| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
Short Communication |
1 Department of Urology, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
2 Department of Urology, Tokyo Women's Medical University, Tokyo, Japan
3 Department of Urology, Iwate Medical University School of Medicine, Morioka, Japan
4 Japanese Foundation for AIDS Prevention, Tokyo, Japan
5 Kobe Institute of Health, Kobe, Japan
Correspondence
Yoshiaki Yogo
yogo-tky{at}umin.ac.jp
 |
ABSTRACT |
|---|
 TOP ABSTRACT MAIN TEXTREFERENCES |
|---|
The GenBank/EMBL/DDBJ accession numbers of the sequences reported in this paper are AB217917–AB217921.
|
MAIN TEXT |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
). Although host factors (e.g. immunological conditions) are important in the pathogenesis of PVAN (de Bruyn & Limaye, 2004), the genetic change of BKPyV may also involve the progression of the disease. Indeed, several authors have reported sequence rearrangements in the transcriptional control region (TCR) of the BKPyV genome derived from diseased tissue (Chen et al., 2001; Randhawa et al., 2003). Furthermore, genetic variations in the BKPyV VP1 gene have been detected in bioptic renal specimens from patients with PVAN (Baksh et al., 2001; Randhawa et al., 2002). Nevertheless, the implications of these genetic changes for the pathogenesis of PVAN remain unclear.
Chen et al. (2004) recently investigated the genetic variability of BKPyV in vivo. They sequenced several full-length viral DNA clones obtained, using PCR, from the striated muscle and heart of a patient with BKPyV-associated capillary leak syndrome (BKPyVCAP) and also from the urine of one human immunodeficiency virus type 2-positive subject (BKPyVHI) and one healthy control subject (BKPyVHC). They detected a high degree of variation (mean difference, 0·29 % per site) in the coding region among clones in BKPyVCAP, and a lower, but still remarkable, degree of variation (mean difference, 0·1–0·2 % per site) among clones in BKPyVHI or BKPyVHC. Non-synonymous nucleotide substitutions (i.e. those resulting in amino acid substitutions) were frequently observed in all subjects. In addition, the authors did not identify a potentially prototypal sequence that might have generated the variant sequences detected in each subject.
The findings reported by Chen et al. (2004) presented a sharp contrast to observations made with JC polyomavirus (JCPyV), a virus closely related to BKPyV. Using the standard method of cloning that allows one to obtain intact viral DNA molecules (Sambrook et al., 1989), Zheng et al. (2004) established and sequenced five to nine complete JCPyV DNA clones in each of 11 healthy individuals (parents and children in five families), and compared the resultant sequences in each individual. Variations in the coding region were detected in six individuals, but not in five individuals. The detected variations were mostly single-nucleotide substitutions, and only three of 10 nt substitutions caused amino acid substitutions. Furthermore, the authors detected possible prototypal sequences at the nodes of family specific clusters of phylogenetic trees.
We examined the stability of the BKPyV genome in RT patients without PVAN, as a basis of future studies analysing possible genetic changes of BKPyV associated with the pathogenesis or progression of PVAV (see above). We established multiple full-sized BKPyV DNA clones from the urine of each of six RT patients with surviving renal allografts, by using the standard method of molecular cloning (Sambrook et al., 1989). In each patient, three to five complete BKPyV DNA clones were sequenced and the resultant sequences were compared in each patient.
RT patients analysed in this study are shown in Table 1. Entire BKPyV DNAs were cloned into pUC19 at the unique BamHI site by the standard method (Sambrook et al., 1989) as described previously (Yogo et al., 1991). The complete BKPyV DNA clones were prepared using a Qiagen Plasmid Maxi kit. Purified plasmids were sequenced as described elsewhere (T. Takasaka and others, unpublished data). The determined and reference sequences were aligned using the CLUSTAL W program (Thompson et al., 1994). Translation of nucleotide sequences into amino acid sequences was performed with GENETYX-MAC version 11.10 (Genetyx). A neighbour-joining (NJ) phylogenetic tree (Saitou & Nei, 1987) was constructed using the CLUSTAL W program (Thompson et al., 1994). Divergences were estimated with the two-parameter method (Kimura, 1980). The phylogenetic tree was visualized using TREEVIEW (Page, 1996). The confidence of branching patterns of the NJ trees was assessed based on 1000 bootstrap replicates (Felsenstein, 1985).
