Comparative study of different methods to genotype hepatitis C virus type 6 variants.

Hepatitis C virus (HCV) genotype 6a is found frequently in Southeast Asia. In Thailand, however, genotype 6 variants may exist which posses a genotype 1 like sequence in the 5′ non-coding region. In order to genotype correctly these viruses, four different methods; INNO-LiPA assay, two RFLP assays on the core region (using different restriction enzymes) and phylogenetic analysis of the core sequences were compared. Samples from 17 chronic HCV patients from the Netherlands and Thailand and 18 anti-HCV positive blood donors recruited from Thailand were tested. The INNO-LiPA could not distinguish genotype 6 variants. The RFLP methods used could not, or only in combination with 5′NCR genotyping methods, identify type 6 variants. In conclusion, for identification of type 6 variants at least two different regions of the HCV genome have to be analyzed (both 5′NCR and core).