RAPID GENOTYPING OF HEPATITIS-C VIRUS RNA-ISOLATES OBTAINED FROM PATIENTS RESIDING IN WESTERN-EUROPE

Two rapid genotyping methods for hepatitis C virus (HCV), the line pro be assay (Inno-LiPA) and the subtype-specific core amplification syste m [Okamoto et al., (1992b) Journal of General Virology 73:673-679], we re applied to 58 HCV isolates which were typed as type 1 (n = 37) acid type 2 (n = 21) by sequence analysis of the 5' untranslated region (5 'UTR). The line probe assay targets the 5'UTR and recognized 12 subtyp e 1a, 25 subtype 1b, 18 subtype 2a, 2 subtype 2b and 1 subtype 2d in a ccordance with sequence analysis of this region. Subtype-specific core amplification revealed 7 discrepancies among the 37 type 1 isolates w hen compared to LIPA. A different subtype was observed in 3 isolates ( 1a versus 1b), 2 isolates remained untyped and 2 isolates showed a coi nfection of subtype 1a and 1b. The first 5 discrepancies were confirme d by sequence analysis of the core region whereas the coinfection coul d not be confirmed. Of the 21 type 2 isolates only one could be typed by subtype-specific core amplification. HCV RNA was detected in all 21 cases after the general first round of polymerase chain reaction (PCR ). Direct sequencing of the core region indicated sequence variation a s a source of failure. It is concluded that LiPA results are conclusiv e for typing of HCV. However, LiPA is hampered occasionally for subtyp ing by lack of subtype-specific sequence variation in 5'UTR. Subtyping results by subtype-specific core amplification were accurate. However , it seems that this assay is not suitable for the identification of g enotype 2 isolates that circulate in patients living in Western Europe . (C) 1995 Wiley-Liss, Inc.