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Polyomaviruses are widespread, with BK viruses being most common in humans who require immunosuppression due to allotransplantation. Infection with BK polyomavirus (BKV) may manifest as BK virus-associated nephropathy and hemorrhagic cystitis. Established diagnostic methods include the detection of polyomavirus in urine and blood by PCR and in tissue biopsies via immunohistochemistry. In this study, 79 patients with pathological renal retention parameters and acute kidney injury (AKI) were screened for BK polyomavirus replication by RNA extraction, reverse transcription, and virus-specific qPCR in urine sediment cells. A short fragment of the VP2 coding region was the target of qPCR amplification; patients with (n = 31) and without (n = 48) a history of renal transplantation were included. Urine sediment cell immunofluorescence staining for VP1 BK polyomavirus protein was performed using confocal microscopy. In 22 patients with acute renal injury, urinary sediment cells from 11 participants with kidney transplantation (KTX) and from 11 non-kidney transplanted patients (nonKTX) were positive for BK virus replication. BK virus copies were found more frequently in patients with AKI stage III (n = 14). Higher copy numbers were detected in KTX patients having experienced BK polyoma-nephropathy (BKPyVAN) in the past or diagnosed recently by histology (5.6 × 10⁹–3.1 × 10¹⁰). One patient developed BK viremia following delayed graft function (DGF) with BK virus-positive urine sediment. In nonKTX patients with BK copies, decoy cells were absent; however, positive staining of cells was found with epithelial morphology. Decoy cells were only found in KTX patients with BKPyVAN. In AKI, damage to the tubular epithelium itself may render the epithelial cells more permissive for polyoma replication. This non-invasive diagnostic approach to assess BK polyomavirus replication in urine sediment cells has the potential to identify KTX patients at risk for viremia and BKPyVAN during AKI. This method might serve as a valuable screening tool for close monitoring and tailored immunosuppression decisions. Full article

Decoy cells that can be detected in the urine sediment of immunosuppressed patients are often caused by the uncontrolled replication of polyomaviruses, such as BK-Virus (BKV) and John Cunningham (JC)-Virus (JCV), within the upper urinary tract. Due to the wide availability of highly sensitive BKV and JCV PCR, the diagnostic utility of screening for decoy cells in urine as an indicator of polyomavirus-associated nephropathy (PyVAN) has been questioned by some institutions. We hypothesize that specific staining of different infection time-dependent BKV-specific antigens in urine sediment could allow cell-specific mapping of antigen expression during decoy cell development. Urine sediment cells from six kidney transplant recipients (five males, one female) were stained for the presence of the early BKV gene transcript lTag and the major viral capsid protein VP1 using monospecific antibodies, monoclonal antibodies and confocal microscopy. For this purpose, cyto-preparations were prepared and the BK polyoma genotype was determined by sequencing the PCR-amplified coding region of the VP1 protein. lTag staining began at specific sites in the nucleus and spread across the nucleus in a cobweb-like pattern as the size of the nucleus increased. It spread into the cytosol as soon as the nuclear membrane was fragmented or dissolved, as in apoptosis or in the metaphase of the cell cycle. In comparison, we observed that VP1 staining started in the nuclear region and accumulated at the nuclear edge in 6–32% of VP1⁺ cells. The staining traveled through the cytosol of the proximal tubule cell and reached high intensities at the cytosol before spreading to the surrounding area in the form of exosome-like particles. The spreading virus-containing particles adhered to surrounding cells, including erythrocytes. VP1-positive proximal tubule cells contain apoptotic bodies, with 68–94% of them losing parts of their DNA and exhibiting membrane damage, appearing as “ghost cells” but still VP1⁺. Specific polyoma staining of urine sediment cells can help determine and enumerate exfoliation of BKV-positive cells based on VP1 staining, which exceeds single-face decoy staining in terms of accuracy. Furthermore, our staining approaches might serve as an early readout in primary diagnostics and for the evaluation of treatment responses in the setting of reduced immunosuppression. Full article

Human polyoma BK virus (BKV) prevalence has been increasing due to the introduction of more potent immunosuppressive agents, mostly in immunocompromised patients. BKV has been linked mostly to polyomavirus-associated hemorrhagic cystitis, and polyomavirus-associated nephropathy. BKV is a circular double stranded DNA virus (cdsDNA) with an average genome size of 5100 bp and an average GC content of 40%. Its genome codifies for five proteins: VP1, VP2, VP3, Angio gene, and the antigen T (which includes an event of alternative splicing, yielding a short and a large antigen T transcript). Additionally, it contains the non-coding control region (NCCR), known to be highly repetitive and to vary in number, length, and location of the repeats. Subtyping of BKV has been mainly studied in VP1 and the NCCR. Subtyping and subgrouping of BKV is conducted routinely in diagnostic assays and in epidemiological studies. Recently, Morel et al. published (Journal of Clinical Microbiology 2017; 55, 4) a strategy to subtype BKV through 100 bp VP1 amplicon. NCCR diversity is more complex than VP1, as it is configured by five repeat blocks (O, P, Q, R, and S). NCCR blocks can vary in number and length, resulting in a gradient of infectivity and replication. Rearranged NCCR have been linked to diverse patient etiologies, although any specific arrangement has failed to correlate with disease outcome or to have any predictive value. Due to the high abundance of BKV individuals and the clinical implications for human health that may represent BKV typing, a reliable, automatic, and free typing tool would be of great interest. Here, BKTyper is presented, a whole genome genotyper for polyoma BKV, based on a VP1 typing by Morel’s algorithm and NCCR block identification. BKTyper can accept both whole BKV genome or regions of interest in fasta format to generate the typing profile and phylogenetic analysis. Full article