{'fraction_non_alphanumeric': 0.040619547583335885, 'fraction_numerical': 0.02292693379044354, 'mean_word_length': 4.710540115364447, 'pattern_counts': {'":': 0, '<': 16, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 3, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
Polyomavirus BK with rearranged noncoding control region emerge in vivo in renal transplant patients and increase viral replication and cytopathology

Immunosuppression is required for BK viremia and polyomavirus BK–associated nephropathy (PVAN) in kidney transplants (KTs), but the role of viral determinants is unclear. We examined BKV noncoding control regions (NCCR), which coordinate viral gene expression and replication. In 286 day–matched plasma and urine samples from 129 KT patients with BKV viremia, including 70 with PVAN, the majority of viruses contained archetypal (ww-) NCCRs. However, rearranged (rr-) NCCRs were more frequent in plasma than in urine samples (22 vs. 4%; P < 0.001), and were associated with 20-fold higher plasma BKV loads (2.0 × 104/ml vs. 4.4 × 105/ml; P < 0.001). Emergence of rr-NCCR in plasma correlated with duration and peak BKV load (R2 = 0.64; P < 0.001). This was confirmed in a prospective cohort of 733 plasma samples from 227 patients. For 39 PVAN patients with available biopsies, rr-NCCRs were associated with more extensive viral replication and inflammation. Cloning of 10 rr-NCCRs revealed diverse duplications or deletions in different NCCR subregions, but all were sufficient to increase early gene expression, replication capacity, and cytopathology of recombinant BKV in vitro. Thus, rr-NCCR BKV emergence in plasma is linked to increased replication capacity and disease in KTs.

Polyomavirus BK -associated nephropathy (PVAN) has emerged as the most challenging infectious cause of irreversible kidney transplant (KT) failure ( 1,2 ). PVAN is diagnosed in up to 10% of KT patients around the world, causing premature graft loss in the 6 -60 mo after transplant ( 3,4 ). Histologically, progression from a mainly cytopathic pattern (PVAN A) to extensive cytopathic/infl ammatory changes of interstitial nephritis (PVAN B) is associated with increasing graft loss from < 10 to 50%, exceeding 80% for PVAN C when tubular atrophy and fi brosis predominate ( 5 ). Histological studies have demonstrated extensive BKV replication in the urothelial cell layer ( 6 ); however, unlike in bone marrow transplant patients, BKV-associated hemorrhagic cystitis is rarely encountered in KT patients, despite high urine viral loads ( 7 ). The emer gence of PVAN is remarkable in view of the 50 yr of experience in kidney transplantation and the basically unchanged high prevalence of BKV infection in the general population ( 8 -10 ). The " net state of immunosuppression " seems crucial for PVAN pathogenesis and refl ects the use of more potent immunosuppressive drugs synergizing with other factors, such as older age, negative BKV recipient and positive BKV donor status, higher number of HLA mismatches, and prior rejection episodes ( 7, 11 -14 ). The role of viral determinants is presently unclear. As no antiviral drug of proven effi cacy is available ( 15 ), current treatment is based on reducing immunosuppression to regain immune control over BKV replication and disease ( 16,17 ). This maneuver bears the risk of rejection and entry into a vicious cycle with eventual graft loss ( 18 ). respectively ( Table I , rr-NCCR architecture in samples column). The number of patients with rr-NCCR BKV in plasma represented a signifi cant fraction (P < 0.0005, Kolmogorov-Smirnov; see footnote a in Table I , Patients column) compared with the fraction of patients with rr-NCCR in urine (P = 0.45, Kolmogorov-Smirnov). The higher frequency of patients with rr-NCCR in plasma compared with urine was statistically signifi cant (P < 0.0001, 2 test; see footnote b in Table I , Patients column). The same was true when the analysis was restricted to patients with the histological diagnosis of PVAN in biopsies ( n = 70; rr-NCCR in plasma 35, 50%; ww-NCCR in urine 67, 96%; P < 0.0001, 2 test). When we compared the NCCR architecture in 129 patients with ( n = 70) and without histologically defi ned PVAN ( n = 59; Table I , Patients column), the detection of rr-NCCR in plasma was significantly associated with a positive biopsy (35 of 70 vs. 9 of 59; P < 0.0001, 2 test).
