Comparative evaluation of five rapid methods for identifying subtype 1b and 2c hepatitis C virus isolates

A panel of 61 HCV isolates belonging to five different subtypes were used to evaluate five methods for rapid typing of HCV RNA: an in-house type-specific polymerase chain reaction based on the core region (type-specific PCR), a commercial amplification of the core region followed by hybridisation to probe coated wells (DEIA), a commercial amplification of the 5'-UTR region followed by hybridisation to probes immobilised on strips (LiPA), an in-house restriction fragment polymorphism analysis of the 5'UTR (RFLP), and a commercial serological method using synthetic peptides from the NS4 region (serotyping). The correct viral type was identified in 90% of cases by DEIA, in 82% of cases by type-specific PCR, in 80% of cases by LiPA and RFLP, and in 67% of cases by serotyping. Correct identification of the virus subtype was much less frequent and was beyond the performance characteristics of some assays. Major problems were found in the identification of isolates belonging to type 2. This was probably at least partly due to the fact that all type 2 isolates in the viral panel were of subtype 2c, which has been considered rare until recently.