title: Hepatitis B virus genotypes and genome characteristics in China.
abstract: OBJECTIVE
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Hong-Mei Li, Rui Wang, College of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, Yunnan Province, China.
authors.forename: Hong-Mei
authors.initials: HM
authors.lastname: Li
authors.affiliation: Hong-Mei Li, Rui Wang, College of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, Yunnan Province, China.
authors.forename: Jian-Qiong
authors.initials: JQ
authors.lastname: Wang
authors.affiliation: Hong-Mei Li, Rui Wang, College of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, Yunnan Province, China.
authors.forename: Rui
authors.initials: R
authors.lastname: Wang
authors.affiliation: Hong-Mei Li, Rui Wang, College of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, Yunnan Province, China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Zhao
authors.affiliation: Hong-Mei Li, Rui Wang, College of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, Yunnan Province, China.
authors.forename: Li
authors.initials: L
authors.lastname: Li
authors.affiliation: Hong-Mei Li, Rui Wang, College of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, Yunnan Province, China.
authors.forename: Jin-Ping
authors.initials: JP
authors.lastname: Zhang
authors.affiliation: Hong-Mei Li, Rui Wang, College of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, Yunnan Province, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Shen
mesh_terms: D002681:China / Q000453:epidemiology; D018388:Codon, Terminator; D019295:Computational Biology; D004252:DNA Mutational Analysis; D004279:DNA, Viral / Q000235:genetics*; D030541:Databases, Genetic; D005787:Gene Frequency; D005838:Genotype; D006509:Hepatitis B / Q000175:diagnosis / Q000453:epidemiology / Q000821:virology*; D006515:Hepatitis B virus / Q000235:genetics* / Q000472:pathogenicity; D006801:Humans; D009154:Mutation; D016366:Open Reading Frames; D010641:Phenotype; D010802:Phylogeny; D012189:Retrospective Studies; D012984:Software; D014764:Viral Proteins / Q000235:genetics*
chemical_list: D018388:Codon, Terminator; D004279:DNA, Viral; D014764:Viral Proteins
keywords: Clinical symptoms; Codon usage bias; Genotype; Hepatitis B virus; Mutation; Phylogenetic tree