title: Evolution and genetic characterization of hepatitis A virus isolates in China.
abstract: OBJECTIVE
  Hepatitis A virus (HAV), transmitted mainly through the fecal-oral route, is one of the major causes of acute viral hepatitis worldwide. HAV is endemic in China. This study performed genetic and evolutionary analysis of HAV isolates circulated in the country.
  
  
  METHODS
  Clinical samples were collected and HAV nucleotide and deduced amino acid sequences were analyzed. 70 representative sequences of HAV VP3-VP1-2A regions sampled from 1988 to 2014 were compared and characterized using the Bayesian Markov Chain Monte Carlo approach (BEAST software, Version1.7.5).
  
  
  RESULTS
  All isolates from China in this study belonged to genotype I, with most of the samples clustering in subgenotype IA, while several unique amino acid variants were observed. The estimated mean substitution rate was 5.56×10(-4) substitutions / site / year, the time to the most recent common ancestor of genotype I isolates in China was calculated to be around 180 years ago. Skyline plots showed the incidence of HAV went down gradually from the mid-1990s.
  
  
  CONCLUSIONS
  The evolution estimations were consistent with the laboratory and epidemiological results. Several isolates from China showed amino acid changes close to the immunodominant sites, which needs to be further analyzed. The study results have indicated the effectiveness of improving economic and sanitation levels together with HAV vaccination to control HAV-related infections in China.
authors.affiliation: National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China.
authors.forename: Hao
authors.initials: H
authors.lastname: Wang
authors.affiliation: National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China.
authors.forename: Xin-Ying
authors.initials: XY
authors.lastname: Wang
authors.affiliation: National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China.
authors.forename: Hui-Hui
authors.initials: HH
authors.lastname: Zheng
authors.affiliation: National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China. Electronic address: caojy@126.com.
authors.forename: Jing-Yuan
authors.initials: JY
authors.lastname: Cao
authors.affiliation: National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China.
authors.forename: Wen-Ting
authors.initials: WT
authors.lastname: Zhou
authors.affiliation: National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China. Electronic address: shengli_bi@163.com.
authors.forename: Sheng-Li
authors.initials: SL
authors.lastname: Bi
mesh_terms: D000595:Amino Acid Sequence; D001499:Bayes Theorem; D002681:China; D019143:Evolution, Molecular; D005838:Genotype; D030041:Hepatitis A virus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D010802:Phylogeny; D012367:RNA, Viral / Q000737:chemistry
chemical_list: D012367:RNA, Viral
keywords: China; Genotype; Hepatitis A virus; MCMC; Substitution rates