Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2017 Apr;55(4):1177-1185.
doi: 10.1128/JCM.01180-16. Epub 2017 Feb 1.

A Simple and Reliable Strategy for BK Virus Subtyping and Subgrouping

Virginie Morel  1   2 , Elodie Martin  2 , Catherine François  1   2 , François Helle  2 , Justine Faucher  3 , Thomas Mourez  4   5 , Gabriel Choukroun  3   6 , Gilles Duverlie  1   2 , Sandrine Castelain  1   2 , Etienne Brochot  7   2
Affiliations

A Simple and Reliable Strategy for BK Virus Subtyping and Subgrouping

Virginie Morel et al. J Clin Microbiol. 2017 Apr.

Abstract

BK virus (BKV)-associated diseases in transplant recipients are an emerging issue. However, identification of the various BK virus subtypes/subgroups is a long and delicate process on the basis of currently available data. Therefore, we wanted to define a simple and effective one-step strategy for characterizing all BK virus strains from the VP1 gene sequence. Based on the analysis of 199 available complete DNA VP1 sequences, phylogenetic trees, alignments, and isolated polymorphisms were used to define an effective strategy for distinguishing the 12 different BK virus subtypes/subgroups. Based on the 12 subtypes identified from the 199 complete BKV VP1 sequences (1,089 bp), 60 mutations that can be used to differentiate these various subtypes/subgroups were identified. Some genomic areas were more variable and comprised mutational hot spots. From a subregion of only 100 bp in the VP1 region (1977 through 2076), we therefore constructed an algorithm that enabled rapid determination of all BKV subtypes/subgroups with 99% agreement (197/199) relative to the complete VP1 sequence. We called this domain of the BK viral genome the BK typing and grouping region (BKTGR). Finally, we validated our viral subtype identification process in a population of 100 transplant recipients with 100% efficiency. The new simpler method of BKV subtyping/subgrouping reported here constitutes a useful tool for future studies that will help us to more clearly understand the impact of BKV subtypes/subgroups on diagnosis, infection, and BK virus-associated diseases.

Keywords: BK virus; BK virus strains; subtyping; transplantation.

PubMed Disclaimer

Figures

FIG 1
FIG 1
Phylogenetic tree constructed by the maximum likelihood method using 199 complete BKV VP1 gene sequences available in GenBank. The asterisk indicates the strain for which subtyping/subgrouping showed discordant results according to the BKTGR scheme.
FIG 2
FIG 2
BKV subtyping/subgrouping algorithm based on the mutations detected in the BKTGR region of VP1.
See this image and copyright information in PMC

References

    1. Hirsch HH, Knowles W, Dickenmann M, Passweg J, Klimkait T, Mihatsch MJ, Steiger J. 2002. Prospective study of polyomavirus type BK replication and nephropathy in renal-transplant recipients. N Engl J Med 347:488–496. doi:10.1056/NEJMoa020439. - DOI - PubMed
    1. Dropulic LK, Jones RJ. 2008. Polyomavirus BK infection in blood and marrow transplant recipients. Bone Marrow Transplant 41:11–18. doi:10.1038/sj.bmt.1705886. - DOI - PMC - PubMed
    1. Jin L. 2001. Molecular methods for identification and genotyping of BK virus. Methods Mol Biol 165:33–48. - PubMed
    1. Krumbholz A, Bininda-Emonds OR, Wutzler P, Zell R. 2008. Evolution of four BK virus subtypes. Infect Genet Evol 8:632–643. doi:10.1016/j.meegid.2008.05.006. - DOI - PubMed
    1. Zhong S, Randhawa PS, Ikegaya H, Chen Q, Zheng HY, Suzuki M, Takeuchi T, Shibuya A, Kitamura T, Yogo Y. 2009. Distribution patterns of BK polyomavirus (BKV) subtypes and subgroups in American, European and Asian populations suggest co-migration of BKV and the human race. J Gen Virol 90:144–152. doi:10.1099/vir.0.83611-0. - DOI - PubMed

Publication types

Substances

LinkOut - more resources