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Background: Human polyomaviruses (HPyVs), JC polyomavirus (JCPyV) and BK polyomavirus (BKPyV), have been found in upper tract urothelial carcinoma UTUC; however, the association of the viral oncogenic factors and clinical characteristics of UTUC remains unclear. This study aimed to investigate the prevalence of JCPyV and BKPyV in UTUC and their correlation with cancer progression among the southwest Taiwanese population from 2020 to 2022., Methods: A total of 72 paraffin-embedded UTUC tissue samples and 41 adjacent tissue samples were collected from 72 patients. Nested polymerase chain reaction and DNA sequencing were used to detect viral DNA and genotypes. Immunohistochemistry was performed using anti- large T (LT) and anti-p53 monoclonal antibodies to detect the expression of viral early LT protein and cellular p53 protein, respectively., Results: The overall prevalence of JCPyV and BKPyV were higher in UTUC than in adjacent tissue samples (65.3% [47/72] vs. 17.1% [7/41]). JCPyV and BKPyV were detected in 95.7% (45/47) and 4.3% (2/47) of the HPyVs-positive UTUC samples, respectively. JCPyV-TW-3 was the predominant strain of JCPyV infection. In UTUC samples, the LT protein of JCPyV and BKPyV positivity rate was 65.3%, while that of mutant p53 protein was 52.7%. JCPyV infection and LT protein expression increased the odds ratio (OR) of UTUC by 9.13-fold. The OR of UTUC was higher by 10.34-fold in patients with mutant p53 and by 10.37-fold in those with simultaneous LT and mutant p53 expression. The presence of LT protein in UTUC patients may increase the OR of mutant p53 protein expression by 2.93-fold compared to its absence. Women had a 5.19-fold higher superiority of JCPyV infection and LT expression than men. Patients with chronic kidney disease (CKD) had a 3.15-fold higher OR for mutant p53 protein expression than those without it. In the UTUC advanced stages, the OR of virus and LT expression was 3.18-fold higher compared to those who do not require chemotherapy., Conclusions: JCPyV infection is highly prevalent in UTUC, and the presence of CKD concurrent with high expressions of LT and mutant p53 proteins in patients may be a useful indicator for chemotherapy and poor prognosis., Competing Interests: Declarations. Ethics approval and consent to participate: This study was approved by the review board of the Chia-Yi Christian Hospital (IRB number 2021103). This study was conducted in accordance with the guidelines prescribed in Good Clinical Practice Procedures and the Declaration of Helsinki. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

To date, no drugs are approved for BK polyomavirus (BKPyV) reactivation, a major cause of nephropathy after kidney transplantation. Recently, tumor necrosis factor-α (TNF-α) blockade has been proposed as a promising therapy, however, the effect of TNF-α on the clinically most common archetype (ww) BKPyV remained unclear. Assays in primary renal proximal tubule epithelial cells (RPTEC) allowed efficient replication only of BKPyV strains with rearranged (rr) non-coding control regions (NCCR), which may develop at later disease stages, but not of ww-BKPyV. Here, we optimized culture conditions allowing robust replication of patient-derived ww-BKPyV, while efficiently preserving their ww-NCCR. TNF-α promoted rr-BKPyV replication, while the T H 1 cytokine IFN-γ suppressed it, also in the presence of TNF-α. Surprisingly, TNF-α alone was sufficient to suppress all ww-BKPyV strains tested. Comprehensive analysis using siRNAs, and chimeric or mutated BKPyV-strains revealed that the response to TNF-α depends on the NCCR type, and that the NF-κB p65 pathway but not the conserved NF-κB binding site is essential for the TNF-α-induced enhancement of rr-BKPyV replication. Our data suggest that in immunosuppressed patients with archetype-dominated infections, TNF-α blockade could interfere with natural TNF-α-mediated anti-BKPyviral control, and this could be detrimental when IFN-γ-driven T H 1 responses are impaired. Ongoing inflammation, however, could lead to the selection of rearrangements responding to NCCR-activating pathways downstream of NF-κB p65 signaling, that may overcome the initial TNF-α-mediated suppression. Our findings also highlight the importance of using clinically relevant BKPyV isolates for drug testing and discovery, for which this new assay paves the way., (© 2025 The Author(s). Journal of Medical Virology published by Wiley Periodicals LLC.)

BK virus is implicated in polyomavirus-associated nephropathy (PVAN) and hemorrhagic cystitis, particularly in kidney transplant recipients, affecting the functionality of the transplanted kidney and posing a risk of graft loss. Despite these challenges, specific antiviral drugs targeting BK virus remain elusive. Agnoprotein, a small, positively charged protein encoded by the BK virus late gene, functions in the assembly, maturation, and release of the virus. Consequently, agnoprotein emerges as a promising target for potential anti-BK virus drugs. Utilizing phage display technology, we conducted screening to identify specific binding peptides against the agnoprotein. The primary objective of screening binding peptides is to utilize them to disrupt the virus's life cycle, impeding its replication and transmission, thereby achieving antiviral effects. In the current experimental study, a combination of phage 7 peptide libraries and 12 peptide libraries was employed for screening purposes. Following four rounds of screening, seven positive phages demonstrating the ability to bind Agnoprotein were successfully isolated. Following ELISA validation, it was observed that the optical density (OD) values for Agnoprotein binding of the seven positive clones significantly exceeded three times the value of the negative control (NC). Subsequent analysis identified one 7-peptide and six 12-peptides within the binding peptides. Moreover, OD values of dodecapeptide phage clones bound to agnoprotein were generally higher than those of heptapeptide phage clones.In conclusion, our study demonstrates the successful identification of specific binding peptides against agnoprotein, a crucial component in the BK virus life cycle., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Acute kidney injury (AKI) is a condition that can result in changes in both urine production and creatinine levels in the bloodstream, complicating the treatment process and worsening outcomes for many hospitalized patients. BK polyomavirus (BKPyV), a member of the Polyomaviridae family, is prevalent in the population and remains latent in the body. It can reactivate in individuals with a compromised immune system, particularly post-kidney transplant, and can activate various transcription factors and immune mediators. Although reactivation is often asymptomatic, it can present as AKI, which is a risk factor for early loss of the transplanted organ. The immune response to BKPyV is crucial in controlling the virus and safeguarding organs from damage during infection. Understanding BKPyV pathways may offer novel opportunities for effectively treating BKPyV-associated complications. This review seeks to elucidate the potential mechanisms by which BKPyV reactivation can lead to AKI by analyzing various signaling pathways, as well as the identification of molecular mechanisms that BKPyV may utilize to induce AKI., Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

The polyomavirus family consists of a highly diverse group of small DNA viruses isolated from various species, including humans. Some family members have been used as model systems to understand the fundamentals of modern biology. After the discovery of the first two human polyomaviruses (JC virus and BK virus) during the early 1970s, their current number reached 14 today. Some family members cause considerably severe human diseases, including polyomavirus-associated nephropathy (PVAN), progressive multifocal leukoencephalopathy (PML), trichodysplasia spinulosa (TS) and Merkel cell carcinoma (MCC). Polyomaviruses encode universal regulatory and structural proteins, but some members express additional virus-specific proteins and microRNA, which significantly contribute to the viral biology, cell transformation, and perhaps progression of the disease that they are associated with. In the current review, we summarized the recent advances in discovery, and functional and structural analysis of those viral proteins and microRNA., Competing Interests: Declaration of competing interest Authors declare no conflict of interest., (Copyright © 2024. Published by Elsevier Inc.)

The increasing use of immune suppressive monoclonal antibodies in the treatment of organ transplant recipients and patients with oncologic, neurological, and autoimmune diseases can lead to serious morbidity and mortality from the reactivation of viral agents that persist in humans. The squirrel monkey polyomaviruses are naturally found in Bolivian squirrel monkeys (SQM) and may be a useful model for the study of polyomavirus-associated pathogenesis and experimental treatment and prevention strategies. Two diverse groups of squirrel monkeys were given, a single dose of an anti-B cell antibody (rituximab) resulting in complete depletion of B cells (CD20+), while an anti-CD8 monoclonal antibody (7 pt-3F9) resulted in a transient depletion of CD8+ lymphocytes compared with control animals (group with no infusion with either of the monoclonal antibodies). The animals remained clinically healthy, with no pathological symptoms suggesting that the intensity and/or duration of immune suppression were inadequate to trigger pathogenic reactivation of the latent polyoma and herpes viruses. We observed a transient reduction in circulating plasma cytokines, IL-2, IFN-γ, and IL-12 reduced JC and BK viral protein-specific proliferative responses in both the CD8 and CD20 depletion groups. This study clearly elucidates the consequences of the use of depletion monoclonal antibodies in immune suppression modalities in the treatment of human malignancies and during transplantation, and SQM acts as a good model in the selection of dosage at which activation of latent viruses is at a minimum, with no pathological consequences.

