title: Transcriptional control region rearrangements associated with the evolution of JC polyomavirus.
abstract: JC polyomavirus (JCV) isolates worldwide are classified into three super-lineages (A, B and C), with A and B further split into several lineages and sub-lineages. The transcriptional control region (TCR) of the JCV genome generally has the archetypal configuration, but rearranged TCRs have occasionally been detected in isolates from immunocompetent individuals. To investigate the phylogenetic significance of these rearrangements, we analyzed 298 TCR sequences all derived from complete JCV genomes directly cloned from the urine of non-immunocompromised individuals. While sporadic rearrangements were found in many lineages and sub-lineages, common rearrangements were identified in all, or essentially all, isolates belonging to particular lineages or sub-lineages. Interestingly, several common rearrangements were also detected as sporadic rearrangements in other lineages or sub-lineages. This observation suggests that during the course of JCV evolution, JCV strains with sporadic rearrangements became predominant over archetypal TCRs in some JCV lineages or sub-lineages.
authors: Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan. yogo-tky@umin.ac.jp
authors: Yoshiaki
authors: Y
authors: Yogo
authors: Shan
authors: S
authors: Zhong
authors: Ayako
authors: A
authors: Shibuya
authors: Tadaichi
authors: T
authors: Kitamura
authors: Yukio
authors: Y
authors: Homma
mesh_terms: D004279:DNA, Viral / Q000032:analysis / Q000235:genetics; D019143:Evolution, Molecular; D015967:Gene Expression Regulation, Viral; D015321:Gene Rearrangement; D016679:Genome, Viral; D007577:JC Virus / Q000737:chemistry* / Q000145:classification* / Q000235:genetics; D014158:Transcription, Genetic; D014412:Tumor Virus Infections / Q000453:epidemiology / Q000821:virology
chemical_list: D004279:DNA, Viral