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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...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2017
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.
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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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