BK polyomavirus (BKPyV) is an important opportunistic viral infection that complicates kidney transplantation. Uncontrolled viral replication may result in BKPyV-associated nephropathy (BKPyVAN), a major cause of premature allograft damage and failure. In the continued absence of proven treatments, management relies on the empirical reduction of immunosuppression to facilitate an effective host immune response to clear the virus. This may be complicated by the risk of allograft rejection. There is compelling evidence that cellular immune responses are key to establishing control after viral reactivation. Measurable peripheral BKPyV-specific T cell responses temporally correlate with declining viral loads and subsequent clearance. Conversely, these responses are delayed or absent in BKPyVAN. How these peripheral findings correspond to the intragraft response, and whether BKPyV-specific T cells contribute to the immunopathology of BKPyVAN, remains poorly understood. Molecular techniques have provided some insights; however, these have been unable to fully discriminate BKPyVAN from cellular rejection to date. Furthermore, the contributions of components of innate cellular immunity, such as natural killer cells, are not known. Herein, we review the role of cellular immunity in BKPyV infection in kidney transplant recipients. We discuss advances in the understanding of how the development, phenotype, and functionality of these responses may determine the balance between viral control and immunopathology, and how this knowledge is being translated into tools to prognosticate and guide individualized immunosuppression reduction. Lastly, we consider how further elucidation of these responses may inform the design of therapies that would revolutionize how BKPyV is managed after transplantation., (© 2024 The Author(s). Transplant Infectious Disease published by Wiley Periodicals LLC.)

Background: Merkel cell carcinoma (MCC) is associated with Merkel cell polyomavirus (MCPyV) infection. MCPyV antibodies (MCPyV-Ab) in plasma correlate with survival, while MCPyV-Ab within the tumor has never been investigated. This study evaluated plasma MCPyV-Ab and tumor MCPyV-Ab titers to evaluate their role in outcomes and prognostication., Methods: A single-institution, prospective database was retrospectively reviewed for patients diagnosed with MCC from 2014 to 2021. MCPyV-Ab plasma and tumor titers, as well as patient and treatment factors, were collected. Two-year overall survival (OS) and disease-free survival (DFS) were examined based on MCPyV-Ab presence in tumor., Results: Forty patients were identified, with a median follow-up of 27.6 months. Patients were stratified into four groups based on the presence of MCPyV-Ab in plasma (P+, P-) and tumor (T+, T-). Most patients (60.0%) were P-/T-. Of the remaining patients, 22.5% were P+/T+, 12.5% were P-/T+, and 5.0% were P+/T-. Two-year DFS of the P-/T- group was 16.6 months, which was not different from the other groups (p = 0.79). Two-year OS of P-/T- was 18.3 months, and 2-year OS of P-/T+ was 28.1 months, which was similar between groups (p = 0.80)., Conclusions: Most patients P+ for MCPyV had antibody-positive tumors (T+), and P- patients were also T-; however, there was a subset of patients where plasma and tumor antibody findings were incongruent. Patients with MCPyV-Ab in either plasma or tumor had a trend toward improved 2-year DFS and OS, but was limited by a small cohort. This study offers an exploratory investigation into the relationship between plasma and tumor antibodies to MCPyV on which to base future work., Competing Interests: Disclosure: James Lewis is on the speaker’s bureaus of Castle Biosciences and Regeneron, and Andrew Ward is on the speaker’s bureau for Castle Biosciences. Ryan K. Schmocker, Laurentia Nodit, James M. McLoughlin, and Laura M. Enomoto have no conflicts of interest to disclose., (© 2024. Society of Surgical Oncology.)

Kidney transplant recipients require a lifelong protocol of immunosuppressive therapy to prevent graft rejection. However, these same medications leave them susceptible to opportunistic infections. One pathogen of particular concern is human polyomavirus 1, also known as BK virus (BKPyV). This virus attacks kidney tubule epithelial cells and is a direct threat to the health of the graft. Current standard of care in BK virus-infected transplant recipients is reduction in immunosuppressant therapy, to allow the patient's immune system to control the virus. This requires a delicate balance; immune suppression must be strong enough to prevent rejection, yet weak enough to allow viral clearance. We seek to model viral and immune dynamics with the ultimate goal of applying optimal control methods to this problem. In this paper, we begin with a previously published model and make simplifying assumptions that reduce the number of parameters from 20 to 14. We calibrate our model using newly available patient data and a detailed sensitivity analysis. Numerical results for multiple patients are given to show that the newer model reflects observed dynamics well.

Background: Severe acute respiratory syndrome coronavirus 2 was found first in Wuhan and declared a pandemic by the World Health Organization. Coinfection with other respiratory viruses may occur, complicating the diagnosis and treatment of coronavirus disease 2019 . Herein, we identified a Karolinska Institute polyomavirus Stockholm 60 present in a nasopharyngeal swab of a patient with severe acute respiratory syndrome coronavirus 2 infection using next-generation sequencing with an enrichment method., Case Presentation: A 24-year-old Indonesian woman was admitted to our institution due to a cough, cold, and sore throat. She had no family history of hypertension and diabetes mellitus, and she was well. Her vital signs were as follows: heart rate, 84 beats per minute; respiratory rate, 22 breaths per minute; temperature, 39 °C; and pulse oximetry, 96% on room air. She had runny nose and slightly inflamed pharynx. Her nasopharyngeal swab and real-time polymerase chain reaction were positive for the coronavirus disease 2019 nucleocapsid and open reading frame genes, with cycle threshold values of 32.33 and 33.74, respectively. Whole-genome sequencing of severe acute respiratory syndrome coronavirus 2 was performed using the Nextera DNA Flex for Enrichment using the Respiratory Virus Oligos Panel, Illumina MiSeq instruments, and Illumina MiSeq reagent v3 150 cycles (2 × 75 cycles). The full genomes were aligned to the reference genome (NC_045512.2) by the Burrow-Wheeler aligner algorithm. The whole-genome sequencing showed coinfection of Karolinska Institute polyomavirus Stockholm 60 (NC_009238.1) with an overall coverage of 3561x. The patient was given acetaminophen, vitamin C, vitamin D, and zinc for the treatment and discharged uneventfully from the hospital 4 days after admission. Then, 2 weeks after discharge, she visited the outpatient clinic without any further concerns., Conclusion: This report presents a case of Karolinska Institute polyomavirus and severe acute respiratory syndrome coronavirus 2 coinfection in a patient with nonspecific clinical manifestation. Further studies with a larger sample size are mandatory to clarify the association between severe acute respiratory syndrome coronavirus 2 and Karolinska Institute polyomavirus coinfection, particularly on patient outcomes. Moreover, the results propose the usefulness of enrichment-based next-generation sequencing in detecting viral coinfection in patients with severe acute respiratory syndrome coronavirus 2., Competing Interests: Declarations. Ethics approval and consent to participate: The Ethical Committee of the Faculty of Medicine, Public Health and Nursing at Universitas Gadjah Mada/Dr. Sardjito Hospital approved this study (KE/FK/0124/EC/2020). The patient had completed a written informed consent before participating in this study. The study was conducted under the Declaration of Helsinki. Consent for publication: Written informed consent was obtained from the patient for the publication of this case report and any accompanying images. A copy of the written consent is available for review by the Editor-in-Chief of this journal. Competing interests: The authors declared no potential conflicts of interest for this article’s research, authorship, and/or publication., (© 2024. The Author(s).)

JC polyomavirus (JCPyV) establishes a persistent, asymptomatic kidney infection in most of the population. However, JCPyV can reactivate in immunocompromised individuals and cause progressive multifocal leukoencephalopathy (PML), a fatal demyelinating disease with no approved treatment. Mutations in the hypervariable non-coding control region (NCCR) of the JCPyV genome have been linked to disease outcomes and neuropathogenesis, yet few metanalyses document these associations. Many online sequence entries, including those on NCBI databases, lack sufficient sample information, limiting large-scale analyses of NCCR sequences. Machine learning techniques, however, can augment available data for analysis. This study employs a previously compiled dataset of 989 JCPyV NCCR sequences from GenBank with associated patient PML status and viral tissue source to train multilayer perceptrons for predicting missing information within the dataset. The PML status and tissue source models were 100% and 87.8% accurate, respectively. Within the dataset, 348 samples had an unconfirmed PML status, where 259 were predicted as No PML and 89 as PML sequences. Of the 63 sequences with unconfirmed tissue sources, eight samples were predicted as urine, 13 as blood, and 42 as cerebrospinal fluid. These models can improve viral sequence identification and provide insights into viral mutations and pathogenesis.

BK polyomavirus (BKPyV) contributes to premature renal failure in 10%-20% of kidney transplant recipients. Current treatment relies on reducing immunosuppression to regain BKPyV-specific immune control. Subsequently, declining allograft function may result from persisting viral cytopathology, BKPyV-specific immune reconstitution, or alloimmunity/rejection, all being poorly distinguishable by current histological or molecular approaches. To reduce the complexity encountered in BKPyV-replicating kidneys, we analyzed differentially expressed genes (DEGs) in primary human renal proximal tubular epithelial cells at 24 and 48 h post-infection (hpi) using single-cell RNA-sequencing (10x-Genomics-3´ kit). At 24 hpi, viral transcript reads predominantly mapped to the early viral gene region ( EVGR ) and shifted to >100-fold higher late viral gene region ( LVGR ) levels at 48 hpi, matching the sequential bi-directional viral protein expression from the circular double-stranded BKPyV-DNA genome. Besides expected coverage "hills" at viral 3´-poly-A sites, unexpected "spike" and "pulse" reads resulted from off-target TSO priming. "Spike" and "pulse" patterns were rare for the mostly unidirectional reads mapping to the circular mitochondrial genome. Bioinformatic curation removed "spikes" and "pulses" and reclassified 10% of DEGs in renal proximal tubular epithelial cells (RPTECs). Up-regulated gene ontologies included S and G2/M phase, double-stranded DNA repair, proximal tubulopathy, and renal tubular dysfunction, whereas allograft rejection, antigen presentation, innate immunity, translation, and autophagy were down-regulated. BKPyV- LVGR expression induced a novel mitochondrial cell stress pattern consisting of discordant up-regulation and down-regulation of mitochondria-encoded and nucleus-encoded mitochondrial genes, respectively. We explored which top-scoring gene sets of late-phase BKPyV-replicating RPTECs can identify BKPyV-associated nephropathy in kidney transplant biopsies. The results should facilitate distinguishing BKPyV-associated pathology from other entities in kidney transplant biopsies.IMPORTANCEBK polyomavirus (BKPyV) infects more than 90% of the general population and then persists in the reno-urinary tract. Subsequently, low-level urinary shedding is seen in 10% of healthy BKPyV-seropositive persons, indicating that BKPyV replication occurs despite the presence of virus-specific cellular and humoral immunity. Notably, transplantation of donor kidneys with low-level BKPyV replication is a risk factor for progression to high-level BKPyV viruria, new-onset BKPyV-DNAemia and biopsy-proven BKPyV nephropathy. Here, we identify a short list of robust up- and down-regulated nucleus-encoded differentially expressed genes potentially allowing to discriminate viral from allograft immune damage. By carefully curating viral and mitochondrial transcriptomes, we identify a novel virus-associated mitochondrial stress pattern of up-regulated mitochondria-encoded and down-regulated nucleus-encoded mitochondrial transcripts which heralds the BKPyV-agnoprotein-mediated immune escape by breakdown of the mitochondrial membrane potential and network and mitophagy. The results may prove useful when assessing the role of BKPyV replication in kidney transplant patients with suspected acute rejection and/or BKPyV nephropathy., Competing Interests: The authors declare no conflict of interest.