|
). (i) Three sequences, TW-1, TW-1a and TW-1b, were detected in patient 1. In reference to TW-1, TW-1a and TW-1b carried single nucleotide substitutions at nt 1807 and 1744, respectively, within the VP1 gene [nucleotide numbers are those of the strain Dunlop (Seif et al., 1979)]. Both nucleotide substitutions resulted in amino acid substitutions within a predicted outer loop (the BC loop) of the VP1 protein (Chang et al., 1996) (Table 2). (ii) Two sequences, TW-3 and TW-3a, were detected in patient 2. In reference to TW-3, TW-3a carried a single nucleotide substitution at nt 410 within the agnogene. This nucleotide substitution resulted in an amino acid substitution. (iii) A single sequence, TW-4, was detected in patient 3. (iv) Similarly, a single sequence, TW-5, was detected in patient 4. (v) Two sequences, TW-8 and TW-8a, were detected in patient 5. In reference to TW-8, TW-8a carried a single nucleotide substitution at nt 1156 within the VP2/3 gene. This nucleotide substitution inserted a stop codon. (vi) Finally, two sequences, THK-9 and THK-9a, were detected in patient 6. In reference to THK-9, THK-9a carried a single nucleotide substitution at nt 1127 within the VP2/3 gene. This nucleotide substitution did not result in any amino acid substitution.
|
). In the present study, we did not detect any difference in the TCR among clones derived from each patient.
To elucidate the evolutionary relationships among several unique sequences detected in patients 1, 2, 5 and 6, we constructed an NJ phylogenetic tree from the BKPyV DNA sequences detected in these patients together with reference sequences reported previously (Seif et al., 1979; Tavis et al., 1989; T. Takasaka and others, unpublished data). On the resultant tree (Fig. 1), the BKPyV DNA sequences in patients 1, 2, 5 and 6 formed individual clusters. We detected a sequence (TW-1, TW-3a, TW-8 or THK-9) at the node of each cluster, probably representing the prototypal sequence that generated variant sequences in each patient. It may be worth noting that the prototypal sequences were usually the major ones (Table 2
).
|
The finding noted immediately above is contradictory to a high intra-strain genetic diversity in BKPyV suggested by Chen et al. (2004). This discrepancy may be related to the difference in the methods used to obtain a full-sized genome. We used standard molecular cloning (Sambrook et al., 1989), whereas Chen et al. (2004) used PCR amplification. Standard molecular cloning warrants the isolation of intact complete viral genomes, while PCR amplification inevitably involves replication errors, even though the frequency of errors may be reduced by using a thermostable DNA polymerase with proofreading activity. The frequently detected variations in BKPyV (Chen et al., 2004) (see above) could have been introduced by the authors during PCR. Nevertheless, it remains to be elucidated whether the BKPyV genome undergoes a high variability in a specific disease, i.e. BKPyVCAP.
In this study, we detected four non-synonymous nucleotide substitutions and one synonymous substitution. Of the four non-synonymous substitutions, three resulted in amino acid changes in VP1 and the agnoprotein, and one generated an incomplete VP2/3 protein due to the insertion of a stop codon. While viruses with incomplete VP2/3 proteins may not be infectious, it remains to be elucidated whether the amino acid changes in VP1 and the agnoprotein cause alterations in the properties of BKPyV.
|
ACKNOWLEDGEMENTS |
|---|
|
REFERENCES |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
Chang, D., Liou, Z.-M., Ou, W.-C., Wang, K.-Z., Wang, M., Fung, C.-Y. & Tsai, R.-T. (1996). Production of the antigen and the antibody of the JC virus major capsid protein VP1. J Virol Methods 59, 177–187.[CrossRef][Medline]
Chen, C.-H., Wen, M.-C., Wang, M., Lian, J.-D., Wu, M.-J., Cheng, C.-H., Shu, K.-H. & Chang, D. (2001). A regulatory region rearranged BK virus is associated with tubulointerstitial nephritis in a rejected renal allograft. J Med Virol 64, 82–88.[CrossRef][Medline]
Chen, Y., Sharp, P. M., Fowkes, M., Kocher, O., Joseph, J. T. & Koralnik, I. J. (2004). Analysis of 15 novel full-length BK virus sequences from three individuals: evidence of a high intra-strain genetic diversity. J Gen Virol 85, 2651–2663.
de Bruyn, G. & Limaye, A. P. (2004). BK virus-associated nephropathy in kidney transplant recipients. Rev Med Virol 14, 193–205.[CrossRef][Medline]
Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111–120.[CrossRef][Medline]
Page, R. D. M. (1996). TREEVIEW: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12, 357–358.
