title: Reduced genetic distance and high replication levels increase the RNA recombination rate of hepatitis delta virus.
abstract: Hepatitis delta virus (HDV) replication is carried out by host RNA polymerases. Since homologous inter-genotypic RNA recombination is known to occur in HDV, possibly via a replication-dependent process, we hypothesized that the degree of sequence homology and the replication level should be related to the recombination frequency in cells co-expressing two HDV sequences. To confirm this, we separately co-transfected cells with three different pairs of HDV genomic RNAs and analyzed the obtained recombinants by RT-PCR followed by restriction fragment length polymorphism and sequencing analyses. The sequence divergence between the clones ranged from 24% to less than 0.1%, and the difference in replication levels was as high as 100-fold. As expected, significant differences were observed in the recombination frequencies, which ranged from 0.5% to 47.5%. Furthermore, varying the relative amounts of parental RNA altered the dominant recombinant species produced, suggesting that template switching occurs frequently during the synthesis of genomic HDV RNA. Taken together, these data suggest that during the host RNA polymerase-driven RNA recombination of HDV, both inter- and intra-genotypic recombination events are important in shaping the genetic diversity of HDV.
authors.affiliation: Division of Mcrobiology, Graduate Institue of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-yang 333, Taiwan. Electronic address: d9801203@stmail.cgu.edu.tw.
authors.forename: Chia-Chi
authors.initials: CC
authors.lastname: Lin
authors.affiliation: Division of Mcrobiology, Graduate Institue of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-yang 333, Taiwan. Electronic address: russelltools1201@gmail.com.
authors.forename: Zhi-Wei
authors.initials: ZW
authors.lastname: Yang
authors.affiliation: Division of Mcrobiology, Graduate Institue of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-yang 333, Taiwan. Electronic address: isbisb@mail.cgu.edu.tw.
authors.forename: Shan-Bei
authors.initials: SB
authors.lastname: Iang
authors.affiliation: Division of Mcrobiology, Graduate Institue of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-yang 333, Taiwan; Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Tao-yang 333, Taiwan. Electronic address: pa0728@mail.cgu.edu.tw.
authors.forename: Mei
authors.initials: M
authors.lastname: Chao
mesh_terms: D014644:Genetic Variation; D003698:Hepatitis Delta Virus / Q000235:genetics* / Q000502:physiology*; D006801:Humans; D012150:Polymorphism, Restriction Fragment Length; D012367:RNA, Viral / Q000235:genetics*; D011995:Recombination, Genetic; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014162:Transfection; D014779:Virus Replication
chemical_list: D012367:RNA, Viral
keywords: Hepatitis delta virus; RNA recombination; Template-switching; Viral evolution