BK polyomavirus (BKPyV) is a major cause of kidney transplant failure, for which there are no antivirals. The current model is that BKPyV expresses TAg (large T antigen) early during infection, promoting cells to enter S phase where the viral DNA can access the host replication machinery. Here, we performed a single-cell analysis of viral TAg expression throughout the cell cycle to reveal that robust TAg expression required replication of the host DNA first. By using inhibitors that only affect host and not viral replication, we show that both TAg expression and viral production rely on an initial S phase. BKPyV is known to promote cellular re-replication, where the cell re-enters S phase from G2 phase (without passing through mitosis or G1 phase) to prolong S phase for viral replication. Thus, BKPyV infection results in cells with greater than 4N DNA content. We found that these subsequent rounds of replication of the host DNA relied on canonical host cell cycle machinery and regulators despite BKPyV infection. Together, these findings suggest a model for polyomavirus replication, where robust viral TAg expression depends on an initial host S phase and that BKPyV primarily replicates during host re-replication. Having a better understanding of the molecular events that are required for BKPyV production will help identify effective therapeutic targets against BKPyV., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Needham et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: BK polyomavirus (BKV) infection is a critical complication hindering graft survival after kidney transplantation. We aimed to investigate the risk factors and outcome of BKV infection in pediatric kidney transplantation., Methods: The clinical and follow-up data of pediatric kidney transplant recipients at the Children's Hospital of Fudan University from Jan 2015 to June 2023 were retrospectively analyzed., Results: A total of 217 patients were included in the study with mean follow-up time of 24.3 ± 19.9 months. The mean age at transplantation was 9.7 ± 4.2 years. The patient survival rate and graft survival rate were 98.2% and 96.8%, respectively. Twenty-nine patients (13.4%) developed BKV infection, which was detected at 5.8 ± 3.2 months after transplantation. Among these 29 patients with BKV infection, 8 patients (3.6%) developed BKV nephropathy (BKVN), which was diagnosed at 8.3 ± 2.9 months after transplantation, and 2 patients developed graft failure eventually. Compared with the non-BKV infection group (eGFR 76.7 ± 26.1 mL/min/1.73 m 2 ) and BKV infection without BKVN group (eGFR 85.2 ± 23.8 mL/min/1.73 m 2 ), BKVN group had lowest eGFR during follow-up (33.5 ± 11.0 ml/min/1.73 m 2 , P < 0.001). Younger age at transplant (OR 0.850, 95%CI 0.762-0.948, P = 0.005), CAKUT disease of primary etiology (OR 2.890, 95%CI 1.200-6.961, P = 0.018), and CMV negative recipient serostatus before transplantation (OR 3.698, 95%CI 1.583-8.640, P = 0.003) were independent risk factors for BKV infection., Conclusions: Incidence of BKV infection is quite high within 12 months after pediatric kidney transplantation and children with BKVN have poor graft function. Younger age at transplant, CAKUT disease, and CMV negative recipient serostatus before transplantation increase the risk of BKV infection after kidney transplantation., (© 2024. The Author(s), under exclusive licence to International Pediatric Nephrology Association.)

Background: BK polyomavirus (BKV) DNAaemia occurs in 10% of recipients of kidney transplants, contributing to premature allograft failure. Evidence suggests disease is donor derived. Hypothetically, recipient infection with a different BKV serotype increases risk due to poorer immunological control. Thus, understanding the composition and activity of the humoral anti-BKV responses in donor/recipient (D/R) pairs is critical., Methods: Using 224 paired pre-transplant D/R samples, BKV VP1 genotype-specific pseudoviruses were employed to define the breadth of the antibody response against different serotypes (ELISA) and, to characterise specific neutralising activity (nAb) using the 50% inhibitory concentration (LogIC50). Mismatch (MM) ratios were calculated using the ratio of recipient ELISA or nAb reactive BKV serotypes relative to the number of donor reactive serotypes., Findings: BKV DNAaemia was observed in 28/224 recipients of kidney transplants. These recipients had lower nAb titres against all the serotypes, with median logIC50 values of 1.19-2.91, compared to non-viraemic recipients' median logIC50 values of 2.13-3.30. nAb D/R MM ratios >0.67 associated with significantly higher risk of BKV viraemia, with an adjusted odds ratio of 5.12 (95% CI 2.07 to 13.04; p < 0.001). Notably, a mismatch against donor serotype Ic and II associated with adjusted odds ratios of 8.12 (95% CI 2.10 to 35.61; p = 0.002) and 4.52 (95% CI 1.19 to 19.23; p = 0.03) respectively. 21 recipients demonstrated broadly neutralising responses against all the serotypes, none of whom developed BKV DNAaemia post-transplant. In contrast, there was poor concordance with PsV-specific ELISA data that quantified the total antibody response against different serotypes., Interpretation: BKV nAb mismatch predicts post-transplant BKV DNAaemia. Specific mismatches in nAb, rather than total seroreactivity, are key indicators of BKV risk post-transplant. This has the potential to risk-stratify individuals and improve clinical outcomes by influencing the frequency of monitoring and individualised tailoring of immunosuppression. Furthermore, detailed examination of individuals with broadly neutralising responses may provide future therapeutic strategies., Funding: The research was funded by St. Peters Trust, Royal Free Hospital Charity and Wellcome Trust (grant numbers RFCG1718/05, SPT97 and 204870/Z/WT&#95;/Wellcome Trust/United Kingdom)., Competing Interests: Declaration of interests Stephanie Chong was granted funds by HCA healthcare UK to present this work at the British Transplantation Society Annual Congress 2024. The other authors make no further declarations of interests., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Head and neck squamous cell carcinoma (SCC) predisposing factors include smoking and alcohol consumption. However, other agents have been investigated, including viruses. We aimed to investigate the presence of DNA of four different types of human polyomavirus (HPyV) in the oral cavity and oropharyngeal SCC samples from an oncology center in Brazil and evaluate the association between HPyV detection and clinical and sociodemographic characteristics. Sixty fresh frozen samples from three different anatomical sites (tongue, floor of the mouth, and oropharynx, 20 samples for each region) were retrospectively selected. Data from medical records such as age, sex, alcohol consumption, smoking, tumor staging and death in less than 5 years of diagnosis were collected. DNA was extracted for the identification of MCPyV, BKPyV, JCPyV, and TSPyV using PCR followed by Sanger sequencing of positive samples. The identity of the generated DNA sequences was confirmed by alignment reference sequences. The investigation of the presence of HPyV DNA showed positivity of 5% for MCPyV (n = 3), 0% for both BKPyV or TSPyV, and 60% for JCPyV (n = 36). No association was found between the positivity of any HPyV in samples with any clinical or sociodemographic characteristics of the patients, nor with a certain anatomical site, except for the association between death in less than 5 years after diagnosis and positivity for JCPyV (p = 0.009). Positivity for HPyV in oral cavity and oropharyngeal SCC was low for MCPyV, high for JCPyV and null for BKPyV and TSPyV. Further studies should be carried out to better understand the high prevalence of JCPyV found in oral cavity and oropharyngeal SCC., (© 2024 Wiley Periodicals LLC.)

The nuclear lamina is a dense network of intermediate filaments beneath the inner nuclear membrane. Composed of A-type lamins (lamin A/C) and B-type lamins (lamins B1 and B2), the nuclear lamina provides a scaffold for the nuclear envelope and chromatin, thereby maintaining the structural integrity of the nucleus. A-type lamins are also found inside the nucleus where they interact with chromatin and participate in gene regulation. Viruses replicating in the cell nucleus have to overcome the nuclear envelope during the initial phase of infection and during the nuclear egress of viral progeny. Here, we focused on the role of lamins in the replication cycle of a dsDNA virus, mouse polyomavirus. We detected accumulation of the major capsid protein VP1 at the nuclear periphery, defects in nuclear lamina staining and different lamin A/C phosphorylation patterns in the late phase of mouse polyomavirus infection, but the nuclear envelope remained intact. An absence of lamin A/C did not affect the formation of replication complexes but did slow virus propagation. Based on our findings, we propose that the nuclear lamina is a scaffold for replication complex formation and that lamin A/C has a crucial role in the early phases of infection with mouse polyomavirus., (© 2024 The Author(s). The FEBS Journal published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.)

