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Evolution of BK Virus Based on Complete Genome Data

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Abstract

The human polyomavirus BK virus (BKV) is ubiquitous in humans, infecting children asymptomatically. BKV is the only primate polyomavirus that has subtypes (I–IV) distinguishable by immunological reactivity. Nucleotide (nt) variations in a major capsid protein (VP1) gene region (designated the epitope region), probably responsible for antigenic diversity, have been used to classify BKV isolates into subtypes. Here, with all the protein-encoding gene sequences, we attempted to elucidate the evolutionary relationships among 28 BKV isolates belonging to subtypes I, III, and IV (no isolate belonging to subtype II, a minor one, was included). First, using the GTR + Γ + I model, maximum likelihood trees were reconstructed for individual viral genes as well as for concatenated viral genes. On the resultant trees, the 28 BKV isolates were consistently divided into three clades corresponding to subtypes I, III, and IV, although bootstrap probabilities are not always high. Then we used more sophisticated likelihood models, one of which takes account of codon structure, to elucidate the phylogenetic relationships among BKV subtypes, but the phylogeny of the deep branchings remained ambiguous. Furthermore, the possibility of positive selection in the evolution of BKV was examined using the nonsynonymous/synonymous rate ratio as a measure of selection. An analysis based on entire genes could not detect any strong evidence for positive selection, but that based on the epitope region identified a few sites potentially under positive selection (these sites were among those showing subtype linked polymorphisms).

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Acknowledgments

We are grateful to all urine donors. We thank Drs. N. Goya, Y. Ogawa, A. Momose, T. Fujioka, and H. Akiyama for providing urine samples and Drs. J. van der Noordaa and R. Rubinstein for providing BKV DNA clones. This study was supported in part by grants from the Ministry of Health, Labor and Welfare, Japan, from the Japan Society for the Promotion of Science, and from TRIC, Research Organization of Information and Systems.

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Authors and Affiliations

  1. The Institute of Statistical Mathematics, Research Organization of Information and Systems, 4-6-7 Minami-Azabu, Minato-ku, Tokyo, 106-8569, Japan

    Yuriko Nishimoto & Masami Hasegawa

  2. Department of Biosystems Science, Graduate University for Advanced Studies, Hayama, 240-0193, Japan

    Yuriko Nishimoto & Masami Hasegawa

  3. Department of Urology, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan

    Tomokazu Takasaka, Huai-Ying Zheng, Tadaichi Kitamura & Yoshiaki Yogo

  4. Japanese Foundation for AIDS Prevention, 1-23-11 Toranomon, Minato-ku, Tokyo, 105-0001, Japan

    Huai-Ying Zheng & Qin Chen

  5. AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan

    Chie Sugimoto

  6. Tsukuba Primate Research Center, National Institute of Biomedical Innovation, 1 Hachimandai, Tsukuba, Ibaraki, 305-0843, Japan

    Chie Sugimoto

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  1. Yuriko Nishimoto
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  2. Tomokazu Takasaka
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  3. Masami Hasegawa
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  4. Huai-Ying Zheng
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  5. Qin Chen
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  7. Tadaichi Kitamura
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  8. Yoshiaki Yogo
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Correspondence to Yoshiaki Yogo.

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These author Yuriko Nishimoto and Tomokazu Takasaka contributed equally to this article.

[Reviewing Editor: Dr. Rasmus Nielsen]

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Nishimoto, Y., Takasaka, T., Hasegawa, M. et al. Evolution of BK Virus Based on Complete Genome Data. J Mol Evol 63, 341–352 (2006). https://doi.org/10.1007/s00239-005-0092-5

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