DISCREPANCY OF HEPATITIS-C VIRUS GENOTYPES AS DETERMINED BY PHYLOGENETIC ANALYSIS OF PARTIAL NS5 AND CORE SEQUENCES

The use of phylogenetic analyses of partial NS5 and core regions for h epatitis C virus (HCV) genotyping was evaluated by analysing seven Hon duran and 24 European HCV strains. Core primers were designed with whi ch HCV genotypes 1, 2, and 3 were readily amplified. The reliability o f phylogenetic analysis of a Ill-bp core sequence was verified by comp aring the typing results with those obtained using the whole core gene of 52 reference strains. Accordant genotypes (la, Ib, 2b, and 3a) wer e obtained when phylogenetic analyses were undertaken on both the part ial core and a 222-bp NS5 sequence in ail of the European HCV strains. Genotypes la, Ib, and 3a were identified among the Honduran strains b y phylogenetic analysis of the partial NS5 sequence. Interestingly, tw o of three Honduran type 3a strains, as determined by the NS5 sequence analysis, turned out to be type la by core sequence analysis. These t wo strains were also classified as type la, but not 3a, by a core type -specific PCR. Furthermore, the E2/NS1 regions were similar to HCV-PT, a representative strain of genotype la. The results indicate that chi meral HCV strains exist, although in most cases a good concordance is found when phylogenetic analysis of partial core and NS5 sequences are used for genotyping. This finding should be taken into account when H CV is genotyped by phylogenetic analysis of a partial HCV sequence fro m a single genomic region. (C) 1996 Wiley-Liss, Inc.