). Type and subtype could be determined by sequencing for 199 samples (97%). Among them, five were considered as coinfections by the LiPA method. Three LiPA patterns suggesting type 1 and 4 coinfection were not supported by sequence analysis while one 1a/2b and one 1a/3a coinfection was backed up by direct sequencing. For the remaining 194 samples, type assignment was concordant in 100% of the cases. LiPA subtyping was available for 162 samples (83.5%). Sub-typing results concurred in 128 cases (79%). NS5B sequencing of discrepant samples underscored the limitation of the 5'-noncoding region (NCR) in correct subtype assignment. In conclusion, the TRUGENE HCV 5'-NC genotyping kit appeared to be a specific and reliable method that can be used in the current indication of HCV genotyping.
Roque-Afonso
A M
AM
Laboratoire de Virologie and UPRES EA 1596, Hôpital Paul Brousse, VilleJuif, France. anne-marie.roque@pbr.ap-hop-paris.fr
Férey
M-P
MP
Poveda
J-D
JD
Marchadier
E
E
Dussaix
E
E
D020121:5' Untranslated Regions / Q000032:analysis / Q000235:genetics*; D005821:Genetic Techniques; D005838:Genotype; D016174:Hepacivirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D016133:Polymerase Chain Reaction / Q000379:methods; D011446:Prospective Studies; D011933:Reagent Kits, Diagnostic; D012189:Retrospective Studies; D017422:Sequence Analysis, DNA
D020121:5' Untranslated Regions; D011933:Reagent Kits, Diagnostic