1Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing, China.
2Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing, China firstname.lastname@example.org.
The Versant HCV genotype 2.0 assay (LiPA 2.0), based on reverse hybridization, and the Abbott Realtime HCV genotype II assay (Realtime II), based on genotype-specific real-time PCR, have been widely used for analysis of hepatitis C virus (HCV) genotypes. However, their performances for detecting genotype 6 have not been well studied. Here, we analyzed genotype 6 in 63 samples from the China HCV Genotyping Study that were originally identified as genotype 6 using LiPA 2.0. The genotyping results were confirmed by NS5B or core sequence phylogenetic analysis. A total of 57 samples were confirmed as genotype 6 (51 as genotype 6a, five as genotype 6n and one as genotype 6e). Four samples identified as a mixture of genotypes 6 and 4 by LiPA 2.0 were confirmed as genotype 3b. The remaining two samples classified as genotype 6 by LiPA 2.0 were confirmed as genotype 1b, which were intergenotypic recombinants and excluded from further comparison. In 57 genotype 6 samples detected using Realtime II Version 2.00, 47 genotype 6a samples were identified as genotype 6; one 6e sample was misclassified as genotype 1; four 6a and five 6n samples yielded "indeterminate" results. Nine nucleotide profiles in the 5' untranslated region affected the performances of both assays. Therefore, our analysis shows that both assays have limitations in identifying HCV genotype 6. LiPA 2.0 cannot distinguish some 3b samples from genotype 6 samples. Realtime II fails to identify some 6a and all non-6a subtypes and misclassifies genotype 6e as genotype 1.