Comparison of DNA enzyme immunoassay and line probe assays (Inno-LiPA HCV I and II) for hepatitis C virus genotyping

Abstract

Two methods for genotyping hepatitis C virus (DNA enzyme immunoassay [DEIA] and line probe assay [Inno-LiPA HCV I and II]) were compared on 120 samples and of these 87% were assigned to the same subtype by both assays. There were 15 subtyping discrepancies which involved 5% of type 1 isolates and 90% of type 2 isolates. Amplified products from the core and 5' untranslated regions (UTR) were sequenced to resolve conflicts. Type 1 discordant samples had a guanosine at position -99 in the 5' UTR, a characteristic of genotype 1b, and a core region typical of subtype 1a. The eight isolates classified as 2a/2c by LiPA and as subtype 2c by DEIA belonged to type 2.

FIG. 1

Unrooted phylogenetic tree of 63 HCV type 2 isolates derived from an analysis of partial core sequences (nucleotides 159 to 361) retrieved from the EBI database or by using the Entrez software from the National Center for Biotechnology Information (about 600 sequences). The consensus sequences of types 2a, 2b, and 2c were obtained from Bukh et al. (2), and sequences 1F.03, 1F.48, and RC.12 were from Cammarota et al. (3). Sequences were aligned manually, and preliminary phylogenetic analyses were used to identify a subset of 120 sequences representative of each monophyletic taxon. More detailed analyses were restricted to type 2 sequences. The topology was obtained by a maximum-likelihood method (double asterisks indicate branches at P < 0.01). Monophyletic taxons also retrieved in the most-parsimonious tree are indicated by a plus sign. Percentages show branches identified according to a bootstrap resampling (500 replicates) by neighbor-joining analysis. Sequences obtained in this study are shaded.