Typing of hepatitis C virus isolates and characterization of new subtypes using a line probe assay

A reverse-hybridization assay, the line probe assay (LiPA), based on variations found in the 5' untranslated regions of the different hepatitis C virus (HCV) genotypes was developed, permitting simple and fast determination of four HCV genotypes and their subtypes. Using this assay, 61 PCR-positive Brazilian HCV sera were typed. Of the sera, 33% had a type 1 HCV infection, 38% had type 1b (related to HCV-J), 1.5% had type 2a (related to HC-J6), 24.5% had type 3 (related to E-b1 and HCV-T), and 3% of the sera were co-infected. This assay format was further evaluated using 13 sera from Belgium and the Netherlands, and all of these could be classified. Two pools of Japanese sera were classified as either type 2a or were co-infected with types 1b and 2a, but no type 2b sequences were detected. Another eight PCR-positive sera were obtained from Burundi and Gabon. The sequence of the 5' untranslated region of these African viruses was strongly divergent from the three previously described types. Therefore, these isolates were tentatively classified as type 4. These and some of the other non-type 1 sera often demonstrated weaker reactivities than type 1 isolates in currently used second generation antibody confirmation assays.