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Phylogenetic analysis of HCV subgenotypes in patients from Sichuan province in China based on the NS5B region

The classification of hepatitis C virus (HCV) genotypes is of clinical importance as it may help to predict drug therapy responses and estimate treatment duration. The classical method of HCV subgenotype classification is whole genome sequencing (WGS). However, the high cost and time-consuming natur...

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Autores principales: NIE, BIN, ZHANG, GUANGJIONG, GUO, YONGCAN, LI, QINGFENG, LIU, JINBO, TU, ZHIGUANG
Formato: Online Artículo Texto
Lenguaje:English
Publicado: D.A. Spandidos 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4564081/
https://www.ncbi.nlm.nih.gov/pubmed/26311523
http://dx.doi.org/10.3892/ijmm.2015.2321
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author NIE, BIN
ZHANG, GUANGJIONG
GUO, YONGCAN
LI, QINGFENG
LIU, JINBO
TU, ZHIGUANG
author_facet NIE, BIN
ZHANG, GUANGJIONG
GUO, YONGCAN
LI, QINGFENG
LIU, JINBO
TU, ZHIGUANG
author_sort NIE, BIN
collection PubMed
description The classification of hepatitis C virus (HCV) genotypes is of clinical importance as it may help to predict drug therapy responses and estimate treatment duration. The classical method of HCV subgenotype classification is whole genome sequencing (WGS). However, the high cost and time-consuming nature of WGS limits its usage in clinical practice. A number of studies have been conducted to confirm whether specific regions of HCV could replace WGS in the classification of HCV subgenotypes. In the present study, we used the HCV database to select HCV sequences from different countries. The neighbor-joining method was used to construct phylogenetic trees based on different regions of HCV (core, E1, E2 and NS5B), to confirm which region could replace WGS in subgenotype classification. Our results indicated that the core, E1 and E2 regions could not be used to classify the HCV subgenotype correctly (core failed to recognize subgenotypes c and a, E1 failed to discriminate between subgenotypes a and b, and E2 failed to identify subgenotypes a and c). The NS5B region provided the correct subgenotype classification. The HCV samples (n=153) collected from patients in Sichuan province, (Southwest China) were sequenced and classified based on the NS5B region. The results indicated that the major subgenotype of HCV in patients from Sichuan was 1b (51.6%, n=79); other subgenotypes included 3b (30.1%, n=46), 3a (7.8%, n=12), 6a (8.5%, n=13), 2a (n=2) and 6n (n=1). The data from our analysis may prove to be helpful in future epidemiological investigations of HCV, and may aid in the prevention and clinical treatment of HCV.
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spelling pubmed-45640812015-11-30 Phylogenetic analysis of HCV subgenotypes in patients from Sichuan province in China based on the NS5B region NIE, BIN ZHANG, GUANGJIONG GUO, YONGCAN LI, QINGFENG LIU, JINBO TU, ZHIGUANG Int J Mol Med Articles The classification of hepatitis C virus (HCV) genotypes is of clinical importance as it may help to predict drug therapy responses and estimate treatment duration. The classical method of HCV subgenotype classification is whole genome sequencing (WGS). However, the high cost and time-consuming nature of WGS limits its usage in clinical practice. A number of studies have been conducted to confirm whether specific regions of HCV could replace WGS in the classification of HCV subgenotypes. In the present study, we used the HCV database to select HCV sequences from different countries. The neighbor-joining method was used to construct phylogenetic trees based on different regions of HCV (core, E1, E2 and NS5B), to confirm which region could replace WGS in subgenotype classification. Our results indicated that the core, E1 and E2 regions could not be used to classify the HCV subgenotype correctly (core failed to recognize subgenotypes c and a, E1 failed to discriminate between subgenotypes a and b, and E2 failed to identify subgenotypes a and c). The NS5B region provided the correct subgenotype classification. The HCV samples (n=153) collected from patients in Sichuan province, (Southwest China) were sequenced and classified based on the NS5B region. The results indicated that the major subgenotype of HCV in patients from Sichuan was 1b (51.6%, n=79); other subgenotypes included 3b (30.1%, n=46), 3a (7.8%, n=12), 6a (8.5%, n=13), 2a (n=2) and 6n (n=1). The data from our analysis may prove to be helpful in future epidemiological investigations of HCV, and may aid in the prevention and clinical treatment of HCV. D.A. Spandidos 2015-10 2015-08-24 /pmc/articles/PMC4564081/ /pubmed/26311523 http://dx.doi.org/10.3892/ijmm.2015.2321 Text en Copyright: © Nie et al. This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.
spellingShingle Articles
NIE, BIN
ZHANG, GUANGJIONG
GUO, YONGCAN
LI, QINGFENG
LIU, JINBO
TU, ZHIGUANG
Phylogenetic analysis of HCV subgenotypes in patients from Sichuan province in China based on the NS5B region
title Phylogenetic analysis of HCV subgenotypes in patients from Sichuan province in China based on the NS5B region
title_full Phylogenetic analysis of HCV subgenotypes in patients from Sichuan province in China based on the NS5B region
title_fullStr Phylogenetic analysis of HCV subgenotypes in patients from Sichuan province in China based on the NS5B region
title_full_unstemmed Phylogenetic analysis of HCV subgenotypes in patients from Sichuan province in China based on the NS5B region
title_short Phylogenetic analysis of HCV subgenotypes in patients from Sichuan province in China based on the NS5B region
title_sort phylogenetic analysis of hcv subgenotypes in patients from sichuan province in china based on the ns5b region
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4564081/
https://www.ncbi.nlm.nih.gov/pubmed/26311523
http://dx.doi.org/10.3892/ijmm.2015.2321
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