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Journal of Clinical Microbiology, May 2009, p. 1402-1411, Vol. 47, No. 5
0095-1137/09/$08.00+0 doi:10.1128/JCM.02065-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.
High Frequency and Diversity of Rearrangements in Polyomavirus BK Noncoding Regulatory Regions Cloned from Urine and Plasma of Israeli Renal Transplant Patients and Evidence for a New Genetic Subtype 
,
Tsachi Tsadok Perets,1,2
Ilana Silberstein,2
Jana Rubinov,2
Ronit Sarid,1
Ella Mendelson,1,2*,
and
Lester M. Shulman2*,
The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel,1 Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Tel-Hashomer, Israel2
Received 26 October 2008/ Returned for modification 22 December 2008/ Accepted 20 February 2009
Polyomavirus BK (BKV) establishes latent infection in various human tissues, including the kidney. Reactivation following renal transplantation (RT) may cause BKV-associated nephropathy, leading to graft loss. BKV reactivation is often associated with extensive rearrangements in the BKV noncoding regulatory region (NCRR). We explored the formation and predominance of the rearrangements versus the diversity of the rearrangements by cloning and characterizing PCR-amplified NCRR sequences from six Israeli RT patients. We found a high frequency and a high degree of diversity of rearrangements: NCRRs that contained major rearrangements (mrNCRRs), including large insertions and deletions, were detected in 0 to 100% of the clones from individual samples (mean, 50% and 67% in plasma and urine, respectively). In addition, we found a high frequency of mrNCRRs that contained single-nucleotide variations (snvNCRRs) among identical mrNCRRs and archetype clones. mrNCRRs were present in plasma and in concomitantly collected urine samples, but for each patient, only a subset of the mrNCRRs and snvNCRRs were present in both compartments at the same time and/or in subsequent samples from the same compartment. Some mrNCRRs were observed over several months, indicating the continuous replication of the viral genomes carrying them. Phylogenetic analysis based on the snvNCRR in the archetype clones grouped isolates from four of the patients into a new subgroup of genotype IV. Genotypes Ib-1 and Ib-2 were also found. Isolates from two patients had NCRRs from two genotypes, one concurrently with a RT and one after a second RT. Our study prompts further investigation of the functional consequences of NCRR rearrangements to assess their biological significance and their putative role in disease progression and prognosis.
* Corresponding author. Mailing address for Lester M. Shulman: Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Hashomer 52621, Israel. Phone: 972-3-530-2341. Fax: 972-3-535-0436. E-mail: lester.shulman{at}sheba.health.gov.il. Mailing address for Ella Mendelson: Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Hashomer 52621, Israel. Phone: 972-3-530-2421. Fax: 972-3-535-0436. E-mail: ellamen{at}sheba.health.gov.il
Published ahead of print on 4 March 2009.
Supplemental material for this article may be found at http://jcm.asm.org/.
Both L.M.S. and E.M. contributed equally to this study.
Journal of Clinical Microbiology, May 2009, p. 1402-1411, Vol. 47, No. 5
0095-1137/09/$08.00+0 doi:10.1128/JCM.02065-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.
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