Hepatitis C virus genotyping by restriction fragment length polymorphism of polymerase chain reaction products generated with a HCV detection kit

Highly conserved sequence in the 5' untranslated region(UTR) of hepatitis C virus(HCV) genome have been targeted by most nucleic acid amplification-based detection assays, such as Amplicor HCV test, a commercially available assay kit. In this study, we classified HCV genotypes by direct sequencing determination for 5' UTR of nested-PCR after Amplicor HCV test. Then, based on the results of sequence, RFLP analysis after digestion of the nested PCR fragments with Hae III or Sau 3AI to classify HCV genotype was evaluated. RFLP analysis distinguished the type 1, 2a and 2b. Only one of 29 samples was not classified by RFLP analysis due to the point mutation of Hae III recognition site. HCV genotypes commonly found in JAPAN were classified into three types, 1b, 2a, and 2b. Also, RFLP analysis requires fewer resources than serotype grouping test. Hence, the present method provides an adaptable and rapid HCV genotyping in clinical laboratory in JAPAN.