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Journal of Virology, March 2009, p. 2285-2297, Vol. 83, No. 5
0022-538X/09/$08.00+0     doi:10.1128/JVI.02180-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Genotyping Schemes for Polyomavirus BK, Using Gene-Specific Phylogenetic Trees and Single Nucleotide Polymorphism Analysis {triangledown}

Chunqing Luo,1 Marta Bueno,2 Jeffrey Kant,1,3 Jeremy Martinson,4 and Parmjeet Randhawa1*

Departments of Pathology,1 Computational Biology,2 Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania,3 Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania4

Received 15 October 2008/ Accepted 15 December 2008

BK virus (BKV) genotyping has been historically based on nucleotides 1744 to 1812 in the VP1 gene. We reevaluated this practice by making BKV whole-genome and gene-specific phylogenetic trees as well as performing single nucleotide polymorphism (SNP) analysis of 162 sequences available in the public domain. It was found that currently known BKV subtypes and subgroups can no longer be reliably determined by sequencing certain partial gene sequences. Phylogenetic trees based on large T-antigen (LTA) allow separation of subtype I into subgroups Ia, Ib1, Ib2, and Ic, with bootstrap values of 100%, which are better than bootstraps obtained using VP1 sequences (bootstrap values of 71 to 97%). Subtype IV can be subdivided into subgroups, but LTA bootstrap values (33 to 80%) are lower than those obtained by whole-genome analysis (68 to 87%). Subtypes V and VI provisionally identified earlier on the basis of more limited sequence data are better classified as subgroups Ib2 and Ib1, respectively. LTA positions 3634, 3772, 3934, and 4339 can serve as a minimal SNP set to distinguish between the four major BKV subtypes. No subtype II-, IVa-, or IVb-defining SNPs are available in the VP1 gene. However, the overall congruence of viral strain classification based on either VP1 or LTA phylogenetic analysis indicates that these two areas of the viral genome are genetically linked. Interstrain genetic recombination between distant loci in the VP1 and LTA areas is not a common event.

* Corresponding author. Mailing address: Division of Transplant Pathology, Department of Pathology, University of Pittsburgh, E737 UPMC-Montefiore Hospital, 3459 Fifth Ave., Pittsburgh, PA 15213. Phone: (412) 647-7646. Fax: (412) 647-5237. E-mail: randhawapa{at}upmc.edu

{triangledown} Published ahead of print on 24 December 2008.

Journal of Virology, March 2009, p. 2285-2297, Vol. 83, No. 5
0022-538X/09/$08.00+0     doi:10.1128/JVI.02180-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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