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

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.

The nationwide distribution and trends of hepatitis C virus genotypes in mainland China

“…HCV is a single‐stranded, positive‐sense RNA virus with a whole genome of approximately 9400 base pairs in length. This virus shows extraordinary genetic diversity, with a tremendous replication capacity (10 viruses every day in the infected body) and lack of high‐fidelity editing mechanism to correct errors during replication . The HCV genotypes differ from each other in the nucleotide sequences by 31% to 33%, compared with 20% to 25% between subtypes .…”

“…Based on phylogenetic and sequence analyses of the whole viral genome, HCV has been classified into seven confirmed genotypes and 67 subtypes, 20 provisionally assigned subtypes, and 21 unassigned subtypes . Knowledge of the distribution of HCV genotypes can provide abundant information for treatment regimen selection, rational vaccine design, and drug development . HCV genotypes can also be used as epidemiologic markers for tracing the source of an HCV outbreak in a given population or area .…”

“…12 Knowledge of the distribution of HCV genotypes can provide abundant information for treatment regimen selection, rational vaccine design, and drug development. 7,8 HCV genotypes can also be used as epidemiologic markers for tracing the source of an HCV outbreak in a given population or area. 9 However, several studies have shown that substantial regional and demographic differences appear to exist in the distribution of HCV genotypes.…”

Hepatitis C virus genotype/subtype distribution and evolution among Chinese blood donors: Revealing recent viral expansion

“…In Mianyang (Sichuan province), Luoyang (Henan province) and Urumqi (Xinjiang province), the prevalent genotypes were both HCV 1b and 2a. According to the previous reports, the major two HCV subtypes in Sichuan were 1b and 3b or 3a [ 27 – 30 ]. In our study, however, HCV-1b and 2a became the predominant subtypes in Mianyang with the prevalence rate of 1b up to 80%, and the prevalence of 2a was significantly higher than 3a and 3b.…”

Molecular Detection of Hepatitis C Virus amongst Patients in Five Selected Hospitals in Niger State, Nigeria

“…24 It may also constitute a serious obstacle to designing a universal vaccine against HCV infection. Medhat et al 25 and Nie et al 26 reported the circulation of genotypes 1 & 4 in Saudi Arabia and genotypes 2a, 3a, 6n, & 6a in China province respectively. Messina et al 15 documented that genotypes 1, 2, and 3 have a worldwide distribution and HCV subtypes 1a and 1b are the most common prevalent genotypes.…”