We also analyzed 56 BKV-positive urine samples from KT patients without concurrent BKV viremia (median, 14,700 geq/ml; range, 1,000 -8.9 × 10 8 ) and found ww-NCCR BKV in all cases. When examining 264 healthy blood donors, BKV was only detected in urine, but not in plasma in 26 (9.8%) cases, all of which were of archetype ww-NCCR confi guration (median viral load, 2,600 geq/ml; Outside the KT setting, BKV seems well adapt ed to the human host. BKV asymptomatically infects 60 -90% of the world ' s population during childhood and subsequently persists in the renourinary tract ( 9,19 ). After kidney transplantation, BKV viruria rates increase from 5 to 40%, with the percentage of urine viral loads increasing from < 10 5 to > 10 7 genome equivalents (geq)/ml and decoy cell shedding ( 1,5,20 ). Renal allograft function is not aff ected at fi rst, but one third of patients are at high risk of progressing to BKV viremia and overt PVAN ( 1,21 ). In patients with PVAN undergoing allograft nephrectomy, plasma BKV loads drop to undetectable levels with a half-life of < 2 h, indicating that BKV viremia is essentially derived from replication in renal allografts ( 22 ). Accordingly, > 99% of plasma BKV loads in steady state are replaced every day, refl ecting loss of at least 10 6 renal tubular epithelial cells to release progeny virus ( 22 ). After reduced immunosuppression, plasma BKV loads decline over 7 -13 wk ( 22 ), and antiviral cellular immune responses directed against early and late viral proteins become detectable in the peripheral blood ( 23,24 ). Thus, BKV load in plasma is widely accepted as a marker of onset and resolution of PVAN ( 1,17 ).
Polyomavirus genomes are circular dsDNA of 5 kb consisting of the noncoding control region (NCCR) with the origin of replication and promoter/enhancer functions controlling expression of the early proteins, large and small T-antigen, and the late agnoprotein and the capsid proteins VP1-3 ( 25 ). BKV strains excreted in urine of immunocompetent individuals have been reported to be of archetype (ww-) NCCR architecture. Upon propagation of BKV in tissue culture, however, ww-NCCR BKV are readily replaced by BKV variants with genetically rearranged (rr-) NCCR, whereas other areas of the BKV genome remain unchanged ( 26 -28 ). Because of NCCR hypervariability in tissue culture, identifi cation of archetype ww-NCCR requires direct analysis of BKV genomes from biological samples e.g., by PCR amplifi cation and cloning. PCR studies of PVAN biopsies identifi ed rr-NCCR in approximately one fourth of BKV strains, indicating that rr-NCCR BKV were not necessary for histological disease ( 29 -31 ). Given the rapid dynamics of BKV replication and the close correlation of plasma BKV load with PVAN, we compared the occurrence of rr-NCCR variants in BKV-positive plasma and urine samples, and investigated the functional consequences.

