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Discrepancy between Hepatitis C Virus Genotypes and NS4-Based Serotypes: Association with Their Subgenomic Sequences
Determination of hepatitis C virus (HCV) genotypes plays an important role in the direct-acting agent era. Discrepancies between HCV genotyping and serotyping assays are occasionally observed. Eighteen samples with discrepant results between genotyping and serotyping methods were analyzed. HCV serot...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5297804/ https://www.ncbi.nlm.nih.gov/pubmed/28106726 http://dx.doi.org/10.3390/ijms18010172 |
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author | Win, Nan Nwe Nakamoto, Shingo Kanda, Tatsuo Takahashi, Hiroki Takahashi-Nakaguchi, Azusa Yasui, Shin Nakamura, Masato Wu, Shuang Imazeki, Fumio Mikami, Shigeru Yokosuka, Osamu Gonoi, Tohru Shirasawa, Hiroshi |
author_facet | Win, Nan Nwe Nakamoto, Shingo Kanda, Tatsuo Takahashi, Hiroki Takahashi-Nakaguchi, Azusa Yasui, Shin Nakamura, Masato Wu, Shuang Imazeki, Fumio Mikami, Shigeru Yokosuka, Osamu Gonoi, Tohru Shirasawa, Hiroshi |
author_sort | Win, Nan Nwe |
collection | PubMed |
description | Determination of hepatitis C virus (HCV) genotypes plays an important role in the direct-acting agent era. Discrepancies between HCV genotyping and serotyping assays are occasionally observed. Eighteen samples with discrepant results between genotyping and serotyping methods were analyzed. HCV serotyping and genotyping were based on the HCV nonstructural 4 (NS4) region and 5′-untranslated region (5′-UTR), respectively. HCV core and NS4 regions were chosen to be sequenced and were compared with the genotyping and serotyping results. Deep sequencing was also performed for the corresponding HCV NS4 regions. Seventeen out of 18 discrepant samples could be sequenced by the Sanger method. Both HCV core and NS4 sequences were concordant with that of genotyping in the 5′-UTR in all 17 samples. In cloning analysis of the HCV NS4 region, there were several amino acid variations, but each sequence was much closer to the peptide with the same genotype. Deep sequencing revealed that minor clones with different subgenotypes existed in two of the 17 samples. Genotyping by genome amplification showed high consistency, while several false reactions were detected by serotyping. The deep sequencing method also provides accurate genotyping results and may be useful for analyzing discrepant cases. HCV genotyping should be correctly determined before antiviral treatment. |
format | Online Article Text |
id | pubmed-5297804 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-52978042017-02-10 Discrepancy between Hepatitis C Virus Genotypes and NS4-Based Serotypes: Association with Their Subgenomic Sequences Win, Nan Nwe Nakamoto, Shingo Kanda, Tatsuo Takahashi, Hiroki Takahashi-Nakaguchi, Azusa Yasui, Shin Nakamura, Masato Wu, Shuang Imazeki, Fumio Mikami, Shigeru Yokosuka, Osamu Gonoi, Tohru Shirasawa, Hiroshi Int J Mol Sci Article Determination of hepatitis C virus (HCV) genotypes plays an important role in the direct-acting agent era. Discrepancies between HCV genotyping and serotyping assays are occasionally observed. Eighteen samples with discrepant results between genotyping and serotyping methods were analyzed. HCV serotyping and genotyping were based on the HCV nonstructural 4 (NS4) region and 5′-untranslated region (5′-UTR), respectively. HCV core and NS4 regions were chosen to be sequenced and were compared with the genotyping and serotyping results. Deep sequencing was also performed for the corresponding HCV NS4 regions. Seventeen out of 18 discrepant samples could be sequenced by the Sanger method. Both HCV core and NS4 sequences were concordant with that of genotyping in the 5′-UTR in all 17 samples. In cloning analysis of the HCV NS4 region, there were several amino acid variations, but each sequence was much closer to the peptide with the same genotype. Deep sequencing revealed that minor clones with different subgenotypes existed in two of the 17 samples. Genotyping by genome amplification showed high consistency, while several false reactions were detected by serotyping. The deep sequencing method also provides accurate genotyping results and may be useful for analyzing discrepant cases. HCV genotyping should be correctly determined before antiviral treatment. MDPI 2017-01-17 /pmc/articles/PMC5297804/ /pubmed/28106726 http://dx.doi.org/10.3390/ijms18010172 Text en © 2017 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC-BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Win, Nan Nwe Nakamoto, Shingo Kanda, Tatsuo Takahashi, Hiroki Takahashi-Nakaguchi, Azusa Yasui, Shin Nakamura, Masato Wu, Shuang Imazeki, Fumio Mikami, Shigeru Yokosuka, Osamu Gonoi, Tohru Shirasawa, Hiroshi Discrepancy between Hepatitis C Virus Genotypes and NS4-Based Serotypes: Association with Their Subgenomic Sequences |
title | Discrepancy between Hepatitis C Virus Genotypes and NS4-Based Serotypes: Association with Their Subgenomic Sequences |
title_full | Discrepancy between Hepatitis C Virus Genotypes and NS4-Based Serotypes: Association with Their Subgenomic Sequences |
title_fullStr | Discrepancy between Hepatitis C Virus Genotypes and NS4-Based Serotypes: Association with Their Subgenomic Sequences |
title_full_unstemmed | Discrepancy between Hepatitis C Virus Genotypes and NS4-Based Serotypes: Association with Their Subgenomic Sequences |
title_short | Discrepancy between Hepatitis C Virus Genotypes and NS4-Based Serotypes: Association with Their Subgenomic Sequences |
title_sort | discrepancy between hepatitis c virus genotypes and ns4-based serotypes: association with their subgenomic sequences |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5297804/ https://www.ncbi.nlm.nih.gov/pubmed/28106726 http://dx.doi.org/10.3390/ijms18010172 |
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