title: RNA recombination in Hepatitis delta virus: Identification of a novel naturally occurring recombinant.
abstract: OBJECTIVE
  Hepatitis delta virus (HDV) is the only animal RNA virus that has an unbranched rod-like genome with ribozyme activity. It replicates in the nucleus by host RNA polymerase via a rolling circle mechanism. Similar to many RNA viruses encoding their own RNA-dependent RNA polymerases, homologous recombination of HDV occurs in mixed-genotype infections and in cultured cells cotransfected with two HDV sequences, as demonstrated by molecular analyses.
  
  
  METHODS
  Among 237 published complete genomic sequences, 34 sequences were reported from the small and isolated Miyako Island, Japan, and belonged to the Asia-specific genotypes, HDV-2 and HDV-4 (the majority of them belonged to the known Miyako Island-specific subgroup, HDV-4M). We investigated the presence of naturally occurring HDV recombinant in Miyako Island using phylogenetic and recombination analyses.
  
  
  RESULTS
  We identified a two-switch HDV-4/4M intersubtype recombinant with an unbranched rod-like RNA genome.
  
  
  CONCLUSIONS
  Our data suggest that RNA recombination plays an important role in the rapid evolution of HDV, allowing the production of new HDV strains with correct genomic structures.
authors.affiliation: Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan; Department of Microbiology and Immunology, Chang Gung University, Taoyuan, Taiwan.
authors.forename: Chia-Chi
authors.initials: CC
authors.lastname: Lin
authors.affiliation: Bioinformatics Center, Chang Gung University, Taoyuan, Taiwan.
authors.forename: Chi-Ching
authors.initials: CC
authors.lastname: Lee
authors.affiliation: Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan; Department of Microbiology and Immunology, Chang Gung University, Taoyuan, Taiwan.
authors.forename: Siao-Han
authors.initials: SH
authors.lastname: Lin
authors.affiliation: Bioinformatics Center, Chang Gung University, Taoyuan, Taiwan.
authors.forename: Po-Jung
authors.initials: PJ
authors.lastname: Huang
authors.affiliation: Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan; Department of Microbiology and Immunology, Chang Gung University, Taoyuan, Taiwan; Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.
authors.forename: Hsin-Pai
authors.initials: HP
authors.lastname: Li
authors.affiliation: Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan; Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.
authors.forename: Yu-Sun
authors.initials: YS
authors.lastname: Chang
authors.affiliation: Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan; Bioinformatics Center, Chang Gung University, Taoyuan, Taiwan; Department of Parasitology, Chang Gung University, Taoyuan, Taiwan. Electronic address: petang@mail.cgu.edu.tw.
authors.forename: Petrus
authors.initials: P
authors.lastname: Tang
authors.affiliation: Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan; Department of Microbiology and Immunology, Chang Gung University, Taoyuan, Taiwan. Electronic address: pa0728@mail.cgu.edu.tw.
authors.forename: Mei
authors.initials: M
authors.lastname: Chao
mesh_terms: D001483:Base Sequence; D016679:Genome, Viral / Q000235:genetics*; D005838:Genotype; D003699:Hepatitis D / Q000453:epidemiology / Q000821:virology; D003698:Hepatitis Delta Virus / Q000145:classification / Q000235:genetics*; D006801:Humans; D007564:Japan / Q000453:epidemiology; D010802:Phylogeny; D012313:RNA / Q000235:genetics*; D012367:RNA, Viral / Q000235:genetics*; D011995:Recombination, Genetic / Q000235:genetics*; D017423:Sequence Analysis, RNA; D014744:Vietnam / Q000453:epidemiology
chemical_list: D012367:RNA, Viral; C039919:RNA, recombinant; D012313:RNA
keywords: RNA recombination; hepatitis delta virus