rr-NCCRs are associated with higher plasma BKV load
The NCCR architecture was analyzed by PCR in 129 KT patients, including 70 with PVAN-positive biopsy results, providing a total of 286 same day -matched plasma and urine samples ( Table I ). The majority of patients had ww-NCCR detectable in plasma ( n = 85; 66%) and in urine ( n = 119; 92%; Table I , Patients column). rr-NCCRs consisted of larger and shorter amplicons representing insertions (ins-) NCCR in 14%, deletions (del-)NCCR in 42%, and mixtures of ins/ww-and del/ww-NCCR in 6 and 38%, indeed, emerged from initial ww-NCCR BKV strains after prolonged viremia ( Fig. 1 B ). Regression analysis revealed that the time to fi rst rr-NCCR emergence correlated with peak plasma viral load (P < 0.000001; Fig. 1 C ). The linear and the quadratic regression models largely overlapped between BKV loads of 5.5 -7.5 log10 geq/ml. However, the convex shape of the quadratic regression model provided a better fi t of the overall data, suggesting that higher peak plasma BKV loads overproportionally increased the risk of rr-NCCR emergence. Accordingly, rr-NCCRs were detectable in patients with high peak plasma BKV load of 6.5 log10 geq/ml after < 4 mo, whereas 100-fold lower viremia (4.5 log10) required > 7 times as long. The data indicated that duration and peak replication favored the change from ww-to rr-NCCR BKV variants as the majority species. The only case where rr-NCCR BKV was already present in the fi rst BKV-positive plasma sample was a patient retransplanted after allograft loss and nephrectomy after PVAN. This observation was intriguing, and suggested that impaired BKV-specifi c cellular immunity is not only critical for curtailing BKV replication ( 23 ), but possibly range, 1,000 -64,900). We concluded that rr-NCCR BKV variants appeared more frequently in plasma than in urine in viremic KT patients, and were then associated with signifi cantly higher plasma BKV loads. In contrast, the daymatched urine BKV loads were generally 3,000-fold higher than the corresponding plasma BKV loads, regardless of the NCCR architecture. This observation, together with the discordance of rr-and ww-NCCR architecture in daymatched plasma and urine samples provided quantita tive and molecular evidence that renal tubular epithelial cells and urothelial cells in ureters and bladder, indeed, refl ected diff erent viral replication compartments in immuno suppressed KT patients, thereby extending previous histopathology data ( 6 ).

rr-NCCR BKV replace ww-NCCR BKV with persisting viremia
In preceding plasma samples from patients with rr-NCCR variants, we detected ww-NCCR BKV in all but one case. A detailed analysis of 35 PVAN patients with rr-NCCR ( Table I ) revealed that plasma rr-NCCR BKV variants,

rr-NCCR are diverse and without corresponding changes in VP1
To characterize the architecture of rr-NCCR in more detail, we sequenced 5 ins-NCCR and 5 del-NCCR from 10 diff erent patients with PVAN. Insertions consisted of partial duplication of the P-Q region, whereas deletions preferentially aff ected the Q-R-S region ( Fig. 3 ). Thus, NCCR rearrangements changed transcription factor-binding sites and enhancer elements, but no common feature was apparent (Fig. S1, available at http://www.jem.org/cgi/content/full/ jem.20072097/DC1). Sequencing of the antigenic determinants of VP1 revealed BKV serotype I and IV in 8 and 2 rr-NCCR variants, respectively. In all cases, the VP1 sequences were identical with the one detected when the majority species were of archetype ww-NCCR ( Fig. 3 B and Fig. S2). Thus, NCCR rearrangements were not linked to changes in VP1 serotype.

rr-NCCRs are suffi cient to increase early reporter gene expression
To investigate functional eff ects of rr-NCCR in regard to early and late gene expression, we constructed a bidirectional reporter vector phRG, having the red fl uorescent protein (RFP) and GFP in the same positions as the early and late genes in the circular BKV DNA genome ( Fig. 3 A ). Human embryonic kidney (HEK) 293 cells were transfected and assayed for red and green fl uorescence. The expression patterns became detectable as early as 1 d after transfection (dat) and remained stable for at least 10 d of observation (all scored at 2 dat; Fig. 3 B ). Archetype ww-NCCR conferred a strong late gene expression (green signal) and a relatively weak early gene expression (red signal, at ‫ف‬ 1/10 of the green signal). In contrast, all rr-NCCRs increased early gene expression by two-to sevenfold, and decreased late gene expression, irrespective of insertion or deletion architectures. Simple deletions or duplications had eff ects similar to more complex ones, suggesting that the architectural context and not the mere number of transcription factor binding sites might be relevant. We therefore generated two NCCR variants by in vitro mutagenesis that refl ected small insertions or deletions of the natural NCCR sequences. Both ins(P24-37)NCCR and del(R8-18)NCCR aff ected early and late gene expression in a manner similar to in vivo -occurring variants ins(23.1)NCCR or del(15.10)NCCR ( Fig. 3 B ). As NCCR expression might be aff ected by host cell type and diff erentiation, we tested two prototype rr-NCCRs (del 5.3, ins 7.3) in addition to the ww-NCCR (ww 1.4) in cells known to support BKV replication in vitro (Vero monkey kidney cells and human umbilical cord vein endothelial cells) and in vivo (primary human renal proximal tubular epithelial cells [RPTECs]). We found that the expression patterns for all three NCCR prototypes were similar in all tested cell types ( Fig. 3 C ). Northern blot analysis and RNA protection experiments at 2 dat indicated that NCCR-driven RNA expression correlated with RFP and GFP signals (unpublished data). To exclude vector-mediated positional eff ects on gene expression, the del(5.3)NCCR was inserted in reverse also for recurrence of BKV replication and direct emergence of rr-NCCR variants ( 24,32 ).  . We concluded that rr-NCCR BKV variants were of diverse architecture, but all increased early gene expression in vitro as a common hallmark.