Randhawa, P. S., Khaleel-Ur-Rehman, K., Swalsky, P. A., Vats, A., Scantlebury, V., Shapiro, R. & Finkelstein, S. (2002). DNA sequencing of viral capsid protein VP-1 region in patients with BK virus interstitial nephritis. Transplantation 73, 1090–1094.[Medline]
Randhawa, P., Zygmunt, D., Shapiro, R., Vats, A., Weck, K., Swalsky, P. & Finkelstein, S. (2003). Viral regulatory region sequence variations in kidney tissue obtained from patients with BK virus nephropathy. Kidney Int 64, 743–747.[CrossRef][Medline]
Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.[Abstract]
Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989). Molecular Cloning, a Laboratory Manual, 2nd edn. Cold Spring Harbor: Cold Spring Harbor Laboratory.
Seif, I., Khoury, G. & Dhar, R. (1979). The genome of human papovavirus BKV. Cell 18, 963–977.[CrossRef][Medline]
Takasaka, T., Goya, N., Tokumoto, T. & 14 other authors (2004). Subtypes of BK virus prevalent in Japan and variation in their transcriptional control region. J Gen Virol 85, 2821–2827.
Tavis, J. E., Walker, D. L., Gardner, S. D. & Frisque, R. J. (1989). Nucleotide sequence of the human polyomavirus AS virus, an antigenic variant of BK virus. J Virol 63, 901–911.
Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673–4680.
Yogo, Y., Iida, T., Taguchi, F., Kitamura, T. & Aso, Y. (1991). Typing of human polyomavirus JC virus on the basis of restriction fragment length polymorphisms. J Clin Microbiol 29, 2130–2138.
Zheng, H. Y., Kitamura, T., Takasaka, T., Chen, Q. & Yogo, Y. (2004). Unambiguous identification of JC polyomavirus strains transmitted from parents to children. Arch Virol 149, 261–273.[CrossRef][Medline]
Received 22 July 2005;
accepted 4 November 2005.
This article has been cited by other articles:
|
|
 |
|
  N. G. Hoffman, L. Cook, E. E. Atienza, A. P. Limaye, and K. R. Jerome Marked Variability of BK Virus Load Measurement Using Quantitative Real-Time PCR among Commonly Used Assays J. Clin. Microbiol., August 1, 2008; 46(8): 2671 - 2680. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Gosert, C. H. Rinaldo, G. A. Funk, A. Egli, E. Ramos, C. B. Drachenberg, and H. H. Hirsch Polyomavirus BK with rearranged noncoding control region emerge in vivo in renal transplant patients and increase viral replication and cytopathology J. Exp. Med., April 14, 2008; 205(4): 841 - 852. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. A. Shackelton, A. Rambaut, O. G. Pybus, and E. C. Holmes JC Virus Evolution and Its Association with Human Populations J. Virol., October 15, 2006; 80(20): 9928 - 9933. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. M. Sharma, G. Gupta, A. Vats, R. Shapiro, and P. Randhawa Phylogenetic Analysis of Polyomavirus BK Sequences J. Virol., September 15, 2006; 80(18): 8869 - 8879. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Nukuzuma, T. Takasaka, H.-Y. Zheng, S. Zhong, Q. Chen, T. Kitamura, and Y. Yogo Subtype I BK polyomavirus strains grow more efficiently in human renal epithelial cells than subtype IV strains J. Gen. Virol., July 1, 2006; 87(7): 1893 - 1901. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
| INT J SYST EVOL MICROBIOL | MICROBIOLOGY | J GEN VIROL |
| J MED MICROBIOL | ALL SGM JOURNALS | |
50 % are shown). Subtypes Ia, Ib, Ic, III and IV and sequences detected in patients 1, 2, 5 and 6 are indicated.