Retrospective Study
Copyright ©The Author(s) 2015. Published by Baishideng Publishing Group Inc. All rights reserved.
World J Gastroenterol. Jun 7, 2015; 21(21): 6684-6697
Published online Jun 7, 2015. doi: 10.3748/wjg.v21.i21.6684
Hepatitis B virus genotypes and genome characteristics in China
Hong-Mei Li, Jian-Qiong Wang, Rui Wang, Qian Zhao, Li Li, Jin-Ping Zhang, Tao Shen
Hong-Mei Li, Rui Wang, College of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, Yunnan Province, China
Hong-Mei Li, Rui Wang, Qian Zhao, Li Li, Jin-Ping Zhang, Tao Shen, Basic and Clinical Medicine Institute of Yunnan Province, Provincial Key Laboratory for Birth Defects and Genetic Diseases, the First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming 650032, Yunnan Province, China
Jian-Qiong Wang, Clinical Laboratory, the First People’s Hospital of Yunnan Province, affiliated Hospital of Kunming University of Science and Technology, Kunming 650032, Yunnan Province, China
Qian Zhao, Kunming Medical College, Kunming 650500, Yunnan Province, China
Author contributions: Li HM, Li L and Zhang JP were in charge of information collection; Li HM, Wang R and Zhao Q participated in the statistical analysis; Li HM and Wang JQ designed the study and wrote the manuscript; Shen T provided advice and reviewed the manuscript; Li HM and Wang JQ contributed equally to this work.
Supported by National Natural Science Foundation of China, No. 81160352; grants from the Education Department Foundation of Yunnan Province, No. 2012J091; Health Bureau of Yunnan Province, No. D-201203 (partly); and Science and Technology Department of Yunnan Province, No. 2013HB084 (partly).
Conflict-of-interest: The authors declare that they have no conflicting interest regarding this work.
Data sharing: Statistical code from the corresponding author at ts902@126.com. Participants gave informed consent for data sharing.
Open-Access: This article is an open-access article which was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: http://creativecommons.org/licenses/by-nc/4.0/
Correspondence to: Dr. Tao Shen, Basic and Clinical Medicine Institute of Yunnan Province, Provincial Key Laboratory for Birth Defects and Genetic Diseases, the First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming 650032, Yunnan Province, China. ts902@126.com
Telephone: +86-871-63638453 Fax: +86-871-63648772
Received: December 24, 2014
Peer-review started: December 26, 2014
First decision: January 22, 2015
Revised: March 3, 2015
Accepted: April 3, 2015
Article in press: April 3, 2015
Published online: June 7, 2015
Processing time: 168 Days and 18.5 Hours
Abstract

AIM: To analyze the hepatitis B virus (HBV) characters in China, as well as the correlation between several HBV mutation and hepatitis symptoms.

METHODS: A total of 1148 HBV genome sequences from patients throughout China were collected via the National Center For Biotechnology Information database (information including: genotype, territory and clinical status). HBV genotypes were classified by a direct reference from the Genbank sequence annotation, phylogenetic tree and online software analysis (http://www.ncbi.nlm.nih.gov/projects/genotyping/formpage.cgi). The phylogenetic tree was constructed based on the neighbor-joining method by MEGA5.0 software. HBV sequences were grouped based on phylogenetic tree and the distance between the groups was calculated by using the computer between group mean distance methods. Seven hundred and twelve HBV sequences with clear annotation of clinical symptoms were selected to analyses the correlation of mutation and clinical symptoms. Characteristics of sequences were analyzed by using DNAStar and BioEdit software packages. The codon usage bias and RNA secondary structures analysis were performed by RNAdraw software. Recombination analysis was performed by using Simplot software.

RESULTS: In China, HBV genotype C was the predominant in Northeastern, genotype B was predominant in Central Southern areas, genotype B and C were both dominant in Southwestern areas, and the recombinant genotype C/D was predominant in Northwestern areas. C2 and B2 were identified as the two major sub-genotypes, FJ386674 might be a putative sub-genotype as B10. The basal core promoter double mutation and pre-C mutation showed various significant differences between hepatitis symptoms. In addition to ATG, many other HBV initiation codons also exist. HBV has codon usage bias; the termination codon of X, C and P open reading frames (ORF) were TAA, TAG, and TGA, respectively. The major stop codons of S-ORF were TAA (96.45%) and TGA (83.60%) in B2 and C2 subtype, respectively.

CONCLUSION: This study recapitulated the epidemiology of HBV in China, and the information might be meaningful critical for the future prevention and therapy of HBV infections.

Keywords: Hepatitis B virus; Genotype; Phylogenetic tree; Clinical symptoms; Mutation; Codon usage bias

Core tip: This study recapitulated the epidemiology of hepatitis B virus (HBV) in China. Genotype C was the predominant HBV genotype in Northeastern, genotype B was predominant in Central Southern areas, genotype B and C were both dominant in Southwestern areas, and the recombinant genotype C/D was predominant in Northwestern areas. C2 and B2 were identified as the two major subgenotypes, FJ386674 might be a putative sub-genotype as B10. Moreover, the termination codon usage bias of B2 (TAA) and C2 (TGA) subtype and the correlation between HBV sequence mutations and clinical symptoms were also determined.