title: New findings regarding the epidemic history and population dynamics of Japan-indigenous genotype 3 hepatitis E virus inferred by molecular evolution.
abstract: BACKGROUND
  Since previous studies have investigated the population dynamics of Japan-indigenous genotype 3 hepatitis E virus (HEV) using virus sequences, more nucleotide sequences have been determined, and new techniques have been developed for such analysis.
  
  
  OBJECTIVE
  To prevent future hepatitis E epidemic in Japan, this study aimed to elucidate the cause of past HEV expansion.
  
  
  METHODS
  The epidemic history of Japan-indigenous genotype 3 HEV was determined using the coalescent analysis framework. Bayesian skyline plot (BSP) and Bayesian estimate of phylogeny with relaxed molecular clock models were calculated using Markov chain Monte Carlo sampling.
  
  
  RESULTS
  Japan-indigenous strains consist of New World strains (subtype 3a), Japanese strains (3b) and European strains (3e). The oldest lineage, 3b, appeared around 1929. Lineages 3a and 3e appeared around 1960. BSPs indicated similar radical population growth of the 3a and 3b lineages from 1960 to 1980.
  
  
  CONCLUSIONS
  Population dynamics of the three lineages shared some common characteristics, but had distinguishing features. The appearance of 3a and 3e lineages coincides with the increase of large-race pig importation from Europe and the USA after 1960. The epidemic phase of 3a and 3b strains from 1960 to 1980 could be related to increased opportunity for HEV infection arising from large-scale pig breeding since 1960. Our observations revealed new findings concerning the close relationship between the epidemic history of Japan-indigenous genotype 3 HEV and the improvement of the Japanese pig industry. Infection control in pig farms should be an effective method of preventing HEV infection in humans.
authors.affiliation: Department of Internal Medicine, Fujita Health University Nanakuri Sanatorium, Mie, Japan. tanakano@sf.starcat.ne.jp
authors.forename: Tatsunori
authors.initials: T
authors.lastname: Nakano
authors.forename: Kazuaki
authors.initials: K
authors.lastname: Takahashi
authors.forename: Oliver G
authors.initials: OG
authors.lastname: Pybus
authors.forename: Naoaki
authors.initials: N
authors.lastname: Hashimoto
authors.forename: Hideaki
authors.initials: H
authors.lastname: Kato
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Okano
authors.forename: Makoto
authors.initials: M
authors.lastname: Kobayashi
authors.forename: Naoki
authors.initials: N
authors.lastname: Fujita
authors.forename: Katsuya
authors.initials: K
authors.lastname: Shiraki
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Takei
authors.forename: Minoru
authors.initials: M
authors.lastname: Ayada
authors.forename: Masahiro
authors.initials: M
authors.lastname: Arai
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Okamoto
authors.forename: Shunji
authors.initials: S
authors.lastname: Mishiro
mesh_terms: D000818:Animals; D001483:Base Sequence; D001499:Bayes Theorem; D003106:Colon / Q000821:virology; D019143:Evolution, Molecular; D016751:Hepatitis E / Q000453:epidemiology* / Q000821:virology*; D016752:Hepatitis E virus / Q000235:genetics*; D006801:Humans; D007564:Japan / Q000453:epidemiology; D008099:Liver / Q000821:virology; D008390:Markov Chains; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D010802:Phylogeny; D011157:Population Dynamics; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D034421:Sus scrofa / Q000821:virology*; D014764:Viral Proteins / Q000235:genetics*
chemical_list: C400971:ORF2 protein, Hepatitis E virus; D014764:Viral Proteins