To investigate whether the genomic NCCR rearrangement still allowed for modulatory eff ects in trans, we examined the responses of the bidirectional reporter vector phRG to BKV LTag, steroids, and agnoprotein expression, which have been reported to positively and negatively regulate NCCR expression ( 33 ). As shown for the prototype ins(7.3)NCCR ( Fig. 4 ), increasing LTag expression as detected by Western blot raised late gene expression by 5-fold within 24 h (green, Fig. 4 A ). Because glucocorticoid response elements are present in BKV NCCR, we examined whether steroid treatment modulated gene expression in Vero monkey kidney cells that, unlike HEK293, expressed functional glucocorticoid receptors. Treatment with dexamethasone at 10 Ϫ 6 M increased early and late gene expression from the ww-NCCR (3-fold), and to lesser degrees, also from the del(5.3)-(2.5-fold) and ins(7.3)-NCCR (2-fold; Fig. 4 B ). When BKV agnoprotein was cotransfected, both early and late reporter gene expression signals were ‫ف‬ 10-fold reduced for all 3 NCCRs ( Fig. 4 C ). Collectively, these results indicated that rr-NCCR consistently increased early gene expression relative to archetype ww-NCCR, but still remained susceptible to modulatory eff ects in trans conveyed by LTag, steroids, or agnoprotein.  LTag red nuclear stain, arrows in 40 × magnifi cation; agno green cytoplasmic stain) and VP1 expression (not depicted). Thus, we concluded that rr-NCCR were suffi cient to confer increased early gene expression, replication, and cytopathology to recombinant BKV in vitro.

DISCUSSION
The failing balance between BKV replication and antiviral immune control is the hallmark of PVAN in KT recipients ( 17,24 ). Viral factors have been postulated to contribute to PVAN pathogenesis, but determinants, rates, and mechanisms remained speculative ( 7,31 ). In this study, we took advantage of BKV viremia as a noninvasive marker of renal allograft involvement and provide evidence that the NCCR is a relevant viral determinant of BKV replication rate and PVAN pathogenesis. Although BKV variants with rr-NCCR had previously been detected in immunocompromised patients ( 29 -31, 34, 35 ), we show for the fi rst time that rr-NCCR BKV variants emerge and replace archetype ww-NCCR BKV as majority species in vivo in 24% of KT patients with persisting BKV viremia and in 50% of patients with PVAN. The time to emergence of rr-NCCR BKV variants in plasma was inversely correlated to peak plasma BKV loads. Thus, duration and level of BKV replication increased the risk of rr-NCCR BKV emergence. Compared with ww-NCCR strains, rr-NCCR variants were associated with 20-fold higher median plasma BKV loads, a higher probability of a histologically confi rmed disease, and increased viral cytopathology and infl ammatory presentation in these patients.
