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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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
D.A. Spandidos
2015
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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. |
format | Online Article Text |
id | pubmed-4564081 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | D.A. Spandidos |
record_format | MEDLINE/PubMed |
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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