title: Conserved archetypal configuration of the transcriptional control region during the course of BK polyomavirus evolution.
abstract: BK polyomavirus (BKV) is widespread among humans, asymptomatically infecting children and then persisting in renal tissue. The transcriptional control region (TCR) of the BKV genome is variable among clinical isolates. Thus, archetypal TCRs with a common basic configuration generally occur in BKV isolates from the urine of immunocompromised patients, but rearranged TCRs that possibly arise from the archetypal configuration have also been detected in clinical specimens. To examine the hypothesis that archetypal strains represent wild-type strains circulating in the human population (the archetype hypothesis), we analysed 145 complete viral genomes amplified directly from the urine of non-immunocompromised individuals worldwide. These genomes included 82, three, two and 58 sequences classified as belonging to subtypes I, II, III and IV, respectively. Rearranged TCRs with long duplications or deletions were detected from two subtype I and two subtype IV genomes, but not from the other 141 genomes (thus, the TCRs of these genomes were judged to be archetypal). The variations in the archetypal TCRs were nucleotide substitutions and single-nucleotide deletions, most of which were unique to particular subtypes or subgroups. We confirmed that the four complete BKV genomes with rearranged TCRs did not form a unique lineage on a phylogenetic tree. Collectively, the findings demonstrate that the archetypal TCR configuration has been conserved during the evolution of BKV, providing support for the archetype hypothesis. Additionally, we suggest that 'archetype' should be used as a conceptual term that denotes a prototypical structure that can generate various rearranged TCRs during viral growth in vivo and in vitro.
authors.affiliation: Department of Urology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan.
authors.forename: Yoshiaki
authors.initials: Y
authors.lastname: Yogo
authors.affiliation: Department of Urology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan.
authors.forename: Shan
authors.initials: S
authors.lastname: Zhong
authors.affiliation: Department of Cardiovascular Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 301 Yan Chang Road, Shanghai 200072, PR China.
authors.forename: Yawei
authors.initials: Y
authors.lastname: Xu
authors.affiliation: Department of Cardiovascular Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 301 Yan Chang Road, Shanghai 200072, PR China.
authors.forename: Mengyun
authors.initials: M
authors.lastname: Zhu
authors.affiliation: Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 301 Yan Chang Road, Shanghai 200072, PR China.
authors.forename: Yuegen
authors.initials: Y
authors.lastname: Chao
authors.affiliation: Tsukuba Primate Research Center, National Institute of Biomedical Innovation, 1 Hachimandai, Tsukuba, Ibaraki 305-0843, Japan.|AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
authors.forename: Chie
authors.initials: C
authors.lastname: Sugimoto
authors.affiliation: Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Ikegaya
authors.affiliation: Department of Urology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan.
authors.forename: Ayako
authors.initials: A
authors.lastname: Shibuya
authors.affiliation: Department of Urology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan.
authors.forename: Tadaichi
authors.initials: T
authors.lastname: Kitamura
mesh_terms: D000328:Adult; D000368:Aged; D001739:BK Virus / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D001483:Base Sequence; D002681:China / Q000453:epidemiology; D004279:DNA, Viral / Q000032:analysis; D019143:Evolution, Molecular; D015967:Gene Expression Regulation, Viral; D016679:Genome, Viral; D006801:Humans; D007564:Japan / Q000453:epidemiology; D008875:Middle Aged; D008969:Molecular Sequence Data; D027601:Polyomavirus Infections / Q000453:epidemiology / Q000821:virology; D012529:Saudi Arabia / Q000453:epidemiology; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic; D014412:Tumor Virus Infections / Q000453:epidemiology / Q000821:virology
chemical_list: D004279:DNA, Viral