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

  • Authors:
    • Bin Nie
    • Guangjiong Zhang
    • Yongcan Guo
    • Qingfeng Li
    • Jinbo Liu
    • Zhiguang Tu

  • View Affiliations

  • Published online on: August 24, 2015     https://doi.org/10.3892/ijmm.2015.2321
  • Pages: 1028-1034

  • Copyright: © Nie et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

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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October-2015
Volume 36 Issue 4

Print ISSN: 1107-3756
Online ISSN:1791-244X

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  • Impact Factor: 5.4
  • Ranked Medicine Research and Experimental
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  • CiteScore: 10.7
  • CiteScore Rank: Q1: #35/328 Biochemistry, Genetics and Molecular Biology
  • Source Normalized Impact per Paper (SNIP): 0.994
  • SCImago Journal Rank (SJR): 0.922
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Spandidos Publications style
Nie B, Zhang G, Guo Y, Li Q, Liu J and Tu Z: Phylogenetic analysis of HCV subgenotypes in patients from Sichuan province in China based on the NS5B region. Int J Mol Med 36: 1028-1034, 2015
APA
Nie, B., Zhang, G., Guo, Y., Li, Q., Liu, J., & Tu, Z. (2015). Phylogenetic analysis of HCV subgenotypes in patients from Sichuan province in China based on the NS5B region. International Journal of Molecular Medicine, 36, 1028-1034. https://doi.org/10.3892/ijmm.2015.2321
MLA
Nie, B., Zhang, G., Guo, Y., Li, Q., Liu, J., Tu, Z."Phylogenetic analysis of HCV subgenotypes in patients from Sichuan province in China based on the NS5B region". International Journal of Molecular Medicine 36.4 (2015): 1028-1034.
Chicago
Nie, B., Zhang, G., Guo, Y., Li, Q., Liu, J., Tu, Z."Phylogenetic analysis of HCV subgenotypes in patients from Sichuan province in China based on the NS5B region". International Journal of Molecular Medicine 36, no. 4 (2015): 1028-1034. https://doi.org/10.3892/ijmm.2015.2321