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Sequencing Assays for Failed Genotyping with the Versant Hepatitis C Virus Genotype Assay (LiPA), Version 2.0
- Source :
- Journal of Clinical Microbiology. 51:2815-2821
- Publication Year :
- 2013
- Publisher :
- American Society for Microbiology, 2013.
-
Abstract
- For optimal antiviral therapy, the hepatitis C virus (HCV) genotype needs to be determined, as it remains a strong predictor of sustained viral response. In this study, we assessed the number of HCV genotyping results that could not be determined using the commercially available line probe assay (LiPA) (Versant hepatitis C virus genotype 2.0 assay) in a large international panel of samples from 9,874 HCV-positive patients. In-house sequencing assays targeting the 5′ untranslated region (UTR), core region, NS3 region, and NS5B region of the HCV genome and phylogenetic analyses were used to resolve these LiPA failures. Among all cases, the genotypes of 51 samples (0.52%) could not be determined with the LiPA. These undetermined results were observed more frequently among samples from non-European regions (mainly the Arabian Peninsula). The use of sequencing assays coupled with phylogenetic analysis provided reliable genotype results for 86% of the LiPA failures, which exhibited higher rates of genotypes 4, 5, and 6 than did LiPA-resolved genotypes. As expected, the 5′ UTR was not sufficiently variable for clear discrimination between genotypes 1 and 6, but it also resulted in errors in classification of some genotype 3 and 4 cases using well-known Web-based BLAST programs. This study demonstrates the low frequency of genotyping failures with the Versant hepatitis C virus genotype 2.0 assay (LiPA) and also underlines the need for a complex combination of sequences and phylogenetic analyses in order to genotype these particular HCV strains correctly.
- Subjects :
- Adult
Male
Microbiology (medical)
Untranslated region
Genotype
Hepacivirus
Hepatitis C virus
Molecular Sequence Data
medicine.disease_cause
chemistry.chemical_compound
Virology
medicine
Humans
False Negative Reactions
NS5B
Genotyping
Aged
Genetics
NS3
Base Sequence
biology
Genetic Variation
Sequence Analysis, DNA
Hepatitis C
Middle Aged
medicine.disease
biology.organism_classification
Molecular Diagnostic Techniques
chemistry
Mutation
RNA, Viral
Female
Subjects
Details
- ISSN :
- 1098660X and 00951137
- Volume :
- 51
- Database :
- OpenAIRE
- Journal :
- Journal of Clinical Microbiology
- Accession number :
- edsair.doi.dedup.....a35ea8303c5d8a2817559d492c5ee6cc