Avian Polyomaviruses are imposing severe health problems in budgerigars, non-budgerigar Psittacine species, and non-psittacine species all over the world, including Pakistan. It marks future challenges for aviculturists and pet store owners, causing significant financial losses. This study emphasizes the occurrence and molecular characterization of polyomaviruses in budgerigars and non-budgerigar Psittacine species. Thirty-five feather Samples of adult birds and 15 tissue samples of deceased birds were collected for the detection of Avian polyomavirus based on the VP1 gene. Screening of samples by PCR revealed the presence of 550 bp VP1 gene in deceased nestlings of two lovebirds and four budgerigars, while the feather samples of adult birds were all negative for VP1 gene. The overall positive rate of APV in Psittacine birds was 6/50 (12 %), and the distribution frequency of virus among species was 4/19 (20 %) in Budgerigars and 2/31 (6.4 %) in non-budgerigar. Positive samples were subjected to partial sequencing which showed a nucleotide similarity index of VP1 gene between 97.46 % & 99.6 % with reference sequences in GenBank. The main problem that researchers are dealing with is the scarcity of data on the prevalence and identification of APV in Pakistan. This study is a milestone for further research on APV for the diagnosis and development of vaccines., Competing Interests: Declaration of Competing Interest All the authors declare no conflict of interests, (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Simian virus 40 (SV40) is a monkey virus with tumorigenic potential in rodents and is associated with several types of human cancers, including lymphomas. A related Merkel cell polyomavirus causes carcinoma in humans by expressing truncated large tumor antigen (LT), with truncations caused by APOBEC family of cytidine deaminase-induced mutations. AID (activation-induced cytidine deaminase), a member of the APOBEC family, is the initiator of the antibody diversification process known as somatic hypermutation and its aberrant expression and targeting is a frequent source of lymphomagenesis. In this study, we investigated whether AID could cause mutations in SV40 LT. We demonstrate that the SV40 enhancer has strong somatic hypermutation targeting activity in several cell types and that AID-induced mutations accumulate in SV40 LT in B cells and kidney cells and cause truncated LT expression in B cells. Our results argue that the ability of the SV40 enhancer to target somatic hypermutation to LT is a potential source of LT truncation events that could contribute to tumorigenesis in various cell types, thereby linking SV40 infection with malignant development through a novel mutagenic pathway., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Polyomaviruses (PyVs) are small double-stranded DNA viruses able to infect species across all vertebrate taxa. In cetaceans, PyVs have been reported only in short-beaked common dolphin ( Delphinus delphis ), common bottlenose dolphin ( Tursiops truncatus ) and killer whale ( Orcinus orca ). Herein, we surveyed PyV in 119 cetaceans (29 mysticetes and 90 odontocetes) stranded along the Brazilian coast, from 2002 to 2022, comprising 18 species. DNA extracted from the lungs was tested using a nested PCR targeting the major capsid protein gene of PyV. Polyomavirus was detected in lung samples of 1.7% (2/119) cetaceans: two juvenile female Guiana dolphins ( Sotalia guianensis ) stranded in Rio de Janeiro (Rio de Janeiro state) and Guriri (Espírito Santo state), in 2018. Both retrieved sequences were identical and presented 93.3% amino acid identity with Zetapolyomavirus delphini , suggesting a novel species. On histopathology, one of the PyV-positive individuals presented basophilic intranuclear inclusion bodies morphologically consistent with polyomavirus in the lungs. Other available tissues from both cases were PyV-PCR-negative; however, both individuals tested positive for Guiana dolphin morbillivirus. To our knowledge, this is the first report of PyV infection in cetaceans of the Southern Hemisphere and the first description of a co-infection with morbillivirus.

Introduction: BK polyomavirus (BKPyV)-DNAemia is a common complication in kidney transplant recipients (KTRs). The significance of achieving viral clearance at different time intervals is not well understood., Methods: All adult KTRs transplanted between January 1, 2015 and December 31, 2017 who developed BKPyV-DNAemia were included. Outcomes were analyzed based on persistent clearance of BKPyV-DNAemia at 3-month intervals up to 2 years after initial detection, and for recipients with persistent BKPyV-DNAemia at last follow-up. Uncensored graft failure, death-censored graft failure (DCGF), and a composite outcome of DCGF or fall in estimated glomerular filtration rate (eGFR) by ≥50% from the time of initial BKPyV-DNAemia were outcomes of interest., Results: Of 224 KTRs with BKPyV-DNAemia, 58 recipients (26%) achieved viral clearance by 3 months after initial detection, 105 (47%) by 6 months, 120 (54%) by 9 months, 141 (63%) by 12 months, 155 (69%) by 15 months, 167 (75%) by 18 months, 180 (80%) by 21 months, and 193 (86%) by 24 months. Nine recipients (4%) had persistent BKPyV-DNAemia at last follow-up. Compared to recipients who achieved viral clearance by 3 months, those who achieved clearance by 6 months (adjusted odds ratio [aOR]: 3.15; 95% confidence interval [CI]: 1.22-8.12; p = .02) and 9 months (aOR: 3.69; 95% CI: 1.02-13.43; p = .04) had significantly increased risk for uncensored graft failure. There was no significant association between time to viral clearance and DCGF or composite outcomes., Conclusions: We found a trend of increased risk for uncensored graft failure among those who cleared BKPyV-DNAemia more slowly. Aiming to clear viremia early, without risking rejection, may be beneficial for allograft function and patient morbidity and mortality., (© 2024 The Author(s). Transplant Infectious Disease published by Wiley Periodicals LLC.)

Infection with merkel cell polyomavirus (MCPyV) is implicated in the development of merkel cell carcinoma (MCC), a rare but aggressive skin cancer. MCC has a mortality rate near 50%, and incidence has been rapidly increasing in recent decades, making development of improved treatment strategies critical to addressing its growing social burden. The parallel increasing necessity for novel research to better understand MCPyV pathogenesis has prompted numerous studies in recent years, yet the role of intrinsic disorder in MCPyV proteins remains unexplored. This study carries out computational characterization of intrinsic disorder within the MCPyV proteome and suggests mechanisms that may contribute to the oncogenicity of the virus to invade and hijack host immune systems. Our analysis finds that significant levels of intrinsic disorder are present in proteins LT, ALTO, 57kT, and VP1, and suggests that regions of sT may also contain large, disordered regions. The investigation further shows correlation of disorder propensity with the outputs for functional predictors of eukaryotic linear motifs (ELMs), molecular recognition features (MoRFs), and propensity for liquid-liquid phase separation (LLPS). Our findings indicate that MCPyV may use disorder and phase condensation to alter viral function that may accentuate or provide the basis for oncogenic activities. It is intended that this study will inform future experimental validation efforts around the phase separation capacity of MCPyV and its host protein-protein interactions. Furthermore, we hope to inform other investigators on the potential role of disorder in the MCPyV life cycle toward ultimately progressing the development of novel therapeutic agents., (© 2023 Wiley Periodicals LLC.)

Background: BK polyomavirus-associated nephropathy (BKPyVAN) is an important cause of allograft dysfunction and failure in kidney transplant recipients (KTRs) and there are no proven effective treatments. Case reports and in vitro data support the potential activity of cidofovir against BK polyomavirus (BKPyV)., Methods: We report the results of a phase I/II, double-blind, placebo-controlled randomized dose-escalation trial of cidofovir in KTRs with biopsy-confirmed BKPyVAN and estimated glomerular filtration rate ≥30 mL/min. Intravenous cidofovir (0.25 mg/kg/dose or 0.5 mg/kg/dose) or placebo was administered on days 0, 7, 21, and 35, with final follow-up through day 49., Results: The trial was prematurely discontinued due to slow accrual after 22 KTRs had completed the study. Cidofovir was safe and tolerated at the doses and duration studied. The proportion of subjects with any adverse event (AE) was similar between groups (9/14 [64%] in the combined cidofovir dose groups and 6/8 [75%] in the placebo group); 84% of AEs were mild. BKPyV DNAemia reduction by day 49 was similar between groups (>1 log 10 reduction in (2/9 [22.2%] of 0.25 mg/kg group, 1/5 [20%] of 0.5 mg/kg group, and 2/8 [25%] of placebo group)., Conclusions: These preliminary results indicate that low-dose cidofovir was safe and tolerated but had no significant BKPyV-specific antiviral effect in KTRs with BKPyVAN., (© 2024 The Author(s). Transplant Infectious Disease published by Wiley Periodicals LLC.)

BK polyomavirus (BKPyV) is responsible for hemorrhagic cystitis and nephropathy in bone marrow- and kidney transplant recipients, respectively. Monitoring BKPyV DNAuria and/or DNAemia by quantitative molecular tests is thus a common practice in the management of these patients. However, critical issues have been raised regarding these methods and the detection of viral genomes by positive PCR is not always associated with true viral replication. Identification of novel biomarkers and development of new assays are thus needed to help clinicians in patients' follow-up and enable timely and beneficial therapeutic interventions. Here, we describe the development of a urinary lateral flow assay that specifically detects the major BKPyV VP1 protein in a few minutes. This assay was characterized using cell culture-produced virus, pseudoviruses as well as VP1 pentamers representing the four BKPyV genotypes, diluted in urine matrix. The limit of detection was around 1 µg/mL of purified VP1 pentamers. This assay also enabled to detect BKPyV VP1 in frozen urine from transplant patients with high DNAuria. Clinical validation studies are now needed to evaluate the performance of this assay in real life and its relevance for interventions., Competing Interests: Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Etienne Brochot, Pauline Gaboriaud and Antoine Touzé reports a relationship with Spydiag (biotechnology start-up) that includes: board membership. The other authors declare that they have no competing interests., (Copyright © 2025 The Authors. Published by Elsevier B.V. All rights reserved.)

