Heterogeneity of hepatitis C virus genotypes in France

The genotypes of French hepatitis C virus (HCV) isolates were investigated by amplification of a domain from the non-structural region 3 (NS3) using nested PCR, followed by hybridization with two genotype-specific probes, F1 (HCV type I-specific) and F2 (HCV type II-specific). Among 119 HCV RNA-positive sera, 91% of samples were NS3 PCR positive. Most samples (83.2%) hybridized with one or the other probe only, whereas a few samples (4.2%) hybridized with both F1 and F2 probes (HB). A small percentage (3.4%) of samples appeared unable to hybridize with either probe (HN). For some of these samples (HB1, HB2, HN1, HN2, HN3, HN4), part of the NS3, core and envelope regions were sequenced and the corresponding deduced consensus sequences were compared with those of prototype isolates of the four HCV genotypes (types I to IV). A phylogenetic tree was constructed to illustrate the relationship between these isolates. The results obtained showed that (i) HN4 appears to be more closely related to type III than to type IV HCV genotypes, which suggests that in France there may exist additional although minor genotypes besides the two major types, F1 and F2. (ii) HB1, HB2, HN1, HN2 and probably HN3 belong to the type II HCV genotype. The association between sequence diversity and putative biological difference for isolates within the same genotype remains to be elucidated.