Our in vitro studies revealed complex rr-NCCR emerging in vivo without identifi able common alterations. However, using a novel bidirectional reporter gene replicon that exactly recapitulated the polyomavirus NCCR genome architecture relative to early and late gene organization, we could demonstrate that all rr-NCCR augmented early gene expression compared with ww-NCCR, while decreasing late gene expression. Nevertheless, rr-NCCR remained responsive to up-and down-regulation by LTag-, agnoprotein, and most notably steroids, a clinically defi ned risk factor of BKV replication and PVAN ( 1,36,37 ). It has been proposed that rr-NCCR change critical transcription factor binding sites in the ww-NCCR ( 38 ), but the diff erences between various deletions and insertions did not reveal a common alteration. Clearly, further work is needed to unravel the complex molecular organization of BKV NCCR-mediated gene expression.
We demonstrate that rr-NCCR increased viral early gene expression and accelerated viral replication in vitro. The recombinant rr-NCCR BKV strains yielded 1 -3 log10 geq/ml higher viral loads in tissue culture compared with archetype ww-NCCR BKV. Detailed analysis indicated an ‫ف‬ 24 h earlier LTag expression with corresponding eff ects on VP1 expression, a shorter lag phase reducing the BKV generation time from ‫ف‬ 3 to ‫ف‬ 2 d, with prominent cytopathology by day 21. Thus, rr-NCCRs associated with higher plasma BKV   ( 39 ). Because BKV replication requires LTag with its DNA binding and helicase functions, some genomic rearrangements, and especially deletions of ori or LTag binding sequences, are likely to gene rate defective NCCR penalized by negative selection. Conversely, NCCR rearrangements conferring increased early gene expression outcompete archetype ww-NCCR BKV strains by increased replication capacity, a phenomenon termed positive selection ( 39 ). We noted that NCCR rearrangements were unevenly distributed, being less frequent in the vicinity of the early gene promoter (typically sparing the origin of replication and LTag-binding sites), consisting of partial duplication rather than deletions. In contrast, deletions were loads and accelerated pathology in KTs were suffi cient to increase replication capacity and cytopathology of recombinant rr-NCCR BKV in tissue culture.
The molecular mechanisms leading to NCCR rearrangements in a DNA virus at such high frequency are intriguing and as yet unclear. Unlike RNA virus replication generating mutant progeny by lack of proof-reading, DNA virus replication is widely considered a process of high fi delity, particularly for viruses that rely on recruiting host cell DNA polymerases, such as polyomaviruses. The dependence on time and peak plasma BKV load shown here suggests that persistent high-level replication of the circular BKV genome and its associated errors may be crucial for rr-NCCR emergence pression might provide an extended window for cytotoxic immune recognition in immunocompetent hosts, which is lacking in immunosuppressed KT patients, as well as in tissue culture. LTag as a target of cellular immunity has been fi rst identifi ed in experimental SV40 models ( 47 ), in healthy individuals ( 48 ), and, more recently, in peripheral blood of KT patients with declining BKV viremia ( 23 ). The late capsid protein VP1 is also a known target of antiviral immunity, particularly for neutralizing antibodies. As VP1 expression is closely linked to virion assembly and host cell lysis, anti-VP1 -directed CD8-T cells may develop their impact at a later stage of the viral life cycle than anti-LTag CD8-T cells ( 23 ). We speculate that immune surveillance is likely to be more stringent for renal tubular epithelial cells than for the urothelial cells, as with other mucosal surfaces. This notion is also supported by the strong infl ammatory response evolving in the infected renal tubulus and its virtual absence in the heavily BKV replicating transitional cell layer in KT patients. We therefore hypothesize that cellular immunity represents a key barrier to rr-NCCR BKV emergence, rendering less well replicating archetype ww-NCCR BKV evolutionarily more successful in immunocompetent host populations ( Fig. 6 ) ( 39 ).
In summary, our study underlines that genetic plasticity of evolutionarily conserved DNA viruses can be observed in vivo in situations permitting unchecked high-level replication, as in immunocompromised hosts, thereby causing increased cytopathic damage. In KT patients, rr-NCCR BKV emergence is a marker of prolonged viral replication and is specifi cally associated with more advanced PVAN histology. The role of cellular immunity and the prognostic information of rr-NCCR BKV regarding KT function or graft loss has to await properly designed prospective studies. more frequent toward the late gene expression, removing Q-R-S sequences. Interestingly, we did not encounter any poorly replicating rr-NCCRs, as had been reported in previous studies not related to kidney transplantation ( 38,40,41 ). Although these studies support the principle notion that rearrangements as a consequence of replication can also generate defective NCCRs, our results are in line with the fact that we targeted by PCR emerging rr-NCCR majority species that had been positively selected in these immunosuppressed KT patients.
