Comparison of three different HCV genotyping methods: core, NS5B sequence analysis and line probe assay

To evaluate the capacity of Versant HCV genotype assay (LiPA) 2.0 to identify hepatitis C virus (HCV) genotypes, 110 serum samples were collected from chronic hepatitis C patients. Three methods were compared: core sequence analysis, NS5B sequence analysis and the INNO-LiPA assay. The result showed that 102 (92.7%) of the samples were amplified in either or both regions, of which 97 were amplified in the core region and 62 were amplified in the NS5B region. Correlation analysis showed that amplification rates of subgenomic regions were associated with viral loads. Basic local alignment search tool (BLAST) and phylogenetic analysis showed that the 102 samples were classified into 5 categories: subtype 1b, 2a, 3a, 3b and 6a at frequencies of 61.8% (63), 9.8% (10), 3.9% (4), 3.9% (4) and 20.6% (21), respectively. Compared with sequencing methods, 66.7% (68) of the 102 samples were identified completely by LiPA 2.0, whereas 19.6% (20) were assigned incompletely (indistinguishable or not identified subtype) and 13.7% (14) were misclassified. Of 21 genotype 6a samples, 11 were mistyped as 1b. In conclusion, LiPA 2.0 was not suitable for identifying HCV genotypes in the samples tested, whereas core sequence analysis remained an ideal method for genotyping HCV.