Performance of TRUGENEtm hepatitis C virus 5' noncoding genotyping kit, a new CLIPtm sequencing-based assay for hepatitis C virus genotype determination

Publisher Website
Google Scholar
Abstract
Summary. The performance of the recently developed, standardized direct sequencing assay for hepatitis C virus (HCV) genotyping [TRUGENETM 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 °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.