The rapid emergence of rr-NCCR BKV variants with higher replicative capacity in immunosuppressed KT patients is reminiscent of rr-NCCR generation in tissue culture ( 26,27,42 ), and is in striking contrast to the stable colonization of the world ' s population with archetype ww-NCCR BKV strains that do not replicate as well ( 43,44 ). Indeed, our ongoing analysis of BKV seropositive healthy blood donors detected asymptomatic BKV viruria in 9.8%, with ww-NCCR in all cases. This is in line with earlier reports implicating urine as a relevant source of BKV transmission and persistence around the world ( 7,45 ). The discordance of rr-NCCR BKV in plasma and ww-NCCR BKV in urine in immunosuppressed KT patients argues that emergence of rr-NCCR in vivo is at least partially defi ned by host cell properties, i.e., the diff erence between renal tubular epithelial cells and urothelial cells. A precedent for the role of host cells is documented in tissue culture where rr-NCCR emergence required a longer time in human umbilical vein endothelial cells compared with Vero or in HEK293 cells ( 26,27,42 ). Histopathology studies demonstrated in KTs that renal tubular epithelial cells, as well as in the urothelial cells support BKV replication ( 6,46 ), but both host cell types diff er in anatomical location, function, diff erentiation and organization as single cell layer versus multicellular transitional cell layer, respectively. However, a higher rr-NCCR replication capacity in renal tubular epithelial cells may not play out to the same extent in the urothelial cells of ureter and bladder because urine BKV loads were, on average, 3,000-fold higher than plasma BKV loads independent of ww-or rr-NCCR architecture. We therefore conclude that the selective advantage of a higher replication capacity may not be operative to the same extent in the urothelial cell compartment. Diff erent, not mutually exclusive, hypotheses may account for this cell type phenomenon: (a) activation of early gene expression is similar between ww-and rr-NCCR BKV in urothelial cells; (b) less LTag is needed to recruit replication factors in continuously dividing urothelial cells; and (c) ww-NCCR strains are reactivated fi rst and saturate susceptible target cells.
Thus, we suggest that antiviral immunity is another signifi cant barrier that is lacking in tissue culture, as well as in profoundly immunosuppressed KT patients. Because increased early gene expression appears as a common feature of rr-NCCR, cellular immunity directed against early gene encoded epitopes may be the important factor limiting emergence of rr-NCCR BKV in the general immunocompetent population. The rr-NCCR -mediated increase in LTag ex- Figure 6. Emergence of rr-NCCR in the immunocompromised host. Naturally transmitted BKV with archetype ww-NCCR genome (black circles) undergo insertion and deletion errors during replication generating rr-NCCR genomes (red tagged circles). BKV rr-NCCR with increased early gene expression and corresponding higher replication capacity are eliminated in immunocompetent host, but outcompete ww-NCCR BKV in immunodefi cient hosts. LT, LTag; VP1, capsid protein 1.
