Hepatitis B virus genotypes and genome characteristics in China
Hepatitis B virus genotypes and genome characteristics in China
复制标题
中国乙型肝炎病毒基因型及基因组特征
DOI：
10.3748/wjg.v21.i21.6684
复制
发表时间：
2015-06-07
影响因子：
4.3
通讯作者：
Shen, Tao
中科院分区：
文献类型：
--
作者：
Li, Hong-Mei;Wang, Jian-Qiong;Shen, Tao
目的：目的：分析我国B肝炎病毒（HBV）的特征，以及HBV几种变异与肝炎症状的相关性，方法：通过国家生物技术信息中心数据库（包括基因型、地域和临床状态）收集我国1148例HBV全基因组序列。通过直接参考Genbank序列注释、系统发育树和在线软件分析（http：//www.ncbi.nlm.nih.gov/projects/genotyping/formpage.cgi）对HBV基因型进行分类。应用MEGA5.0软件，采用邻接法构建系统发育树。根据系统发育树对HBV序列进行分组，采用计算机组间平均距离法计算组间距离。选取712个有明确临床症状注释的HBV序列，分析变异与临床症状的相关性。用DNAStar和BioEdit软件包分析序列特征。利用RNAdraw软件进行密码子使用偏好性分析和RNA二级结构分析。结果：我国东北地区HBV基因型以C型为主，中南地区以B型为主，西南地区以B、C型为主，西北地区以C/D重组基因型为主。C2和B2是两种主要的亚基因型，FJ 386674可能是B10的一个推定的亚基因型。基础核心启动子双突变和前C区突变在肝炎症状之间存在各种显著性差异。除ATG外，还存在许多其它HBV起始密码子。HBV具有密码子使用偏好性，X、C和P开放阅读框（ORF）的终止密码子分别为TAA、TAG和TGA。结论：本研究基本反映了我国HBV感染的流行病学特征，为今后HBV感染的防治提供了重要信息。
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.