BK Polyomavirus nephropathy (PVN) with definitive diagnosis on biopsy, presents incidentally or with varying degrees of graft dysfunction. Banff working group on PVN has proposed a novel scoring system in renal biopsies, to identify patients with higher risk of graft failure. In this study, we attempted to validate the Banff scoring system at index biopsies and correlate with a novel index score, plasma BK-virus load and graft outcome. 48 patients with index biopsies of PVN diagnosed from 2019 to 2022, with simultaneous plasma BKV-virus loads and SV-40 stains were chosen. Biopsies were scored for Banff PVN Class and by novel PVN index. Inter-observer reproducibility was tested between 3 renal pathologists for all parameters and findings were correlated with graft outcome, in a median follow-up of 42 months. Banff PVN classes 2 and 3 and novel index 3 were associated with higher percentage of graft failure and persistent viremia. The novel index score showed a stronger and consistent temporal association with plasma BK-virus levels. Kappa scores revealed a 68 % agreement for Banff PVN class scoring. Our study highlights the prognostic utility of Banff PVN scheme and novel PVN index in correlation with plasma BKV viremia and graft outcome., Competing Interests: Declaration of competing interest All authors disclose that there is no conflict of interest of any kind. No financial support was obtained for this study. Authors declare that no funding was received from any source for the research study. Corresponding author was a recipient of Fulbright-Nehru Teaching and Research Scholarship and a visiting Professor at the Department of Pathology and Genomic Medicine at Houston Methodist Hospital, Houston, Texas, USA. Institute review board approval was obtained (MOD00006414) for waiver of written informed consent, as the study involved review of pathology slides and medical records for clinical correlation without direct patient contact., (Copyright © 2024 Elsevier Inc. All rights reserved.)

BK polyomavirus (BKPyV) infection of the kidney graft remains a major clinical issue in the field of organ transplantation. Risk factors for BKPyV-associated nephropathy (BKPyVAN) and molecular tools for determining viral DNA loads are now better defined. BKPyV DNAemia in plasma, in particular, plays a central role in diagnosing active infection and managing treatment decisions. However, significant gaps remain in the development of reliable biomarkers that can anticipate BKPyV viremia and predict disease outcomes. Biomarkers under active investigation include urine-based viral load assays, viral antigen detection, and immune responses against BKPyV, which may offer more precise methods for monitoring disease progression. In addition, treatment of BKPyVAN is currently based on immunosuppression minimization, while the role of adjunctive therapies remains an area of active research, highlighting the need for more personalized treatment regimens. Ongoing clinical trials are also exploring the efficacy of T-cell-based immunotherapies. The clinical management of BKPyV infection, based on proactive virological monitoring, immune response assessment, integrated histopathology, and timely immunosuppression reduction, is likely to reduce the burden of disease and improve outcomes in kidney transplantation.

Background: The garden dormouse (Eliomys quercinus) has experienced a significant population decline across Europe in recent decades. While habitat loss and climate change are often cited as primary factors, pathogen exposure, either to novel or to previously known, may play a role in such a decline. This study aimed to investigate the presence of polyomaviruses in garden dormice, given that these viruses are highly prevalent and can cause disease, particularly in immunocompromised individuals., Methods: The carcasses of garden dormice (n = 89) were collected throughout Germany. Kidney samples were tested for the presence of polyomavirus DNA using nested degenerate and specific diagnostic PCRs. Seroprevalence was assessed from chest cavity fluid samples through an enzyme-linked immunosorbent assay using polyomavirus VP1 virus-like particles produced in yeast., Results: A new polyomavirus, related to chimpanzee (Pan troglodytes) polyomaviruses 4 and 5 and human Merkel cell polyomavirus, was identified in the garden dormouse. Two 5,380 bp-length complete viral genomes were sequenced from dormice kidney samples (sequences PQ246041 and PQ246042). Genes encoding the putative structural proteins VP1, VP2, and VP3, as well as the Large, Middle, and small T antigens, containing conserved functional domains were identified. Polyomavirus DNA was detected in 2 of 74 dormice (2.7%, 95% confidence interval: 0-6.4%) through PCR, while 12 of 69 animals (17.4%, 95% confidence interval: 8.4-26.3%) tested positive for polyomavirus-specific antibodies., Conclusions: In conclusion, here we describe a novel polyomavirus in the garden dormouse with molecular and serological detection. Pairwise sequence comparison and phylogenetic analysis suggest that this novel virus may represent a novel species within the genus Alphapolyomavirus. Future work should examine if this virus is garden dormouse-specific and whether it is associated with disease in dormice., Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Chronic kidney disease is a really important heath issue, and transplantation is an intervention that can greatly increase patient quality of life and survival. The aim of this study was to perform a comprehensive evaluation of the BK virus, CMV, and EBV in kidney transplant recipients (KTRs); to assess the prevalence of infections; and to test if our detection method would be feasible for use in follow-ups with KTRs. A total of 157 KTRs registered at the Clinical Hospital "Dr. C. I. Parhon", Iași, Romania, were selected using specific inclusion/exclusion criteria. We tested the blood samples from each patient for BK, EBV, and CMV using a multiplex real-time PCR (qPCR) assay and the TaqMan PCR principle. The highest prevalence was detected for BKV (11/157, 7%), followed by CMV (9/157, 5.7%) and EBV (5/157, 3.2%). By simultaneously detecting three possible nephropathic viruses and oncogenes in KTRs using multiplex real-time PCR, we aimed to optimize their monitoring and follow-up. The prevalence of the tested nephropathogenic viruses-BKV, CMV, and EBV-was comparable to that analyzed in other studies. We demonstrate that the use of qPCR for viral detection in KTRs is a robust, cost-effective method for case monitoring.

Little is known about human polyomavirus 9 (HPyV9). The mode of transmission and the site of replication are unknown, and seroprevalence data have been published with a wide range. A total of 1038 serum samples from individuals aged 0.7-93 years were used for seroprevalence study. We observed that seropositivity increased with age among children and young adults, and a 36.2% adult seroprevalence was detected. The prevalence was examined in samples from the respiratory tract: cancerous and non-cancerous lung tissues, tonsils, adenoids, throat swabs, middle ear discharge and nasopharyngeal samples collected from children and adults. HPyV9 was detected in 5.2% of nasopharyngeal samples and 1% of tonsils. Upon a viral infection, the interaction of viral promoters and cellular factors may determine whether a virus productively replicates in a cell. The early and late promoter activity of HPyV9 and the effect of the large T antigen (LTAg) on it was investigated in respiratory, kidney, endothelial and colon cell lines, fibroblast and primary airway epithelial cells. The highest promoter activity was measured in A549 lung cell line. LTAg expression significantly increased the late promoter activity. Based on our results, the respiratory cells may be suitable for HPyV9 replication., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

BK polyomavirus (BKPyV) is a ubiquitous human virus that establishes a persistent infection in renal tubular epithelial cells and mainly causes disease in kidney transplant recipients. The closely related simian polyomavirus SV40 is known to cause cytoplasmic vacuolization in simian kidney cells, possibly increasing progeny release and cell death. This study aimed to determine whether BKPyV causes cytoplasmic vacuolization in primary human renal proximal tubule epithelial cells (RPTECs) and to investigate its potential role in the replication cycle. Using a large infectious dose (MOI 100-1000), a fraction of RPTECs (10-72%) showed early-wave vacuolization from 3 hours post-infection (hpi), which was mainly reversed by 36 hpi. Independent of the infectious dose, late-wave vacuolization occurred around the timepoint of progeny release. BKPyV receptor binding and internalization were required, as neuraminidase pretreatment and preincubation or treatment with a BKPyV-specific neutralizing antibody prevented early or late-occurring vacuolization. Microscopy revealed that the vacuoles were enlarged acidic endo-/lysosomal structures (dextran, EEA1, Rab5, Rab7, LAMP1, and/or Lysoview positive) that contained membrane-bound BKPyV. Time-lapse microscopy and quantitative PCR revealed that cell death and progeny release preceded late-wave vacuolization, mainly affecting cells directly neighboring the lysed cells. Thus, vacuolization had little impact on cell death or progeny release. Addition of the V-ATPase inhibitor Bafilomycin A1 at 0 hpi blocked vacuolization and BKPyV replication, but addition at 2 hpi only blocked vacuolization, suggesting that continuous endosomal acidification and maturation is needed for vacuole formation, but not for BKPyV replication. Our study shows that a massive uptake of BKPyV in RPTECs induces transient enlargement of endo-/lysosomes and is an early event in the viral replication cycle. Vacuolization gives no clear benefit for BKPyV and is possibly the result of a transiently overloaded endocytic pathway. Focal vacuolization around lysed cells suggests that the spread of BKPyV is preferably local., Competing Interests: The authours have declared that no competing interests exist., (Copyright: © 2024 Lorentzen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Polyomaviruses (PyVs) cause diverse diseases in a variety of mammalian hosts. During the life cycle, PyVs recruit nuclear host factors to viral genomes to facilitate replication and transcription. While host factors involved in DNA replication, DNA damage sensing and repair, and cell cycle regulation have been observed to bind PyV DNA, the complete set of viral and host proteins comprising the PyV replisome remains incompletely characterized. Here, the iPOND-MS technique (Isolation of Proteins on Nascent DNA coupled with Mass Spectrometry) was used to identify the proteome bound to murine PyV (MuPyV) DNA immediately following synthesis and 2 hours post-synthesis. Several novel MuPyV DNA interactors were identified on newly synthesized viral DNA (vDNA), including MCM complex members, DNA primase, DNA polymerase alpha, DNA ligase, and replication factor C. Though displaying partial overlap, the host and viral proteins bound to MuPyV DNA 2 hours post-synthesis lacked many of the replication proteins found on newly synthesized vDNA. These data help distinguish between the host factors critical for MuPyV DNA replication and those involved in downstream processing.IMPORTANCEPolyomaviruses are the causative agents of serious diseases in humans, including progressive multifocal leukoencephalopathy (PML), BK virus nephropathy, and Merkel cell carcinoma. The exact mechanisms by which the virus replicates, and which host cell proteins are required, are incompletely characterized. Identifying the host proteins necessary for efficient viral replication in the cell may reveal targets for downstream targets that may suppress viral replication in vivo ., Competing Interests: The authors declare no conflict of interest.

