AbstractBackgroundBK polyomavirus‐associated nephropathy (BKPyVAN) carries a risk of irreversible allograft injury. While detection of BK viremia and biopsy assessment are the current diagnostic gold standard, the diagnostic value of biomarkers reflecting tissue injury (donor‐derived cell‐free DNA [dd‐cfDNA]) or immune activation (C‐X‐C motif chemokine ligand [CXCL]9 and CXCL10) remains poorly defined.MethodsFor this retrospective study, 19 cases of BKPyVAN were selected from the Vienna transplant cohort (biopsies performed between 2012 and 2019). Eight patients with T cell‐mediated rejection (TCMR), 17 with antibody‐mediated rejection (ABMR) and 10 patients without polyomavirus nephropathy or rejection served as controls. Fractions of dd‐cfDNA were quantified using next‐generation sequencing and CXCL9 and CXCL10 were detected using multiplex immunoassays.ResultsBKPyVAN was associated with a slight increase in dd‐cfDNA (median; interquartile range: .38% [.27%‐1.2%] vs. .21% [.12%‐.34%] in non‐rejecting control patients; p = .005). Levels were far lower than in ABMR (1.2% [.82%‐2.5%]; p = .004]), but not different from TCMR (.54% [.26%‐3.56%]; p = .52). Within the BKPyVAN cohort, we found no relationship between dd‐cfDNA levels and the extent of tubulo‐interstitial infiltrates, BKPyVAN class and BK viremia/viruria, respectively. In some contrast to dd‐cfDNA, concentrations of urinary CXCL9 and CXCL10 exceeded those detected in ABMR, but similar increases were also found in TCMR.ConclusionBKPyVAN can induce moderate increases in dd‐cfDNA and concomitant high urinary excretion of chemokines, but this pattern may be indistinguishable from that of TCMR. Our results argue against a significant value of these biomarkers to reliably distinguish BKPyVAN from rejection.