PCR using primer pairs 5 -6 and 7 -8 and pTRE2hyg as template were joined in a PCR reaction containing primer pair 5 -8. The amplifi cation product was digested with AvrII and BamHI, followed by ligation into AvrII -BamHI-digested pTRE2hyg to yield phyg. Next, BamHI -MluIcleaved dsRed2 (pdsRed2-C1; BD Biosciences) and ClaI-and SalI-digested EGFP (pEGFP-N1; BD Biosciences) were ligated into BamHI -SalIrestricted pTRE2hyg to obtain pTREdsRed-EGFP. Next, the BamHI -SalI dRed2-EGFP fragment was ligated into phyg cleaved with the same enzymes to yield phdsRed-EGFP. In the fi nal step, the AseI -EcoRV ␤ -globin fragment, blunt ended with T4 polymerase, was subcloned into pGEM-3Zf+ (Promega) to yield pGEMglobin. This plasmid was cleaved with SacI -XbaI, and the resulting fragment was ligated into phdsRed-EGFP digested with SacI -SpeI to obtain phRG. In phRG-NCCR plasmids, the expression of RFP (early) and GFP (late) is under control of the inserted BKV NCCR. NCCR sequences were amplifi ed from patient material by nested PCR using primer pairs 9 -10 and 11 -12. The MluI -BssHII-cleaved amplicon was ligated into phRG digested with the same enzymes. The plasmids phRGinsP24-37 and phRGdelR8-18 were generated from the archetype ww-NCCR by a duplication of P24-37 or a deletion of R8-18, respectively, by SOE. The two DNA fragments were generated from phRGww by PCR using primer pairs 11 -13 and 14 -12 (P24-37) or 11 -15 and 16 -12 (R8-18), respectively, and joined in a PCR reaction containing primer pair 11 -12. The amplifi cation products were ligated into MluI -BssHII-digested phRG, as described. To construct recombinant BKV strains, the SacI fragment containing the NCCR was replaced in pBKV Dunlop plasmid (American Type Culture Collection [ATCC] 45025) bearing the full-length genome sequence ( 50 ). A synthetic linker (primer 17 -18) was ligated into SacI-cleaved pGEM3-Zf+ to yield pGEMSacIlinker. The NCCR released from the indicated phRGww, ins, and del constructs by MluI -BssHII digest was ligated into pGEMSacIlinker cleaved with the same enzymes. Finally, the SacI NCCR fragment was ligated into SacI-restricted pBKV to generate the respective recombinant pBKVww-, ins-, and del-NCCR. pCMVAgno encodes the agnoprotein sequence in the pRC/CMV (Invitrogen). The entire agno sequence was amplifi ed from patient material by PCR using primer pair 19 -20. The amplifi cation product was cleaved with BamHI and NotI, followed by ligation into pRC/CMV digested with the same enzymes. The integrity of all plasmid constructs was confi rmed by sequencing.

Patients.
We characterized BKV NCCR in 1,019 plasma and 342 urine samples from 412 KT patients. Day-matched plasma and urine samples were obtained from KT patients as part of the prospective BKV study protocol approved by the University of Maryland Transplant Center. BKV loads had been determined by real-time PCR in same day -matched plasma and urine samples ( n = 286 from 129 patients, including 70 patients with PVAN). The NCCR architecture was determined retrospectively on specimens stored at Ϫ 20 ° C. PVAN was graded based on the Banff classifi cation, as recommended by Hirsch et al. ( 17 ), as follows: PVAN A, minimal to mild viral cytopathic changes (cy1+ -cy2+), insignifi cant infl ammatory infi ltrates ( < i1+), tubular atrophy ( < ct1+), or fi brosis ( < ci1+); PVAN B, viral cytopathic changes scoring from mild to severe (cy2+ -cy4+) and signifi cant infl ammatory infi ltrates scoring from moderate to severe (i1+ -i3+), but only mild tubular atrophy ( ≤ ci2+) and mild fi brosis ( ≤ ci2+); PVAN C, moderate to severe tubular atrophy (ct3+) and interstitial fi brosis (ci2+ -ci3+), variable scores for cytopathic changes (cy1+ -cy4+), and for infl ammatory infi ltrates (i1+ -i3+) ( 17 ). During the years 2005 and 2006, an additional 733 consecutive BKV DNA -positive plasma samples from 227 patients, including 57 with PVAN, had been submitted for BKV testing to the Molecular Diagnostics Laboratory of the Division of Diagnostics, which is an accredited quality controlled laboratory (EN ISO) of the University of Basel (www.zid.ch). If the samples had detectable BKV loads, BKV NCCR sequences were amplified as an independent confirmatory assay to confirm BKV specificity. Patients with suffi cient sampling density defi ned as > 6 consecutive plasma samples collected over > 12 wk were identifi ed ( n = 35, PVAN in 28) to analyze the dependence of rr-NCCR emergence on time and plasma viral load. NCCR architecture was examined in 56 KT patients (median age 44 yr; range 17 -66 yr; 52% female) with urinary BKV shedding, but without concurrent BKV viremia. As controls, we examined BKV in urine and plasma of 264 healthy blood donors (median age 46 yr; range 18 -67 yr; 49% female; IRB approval 267/06).