Background: Polyomavirus (PyV) nephropathy (PyVN) leads to kidney transplant dysfunction and loss. Since a definitive diagnosis requires an invasive kidney biopsy, a timely diagnosis is often hampered. In this clinical dilemma the PyV haufen-test, centering around the detection of 3-dimensional PyV aggregates in the urine, might provide crucial diagnostic information., Methods: A multistep experimental design was used. The hypothesis was that PyV-haufen form within the kidneys under high concentrations of uromodulin, a kidney-specific protein and that PyV-haufen are, therefore, kidney-specific disease biomarkers., Results: The first investigative step showed colocalization of uromodulin with aggregated PyV (1) in 10 kidneys with PyVN by immunohistochemistry, (2) in urine samples containing PyV-haufen by electron microscopy/immunogold labeling (n = 3), and (3) in urine samples containing PyV-haufen by immunoprecipitation assays (n = 4). In the in vitro experiments of the next step, only high uromodulin concentrations (≥1.25 mg/mL) aggregated PyV, as is expected to occur within injured nephrons. In contrast, in voided urine samples (n = 59) uromodulin concentrations were below aggregation concentrations (1.2-19.6 µg/mL). In the third investigative step, none of 11 uromodulin-/- knockout mice (0%) with histologic signs of PyVN showed urinary PyV-haufen shedding, compared with 10 of 14 uromodulin+/+ wild-type mice (71%)., Conclusions: PyV-haufen form within kidneys under high uromodulin concentrations. Thus, PyV-haufen detected in the urine are specific biomarkers for intrarenal disease (ie, definitive PyVN)., Competing Interests: Potential conflicts of interest. All authors: No reported conflicts. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed., (© The Author(s) 2024. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)

The objective of this study was to establish a more sensitive and specific diagnostic method for detecting plasma BK polyomavirus (BKPyV) DNA load in patients after renal transplantation using droplet digital polymerase chain reaction (ddPCR) and to validate the methodology. The linear range, lower limit of detection, accuracy, precision, and specificity of the detection system were evaluated by using the WHO BKPyV standard (7.2 log 10 IU/mL) as a reference, in accordance with the relevant documents of the Clinical and Laboratory Standards Institute. Plasma samples were collected from 74 renal transplantation patients with urinary BKPyV-DNA levels exceeding 7 log 10 copies/mL. Quantitative PCR (qPCR) and ddPCR were performed, and their diagnostic efficacy for BKPyV-DNA in the diagnosis of BK polyomavirus-associated nephropathy was evaluated using a receiver operating characteristic (ROC) curve. The coefficients of variation for the repeated detection of BKPyV standard DNA were 2.55 and 4.71 at concentrations of 6.2 and 3.2 log 10 IU/mL, respectively. The linear range was 2.2-6.2 log 10 IU/mL, and the lowest detection limit was 100 IU/mL. By utilizing histopathological examination of renal biopsy as the gold standard for BKPyV diagnosis, the area under the ROC curve of 74 post-transplantation plasma samples detected by the ddPCR system was found to be 0.875 (95% CI: 0.797-0.953, P < 0.01). The optimal threshold was 512.86 copies/mL, with a sensitivity of 90.0% and a specificity of 67.6%. In comparison, the area under the ROC curve for qPCR was 0.668 (95% CI: 0.583-0.752, P < 0.01), with an optimal threshold of 11,481.54 copies/mL, a sensitivity of 35.0%, and a specificity of 100.0%. Pairwise comparison (Delong test) of the ROC curves of the two systems showed a significant difference in the area under the curve, with a difference of 0.207 and a P -value <0.01. The BKPyV nucleic acid detection system, based on ddPCR, is appropriate for the regular monitoring of the BK polyomavirus, specifically in plasma samples containing low viral DNA loads while it provides the benefits of both absolute quantification and high sensitivity.IMPORTANCEIt was previously believed that droplet digital polymerase chain reaction had limitations, including high cost, limited throughput, and cumbersome operation, which hindered its widespread application in clinical practice. However, the current fully automated digital PCR platform, combined with streamlined operations, can detect 96 samples at once, and the entire process can be completed within an hour, laying a solid foundation for its extensive use., Competing Interests: The authors declare no conflict of interest.

Polyomaviruses are a group of small, non-enveloped, double-stranded DNA viruses that can infect various hosts, including humans. BKPyV causes conditions such as human polyomavirus-associated nephropathy (HPyVAN), human polyomavirus-associated haemorrhagic cystitis (HPyVHC), and human polyomavirus-associated urothelial cancer (HPyVUC). JC polyomavirus (JCPyV), on the other hand, is the causative agent of progressive multifocal leukoencephalopathy (PML), a severe demyelinating disease of the central nervous system. PML primarily affects immunocompromised individuals, including those with HIV, recipients of certain immunosuppressive therapies, and transplant patients. The treatment options for HPyV infections have been limited, but recent developments in virus-specific T cell (VST) therapy have shown promise. Although VST therapy has shown potential in treating both BKPyV and JCPyV infections, several challenges remain. These include the time-consuming and costly preparation of VSTs, the need for sophisticated production facilities, and uncertainties regarding the optimal cell type and infusion frequency. To the best of our knowledge, 85 patients with haemorrhagic cystitis, 27 patients with BKPyV viremia, 2 patients with BKPyV nephritis, 14 patients with haemorrhagic cystitis and BKPyV viremia, and 32 patients with PML have been treated with VST in the literature. The overall response results were 82 complete response, 33 partial response, 35 no response, and 10 no-outcome-reported. This review underscores the importance of VST therapy as a promising treatment approach for polyomavirus infections, emphasising the need for continued research and clinical trials to refine and expand this innovative immunotherapeutic strategy., Competing Interests: Declarations Funding: No external funding was received. Competing Interests: There are no conflicts of interest for all authors. Ethical Approval: Not required. Sequence Information: N/A., (Copyright © 2024 Elsevier Ltd and International Society of Antimicrobial Chemotherapy. All rights reserved.)

Merkel cell carcinoma (MCC) is an extremely rare cutaneous neuroendocrine cancer, with an incidence approximately 40 times lower than that of malignant melanoma; however, its significantly inferior survival rate compared to melanoma establishes MCC as the most lethal form of skin cancer. In recent years, a substantial body of literature has demonstrated a gradual increase in the incidence of MCC. Although the two factors that contribute to MCC, ultraviolet radiation and Merkel cell polyomavirus infection, have been well established, the specific pathogenesis of this disease remains unclear. Additionally, considering the high lethality and recurrence rates of MCC, as well as the absence of specific antitumor drugs, it is crucial to elucidate the factors that can accurately predict patients' outcomes. In this review, we summarized the significant advancements in the epidemiological characteristics, pathogenesis, and the factors that influence patient prognosis of MCC to enhance clinical practices and public health efforts., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

BK polyomavirus-associated nephropathy (BKPyVAN) is a well-known complication of kidney transplantation (KTx). The mainstay of prevention is the reduction of immunosuppression upon detection of BK polyomavirus (BKPyV) DNAemia, which precedes BKPyVAN. However, this reduction may inadvertently increase the risk of alloimmunity particularly in patients with a high BKPyV DNA load, where significant immunosuppression reduction is often necessary. This single-center, retrospective cohort study assesses the risk of de novo donor-specific antibodies (dnDSA) development and biopsy-proven acute rejection (BPAR) following high and low BKPyV DNAemia. All patients who underwent KTx at Leiden University Medical Center between 2011 and 2020 were included. Patients were grouped according to high (maximum BKPyV DNA load > 4log10 copies/mL), low (maximum serum BKPyV DNA load ≤ 10E4 copies/mL), and absent BKPyV DNAemia, and analyzed for the development of dnDSA and BPAR, using Cox regression. Of 1076 KTx recipients included, 108 (10%) developed a BKPyV DNAemia with a maximum DNA load below 4log10 copies/mL, whereas 121 (11.2%) developed a BKPyV DNAemia exceeding 4log10 copies/mL. The risk of dnDSA development was higher in patients with a high BKPyV DNAemia, compared to patients without DNAemia (adjusted hazard ratio of 1.9 (95% CI 1.1-3.2, p = 0.017). No significant difference in dnDSA risk was observed between patients with low and absent BKPyV DNAemia. Risk of BPAR did not differ between groups. Our study shows that higher BKPyV DNA loads in KTx patients are associated with a higher risk for dnDSA development, highlighting the importance of exploring additional strategies for the prevention and treatment of BKPyV infections in KTx recipients., (© 2024 The Author(s). Journal of Medical Virology published by Wiley Periodicals LLC.)

