2ND-GENERATION LINE PROBE ASSAY FOR HEPATITIS-C VIRUS GENOTYPING

Because of the enormous variability of hepatitis C virus (HCV), the de velopment of reliable genotyping assays is a formidable challenge. The optimal genotyping region appears to be the 5' untranslated region (U R) because of high conservation within, but considerable variability b etween, genotypes. In this study, 21 probes dispersed over seven varia ble 5' UR areas were applied to a line probe assay (LiPA) and used to analyze 506 HCV-infected sera from different geographical regions repr esenting a multitude of subtypes. At least 31 different reactivity pat terns emerged, with 404 (80%) of 506 distributed over 11 prototype pat terns, in general corresponding to subtypes 1a, 1b, 2a/2c, 2b, 3a, 5a, and 6a and several type 4 subtypes. Subtyping specificity ranged from 97% in Hong Kong to 90% in Europe but was only 11% in West Africa, wh ile typing specificity was always 100% when samples from Vietnam were excluded. In a second evaluation, the subtype prediction by LiPA of 44 8 GenBank 5' UR HCV sequences was scored. Of the 58 theoretically pred icted patterns, 321 sequences (72%) were covered by the 11 prototype p atterns. We concluded that (i) the selected probes detected the corres ponding signature motifs in the seven variable regions with 100% relia bility; (ii) these motifs allowed correct type interpretation of sampl es collected world,vide, with the exclusion of Vietnam, Thailand, or V ietnamese patients residing in European hospitals; and (iii) subtyping specificities vary according to geographical region, with 11 prototyp e subtyping patterns identifying the majority of samples from Europe a nd the Americas. These results indicate that the LiPA is a reliable as say applicable to routine typing and subtyping of HCV specimens.