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Related Experiment Videos

Evolution of BK virus based on complete genome data.

Yuriko Nishimoto1, Tomokazu Takasaka, Masami Hasegawa

  • 1The Institute of Statistical Mathematics, Research Organization of Information and Systems, Minato-ku, Tokyo, 106-8569, Japan.

Journal of Molecular Evolution
|August 10, 2006
PubMed
Summary
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BK virus (BKV) evolution reveals distinct subtype relationships. Analysis of viral genes showed clear subtype clades, but deeper evolutionary connections remained unclear, with some evidence of positive selection in key regions.

Area of Science:

  • Virology
  • Evolutionary Biology
  • Molecular Genetics

Background:

  • Human polyomavirus BK virus (BKV) is widespread, with subtypes (I-IV) identified by immunological reactivity.
  • Variations in the major capsid protein (VP1) gene's epitope region are linked to BKV's antigenic diversity and subtype classification.

Purpose of the Study:

  • To investigate the evolutionary relationships among 28 BK virus isolates from subtypes I, III, and IV using complete protein-encoding gene sequences.
  • To explore potential positive selection pressures driving BKV evolution, particularly within the VP1 epitope region.

Main Methods:

  • Phylogenetic analysis using maximum likelihood trees (GTR + Gamma + I model) on individual and concatenated viral genes.
  • Application of sophisticated likelihood models, including codon structure, to refine phylogenetic relationships.

Related Experiment Videos

  • Examination of positive selection using the nonsynonymous/synonymous rate ratio across entire genes and the epitope region.

    • Main Results:

    • Phylogenetic trees consistently divided the 28 BKV isolates into three distinct clades corresponding to subtypes I, III, and IV.
    • Deeper phylogenetic branching remained ambiguous even with advanced models accounting for codon structure.
    • Analysis of the epitope region identified specific sites potentially under positive selection, correlating with subtype-specific polymorphisms.

    Conclusions:

    • The study clarifies subtype I, III, and IV evolutionary relationships within BK virus.
    • While overall BKV evolution lacks strong evidence for positive selection, specific sites in the VP1 epitope region show potential selection, contributing to antigenic diversity.