BKV load and NCCR analysis. BKV DNA was quantifi ed after DNA extraction from 200 μ l plasma, urine, or cell culture supernatant using a commercial kit (QIAmp; QIAGEN) and a previously described real-time PCR protocol ( 1 ). NCCR amplifi cation used a standard nested PCR approach with the outer primer pairs BKTT5 5 Ј -GAGCTCCATGGATTCTTC-3 Ј and BKTT6 5 Ј -CCAGTCCAGGTTTTACCA-3 Ј and the inner primer pair BKTT7 5 Ј -CCCTGTTAAGAACTTTATCCATTT-3 Ј and BKTT8 5 Ј -AACTTTCACTGAAGCTTGTCGT-3 Ј . The PCR products were compared after 2%TAE-agarose gel electrophoresis with ww-NCCR controls, and excised for sequence analysis, if indicated. Dilution series of increasing ratios of rr-NCCR versus ww-NCCR and cloning into plasmids indicated that the sensitivity of detecting minority species in NCCR mixtures by the PCR protocol was as low as 5%. Patients were scored as bearing rr-NCCR when one or multiple samples showed rr-NCCR. Samples containing rr-NCCR or mixtures of rr-and ww-NCCR ( Table I , rr-NCCR architecture in samples column) were scored as rr-NCCR.

Plasmids and primers.
In pTRELTag the cDNA coding for the LTag of BKV is under control of a tetracycline-controlled transactivator-dependent promoter. The intron of the LTag was removed by gene splicing by overlap extension (SOE) ( 49 ). Two DNA fragments were generated using primer pairs 1 -2 (Fig. S3, available at http://www.jem.org/cgi/content/full/ jem.200712097/DC1) and 3 -4 and DNA extracted from a BKV-positive urine as template. The two DNA fragments were subsequently joined in a PCR reaction containing primer pair 1 -4. The amplifi cation product was digested with ClaI and NheI, followed by ligation into ClaI -NheI-digested pTRE2pur (BD Biosciences). The dual-reporter vector phRG contains hygromycin selectable marker, the enhanced GFP and RFP dsRed2 occurs in opposite directions with both mRNAs, followed by the same ␤ -globin polyA sequence. Plasmid phRG was generated in a three-step procedure. First, the tetracycline response element/minimal CMV promoter cassette was deleted from pTRE2hyg by SOE. Two DNA fragments generated by Immunofl uorescence. 4 d after infection, RPTEC cells were fi xed in 4% PFA, and then fi xed in methanol. Subsequently, cells were incubated at 37 ° C with primary and secondary antibodies for 30 min. We used the monoclonal mouse anti-SV40 T-antigen (Ab-2; 1:100) and an IgG-fraction of rabbit antiserum directed against BKV-agnoprotein (1:800) ( 51 ). The secondary antibodies were conjugated with Alexa Fluor 568 or 488 (1:500; Invitrogen). Nuclei were labeled in blue with DRAQ5 (Biostatus).
Microscopy and digital image processing. Microscopy was performed using an epifl uorescence microscope (model TE200; Nikon) equipped with suitable fi lters and a digital camera (Hamamatsu). Red and green cells were counted in a minimum of 3 10 × microscopic fi elds. Images were taken at the times indicated in the fi gure legends. Digital images were recorded with Openlab 2.2 software and raw images were processed in Photoshop 6.0 (Adobe). Results are shown as the mean of 3 independent experiments yielding a SD of < 10%. Confocal microscopy analyses and images were obtained using a microscope (Axiovert 200; Carl Zeiss, Inc.) equipped with a LSM510 confocal module and processed using LSM5 software version 3.2 (Carl Zeiss, Inc.).