Abstract: Merkel cell carcinoma (MCC) is known as a rare and highly malignant neuroendocrine skin cancer and often occurs in the sun-exposed parts of the elderly individuals. In this article, we reported 2 cases of MCC and reviewed relative literature. Case 1 was a 91-year-old woman who presented with a half-year history of a brown nodule on the left temple. The histopathological and immunohistochemistry examination diagnosis was MCC with negative staining of Merkel cell polyomavirus large T antigen (CM2B4). Case 2 was a 76-year-old man with a nodule on his right buttock that gradually increased from approximately 3 mm to 1.5 cm in diameter in 1 month without pain. The biopsy diagnosis was MCC with positive staining of CM2B4. Previous studies have found that the genetic mutation and prognosis of polyomavirus-associated MCC (MCCP) and nonviral MCC (MCCN) are significantly different. Large T antigen plays a crucial role in Merkel cell polyomavirus (MCPyV) oncogenesis. Testing for the MCPyV at the onset of MCC is recommended, which is helpful in predicting the prognosis of patients., Competing Interests: The authors declare no conflicts of interest., (Copyright © 2024 The Author(s). Published by Wolters Kluwer Health, Inc.)

Objectives: BK virus-associated hemorrhagic cystitis is a common complication of allogeneic hematopoietic stem cell transplant. It is known to be associated with cyclophosphamide therapy and the intensity of the conditioning regimen as well as infection with the BK virus. Data are limited for BK virus-associated hemorrhagic cystitis in pediatric recipients of allogeneic hematopoietic stem cell transplant. Therefore, we aimed to identify the risk factors and etiology of BK virus-associated hemorrhagic cystitis and determine the factors that may improve the treatment efficacy., Materials and Methods: Data from recipients of allogeneic hematopoietic stem cell transplant were retrospectively analyzed. These data included information about age, sex, underlying disease, the details of ablative conditioning, graft-versus-host disease prophylaxis, donor type, stem cell source, history of acute graft-versus-host disease, and cytomegalovirus reactivation., Results: A total of 50 patients developed BK virus-associated hemorrhagic cystitis among 334 patients. Symptoms associated with BK virus-associated hemorrhagic cystitis manifested an average of 45.3 days after transplant. Most of the patients had grade 2 and grade 3 hemorrhagic cystitis. Risk factor analysis revealed that haploidentical donor type, treatment with busulfan and cyclophosphamide as part of conditioning regimen, and history of total body irradiation increased the risk of BK virus-associated hemorrhagic cystitis in the pediatric recipient population., Conclusions: We found that, despite current condi-tioning regimens, BK virus-associated infection still leads to a considerable incidence rate of hemorrhagic cystitis in pediatric recipients of allogeneic hema-topoietic stem cell transplant. Patients with a haploidentical donor and a history of busulfan and cyclophosphamide treatment or total body irradiation had a higher risk of BK virus-associated hemorrhagic cystitis. Thus, we suggest that patients with these factors should be followed closely after allogeneic hematopoietic stem cell transplant.

BK virus-associated nephritis (BKVAN) is an important cause of graft loss in renal transplant recipients B K viremia occurs in up to 30% of renal transplant recipients. Since the discovery of BKV in 1971, effective prophylaxis and treatment have not been established, and it is not uncommon for a transplant kidney to be lost without cure of BKVAN. BK virus infection is reactivated when cellular immunity is suppressed, which is often during the first year after kidney transplantation when cellular immunity is most suppressed. Clinically, it is caused by reactivation of latent infection or new infection from the donor kidney, leading to viremia, viremia, and transplant nephropathy. BK virus nephropathy is currently diagnosed definitively by measuring the amount of BK virus DNA in the blood and proving SV40-positive cells in transplant kidney tissue obtained by transplant kidney biopsy, but the time required for diagnosis and the low sensitivity of immunohistochemistry using antibodies are problematic. Therefore, we investigated whether the diagnosis of BK virus nephropathy could be made earlier by searching for miRNAs in the urine of renal transplant recipients., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Yuki Nakamura reports a relationship with Department of Surgery Nephrology Center, Toranomon Hospital that includes: funding grants. Tatsuya Chikaraishi reports a relationship with the Okinaka Memorial Institute for Adult Diseases that includes: funding grants. Yuhji Marui reports a relationship with Department of Renal Surgery, Himonya Hospital that includes: funding grants. Yasuo Ishii reports a relationship with Department of Surgery Nephrology Center, Toranomon Hospital that includes: funding grants. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Reactivation of BK polyomavirus (BKPyV) can cause significant kidney and bladder disease in immunocompromised patients. There are currently no effective, BKPyV-specific therapies. MAU868 is a novel, human immunoglobulin (Ig) G1 monoclonal antibody that binds the major capsid protein, VP1, of BKPyV with picomolar affinity, neutralizes infection by the 4 major BKPyV genotypes (EC 50 ranging from 0.009-0.093 μg/mL; EC 90 ranging from 0.102-4.160 μg/mL), and has comparable activity against variants with highly prevalent VP1 polymorphisms. No resistance-associated variants were identified in long-term selection studies, indicating a high in vitro barrier-to-resistance. The high-resolution crystal structure of MAU868 in complex with VP1 pentamer identified 3 key contact residues in VP1 (Y169, R170, and K172). A first-in-human study was conducted to assess the safety, tolerability, and pharmacokinetics of MAU868 following intravenous and subcutaneous administration to healthy adults in a randomized, placebo-controlled, double-blinded, single ascending dose design. MAU868 was safe and well-tolerated. All adverse events were grade 1 and resolved. The pharmacokinetics of MAU868 was typical of a human IgG, with dose-proportional systemic exposure and an elimination half-life ranging between 23 and 30 days. These results demonstrate the potential of MAU868 as a first-in-class therapeutic agent for the treatment or prevention of BKPyV disease., Competing Interests: Declaration of competing interest The authors of this manuscript have conflicts of interest to disclose as described by the American Journal of Transplantation. J. R. Abend, A. Sathe, M. B. Wrobel, M. Knapp, L. Xu, L. Zhao, P. Kim, S. Desai, A. Nguyen, X.-C. Leber, A. Hein, M. Scharenberg, J. Shaul, E. Ornelas, K. Wong, T. Pietzonka, P. Pertel, E. Traggiai, and S. J. Kovacs are or were employees of Novartis and shareholders of Novartis stock when the study was performed. L. M. Sterling was an employee of Celerion when the study was performed. MAU868 was discovered at Novartis Institutes for BioMedical Research and was then acquired by Amplyx Pharmaceuticals, Inc, which became a wholly owned subsidiary of Pfizer. MAU868 was most recently acquired and continues to be held by Vera Therapeutics., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

BK polyomavirus (BKPyV) infection in humans is usually asymptomatic but ultimately results in viral persistence. In immunocompromised hosts, virus reactivation can lead to nephropathy or hemorrhagic cystitis. The urinary tract serves as a silent reservoir for the virus. Recently, it has been demonstrated that human bladder microvascular endothelial cells (HBMVECs) serve as viral reservoirs, given their unique response to infection, which involves interferon (IFN) production. The aim of the present study was to better understand the life cycle of BKPyV in HBMVECs, uncover the molecular pathway leading to IFN production, and to identify the connection between the viral life cycle and the activation of the IFN response. Here, in the early stage of infection, BKPyV virions were found in internalized monopinocytic vesicles, while later they were detected in late endosomes, lysosomes, tubuloreticular structures, and vacuole-like vesicles. The production of viral progeny in these cells started at 36 h postinfection. Increased cell membrane permeability and peaks of virion release coincided with the leakage of viral and cellular DNA into the cytosol at approximately 60 h postinfection. Leaked DNA colocalized with and activated cGAS, leading to the activation of STING and the consequent transcription of IFNB and IFN-related genes; in contrast, the IFN response was attenuated by exposure to the cGAS inhibitor, G140. These findings highlight the importance of the cGAS-STING pathway in the innate immune response of HBMVECs to BKPyV., (© 2024 The Author(s). Journal of Medical Virology published by Wiley Periodicals LLC.)

