Genotyping hepatitis C viruses from Southeast Asia by a novel line probe assay that simultaneously detects core and 5' untranslated regions
| Autor: | Yong Poovorawan, Saskia L. Smits, Bart L. Haagmans, Truong Xuan Lien, Erwin Sablon, Marianne Van Brussel, Jan Brouwer, Albert D. M. E. Osterhaus, Suwanna Noppornpanth, Kathy De Nys |
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| Přispěvatelé: | Virology |
| Rok vydání: | 2006 |
| Předmět: |
Microbiology (medical)
Genotype Sequence analysis Hepacivirus Molecular Sequence Data Polymerase Chain Reaction law.invention chemistry.chemical_compound SDG 3 - Good Health and Well-being law Virology Line Probe Assay Genotyping NS5B Polymerase chain reaction Phylogeny Genetics biology Base Sequence Viral Core Proteins Nucleic Acid Hybridization biology.organism_classification chemistry 5' Untranslated Regions HCV Genotype Assay |
| Zdroj: | Journal of Clinical Microbiology, 44(11), 3969-3974. American Society for Microbiology |
| ISSN: | 0095-1137 |
| Popis: | Hepatitis C viruses (HCVs) display a high level of sequence diversity and are currently divided into six genotypes. A line probe assay (LiPA), which targets the 5′ untranslated region (5′UTR) of the HCV genome, is widely used for genotyping. However, this assay cannot distinguish many genotype 6 subtypes from genotype 1 due to high sequence similarity in the 5′UTR. We investigated the accuracy of a new generation LiPA (VERSANT HCV genotype 2.0 assay), in which genotyping is based on 5′UTR and core sequences, by testing 75 selected HCV RNA-positive sera from Southeast Asia (Vietnam and Thailand). For comparison, sera were tested on the 5′UTR based VERSANT HCV genotype assay and processed for sequence analysis of the 5′UTR-to-core and NS5b regions as well. Phylogenetic analysis of both regions revealed the presence of genotype 1, 2, 3, and 6 viruses. Using the new LiPA assay, genotypes 6c to 6l and 1a/b samples were more accurately genotyped than with the previous test only targeting the 5′UTR (96% versus 71%, respectively). These results indicate that the VERSANT HCV genotype 2.0 assay is able to discriminate genotypes 6c to 6l from genotype 1 and allows a more accurate identification of genotype 1a from 1b by using the genotype-specific core information. |
| Databáze: | OpenAIRE |
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