Background: BK virus-associated nephropathy (BKVAN), caused by infection with or reactivation of BK virus, remains a challenge in kidney transplantation. Screening is recommended for all kidney transplant recipients. For those with clinically significant infection, reduction of immunosuppression is the cornerstone of management. There is no specific antiviral or immunomodulatory therapy sufficiently effective for routine use., Objectives: This review aimed to examine the benefits and harms of interventions for BK virus infection in kidney transplant recipients., Search Methods: We searched the Cochrane Kidney and Transplant Register of Studies up to 5 September 2024 through contact with the Information Specialist using search terms relevant to this review. Studies in the Register are identified through searches of CENTRAL, MEDLINE, and EMBASE, conference proceedings, the International Clinical Trials Registry Platform (ICTRP) Search Portal and ClinicalTrials.gov., Selection Criteria: All randomised controlled trials (RCTs) and cohort studies investigating any intervention for the treatment or prevention of BKVAN for kidney transplant recipients., Data Collection and Analysis: Two authors independently assessed the study quality and extracted data. Summary estimates of effect were obtained using a random-effects model, and results were expressed as risk ratios (RR) and their 95% confidence intervals (CI) for dichotomous outcomes and mean difference (MD) and 95% CI for continuous outcomes. Confidence in the evidence was assessed using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach., Main Results: Twelve RCTs (2669 randomised participants) were included. Six studies were undertaken in single centres, and six were multicentre studies; two of these were international studies. The ages of those participating ranged from 44 to 57 years. The length of follow-up ranged from three months to five years. All studies included people with a kidney transplant, and three studies included people with signs of BK viraemia. Studies were heterogeneous in terms of the type of interventions and outcomes assessed. The overall risk of bias was low or unclear. Intensive screening for the early detection of BK viraemia or BK viruria prevents graft loss (1 study, 908 participants: RR 0.00, 95% CI 0.00 to 0.05) and decreases the presence of decoy cells and viraemia at 12 months (1 study, 908 participants: RR 0.06, 95% CI 0.03 to 0.11) compared to routine care (high certainty evidence). No other outcomes were reported. Compared to placebo, fluoroquinolones may slightly reduce the risk of graft loss (3 studies, 393 participants: RR 0.37, CI 0.09 to 1.57; I 2 = 0%; low certainty evidence), probably makes little or no difference to donor-specific antibodies (DSA), may make little or no difference to BK viraemia and death, had uncertain effects on BKVAN and malignancy, but may increase the risk of tendonitis (2 studies, 193 participants: RR 5.66, CI 1.02 to 31.32; I 2 = 0%; low certainty evidence). Compared to tacrolimus (TAC), cyclosporin (CSA) probably makes little or no difference to graft loss and death, may make little or no difference to BKVAN and malignancy, but probably decreases BK viraemia (2 studies, 263 participants: RR 0.61, 95% CI 0.26 to 1.41; I 2 = 38%) and probably reduces the risk of new-onset diabetes after transplantation (1 study, 200 participants: RR 0.41, 95% CI 0.12 to 1.35) (both moderate certainty evidence). Compared to azathioprine, mycophenolate mofetil (MMF) probably makes little or no difference to graft loss and BK viraemia but probably reduces the risk of death (1 study, 133 participants: RR 0.43, 95% CI 0.16 to 1.16) and malignancy (1 study, 199 participants: RR 0.43, 95% CI 0.16 to 1.16) (both moderate certainty evidence). Compared to mycophenolate sodium (MPS), CSA has uncertain effects on graft loss and death, may make little or no difference to BK viraemia, but may reduce BKVAN (1 study, 224 participants: RR 0.06, 95% CI 0.00 to 1.20; low certainty evidence). Compared to immunosuppression dose reduction, MMF or TAC conversion to everolimus or sirolimus may make little or no difference to graft loss, BK viraemia or BKVAN (low certainty evidence). TAC conversion to sirolimus probably results in more people having a reduced BK viral load (< 600 copies/mL) than immunosuppression reduction (1 study, 30 participants: RR 1.31, 95% CI 0.90 to 1.89; moderate certainty evidence). Compared to MPS, everolimus had uncertain effects on graft loss and BK viraemia, may reduce BKVAN (1 study, 135 participants: 0.06, 95% CI 0.00 to 1.11) and may increase the risk of death (1 study, 135 participants: RR 3.71, 95% CI 0.20 to 67.35) (both low certainty evidence). Compared to CSA, everolimus may make little or no difference to BK viraemia, has uncertain effects on graft loss and BKVAN, but may increase the risk of death (1 study, 185 participants: RR 3.71, 95% CI 0.42 to 32.55; low certainty evidence). Compared to immunosuppression reduction, the leflunomide derivative FK778 may make little or no difference to graft loss, probably results in a greater reduction in plasma BK viral load (1 study, 44 participants: -0.60 copies/µL, 95% CI -1.22 to 0.02; moderate certainty evidence), but had uncertain effects on BKVAN and malignancy. Aggravated hypertension may be increased with KF778 (1 study, 46 participants: RR 8.23, 95% CI 0.50 to 135.40; low certainty evidence). There were no deaths in either group., Authors' Conclusions: Intense monitoring early after transplantation for BK viruria and BK viraemia is effective in improving BK virus infection outcomes as it helps with early detection of the infection and allows for a timely reduction in immunosuppression reduction. There is insufficient evidence to support any other intervention for BK virus infection in kidney transplant recipients., (Copyright © 2024 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.)

Merkel cell polyomavirus (MCPyV) is the foremost causative factor of Merkel cell carcinoma (MCC), a rare yet highly aggressive skin cancer. Although the evaluation of circulating IgG antibodies against Merkel cell polyomavirus (MCPyV) LT/sT oncoproteins is clinically useful for MCC diagnosis/prognosis, a limited number of assays for identifying such antibodies have been developed. Herein, a novel indirect immunoassay with synthetic epitopes/mimotopes of MCPyV oncoproteins was computationally designed and experimentally validated on control sera and sera from healthy individuals and MCC patients. Upon computational design of five synthetic peptides, the performance of the immunoassay in detecting anti-oncoprotein IgGs in MCPyV-positive and -negative control sera was evaluated. The immunoassay was afterwards extended on sera from healthy individuals, and, for longitudinal analysis, MCC patients. Performance properties such as sensitivity and specificity and positive/negative predictive values were adequate. Receiver-operating characteristic (ROC) curves indicated that the areas under the curves (AUCs) were within the low/moderately accurate ranges. Immunoassay was repeatable, reproducible and accurate. As expected, the serum anti-oncoprotein IgG prevalence in healthy individuals was low (2%-5%). Anti-oncoprotein IgGs slightly increased when MCC patients experienced partial tumour remission and/or stable disease, compared to baseline. Our data indicate that the newly developed immunoassay is reliable for detecting circulating anti-oncoprotein IgGs both in healthy individuals and MCC patients., (© 2024 The Author(s). Microbial Biotechnology published by John Wiley & Sons Ltd.)

Merkel cell carcinoma (MCC) is a rare and aggressive neuroendocrine tumor of the skin. Risk factors include extensive sun damage, infection with Merkel cell polyomavirus, and an immunocompromised state. PRAME, also known as preferentially expressed antigen in melanoma, is a cancer-testis antigen recently found to be a useful diagnostic tool in the workup of melanocytic neoplasms. However, the expression pattern of PRAME in Merkel cell carcinoma is unknown. In this study, we examine PRAME expression in Merkel cell carcinoma and explore its prognostic implications. The institutional archives at the University of Virginia were used to search for tumors classified as Merkel cell carcinoma from 2004 to 2022. All potential cases were reviewed to confirm the diagnosis, and electronic medical records were searched for clinical and demographic data. Tumors were subsequently immunostained for PRAME and Merkel cell polyomavirus. Cox proportional hazards regression models were used to estimate relative (all-cause) survival of PRAME positivity and MCPyV positivity in our study as well as MCC-specific survival of PRAME positivity. Univariate and multivariable models were created for each outcome related to all-cause survival. A total of 39 cases were included in the study. Twenty-eight percent (11 cases) demonstrated strong PRAME expression, and 27% of cases were positive for Merkel cell polyomavirus. There was no statistically significant correlation between PRAME expression and virus positivity. With respect to PRAME, the adjusted all-cause mortality hazard ratio was 11.4 (95% CI: 1.8, 70.8). The unadjusted MCC-specific hazard ratio was 4.6 (95% CI: 0.8, 27.5). The adjusted hazard ratio pertaining to Merkel cell polyomavirus infection was 0.25 (95% CI: 0.02, 2.96). In this limited cohort, PRAME expression appears to correlate with worse outcomes in Merkel cell carcinoma., Competing Interests: Conflicts of Interest and Source of Funding: The authors have disclosed that they have no significant relationships with, or financial interest in, any commercial companies pertaining to this article., (Copyright © 2024 Wolters Kluwer Health, Inc. All rights reserved.)

Merkel cell carcinoma (MCC) is a rare, aggressive skin cancer with a tripled incidence in the US and Europe over the past decade. Around 80% of MCC is linked to Merkel cell polyomavirus, but the cell of origin remains unknown. We stably introduced Merkel cell polyomavirus (MCPyV)-sT) and LT antigens to MCC13 and REH cell lines, analyzing DNA methylation and gene transcriptional regulation. Gene ontology analysis assessed MCPyV effects, and integrative analysis correlated gene expression and methylation. Expression patterns were compared with 15 previously sequenced primary MCCs. We found that MCPyV-LT induces DNA methylation changes in both cell lines, while MCPyV-sT only affected REH cells. Greater gene expression changes are observed in MCC13 cells, with upregulated genes associated with cellular components and downregulated genes related to biological processes. Integrative analysis of differentially expressed genes (DEG) and differentially methylated regions (DMR) of REH cell lines revealed that no genes were commonly methylated and differentially expressed. The study compared DEGs and DMG in MCC13 and REH cells to overlapping genes in MCPyV-positive cell lines (MKL1, MKL2, and WaGa), identifying hypomethylated genes in the gene body and hypermethylated genes at TSS1500. GO analysis of the two cell lines showed that MCPyV-TAs can downregulate genes in MHC-I pathways; this downregulation offers a target that can be used to create novel and efficient MCC immunotherapy approaches. Finally, it was confirmed that MCPyV-LT controls gene expression in MCC tissues using an integrative investigation of DNA methylation and gene expression., (© 2024 The Author(s). Journal of Medical Virology published by Wiley Periodicals LLC.)

Aim: The objective of this study was to investigate the pooled prevalence and possible association between polyomavirus infection and lung cancer., Methods: A systematic publication search was conducted by identifying relevant cross-sectional and case-control studies from major online databases. Heterogeneity, OR, and corresponding 95 % CI were applied to all studies through meta-analysis and forest plot. Random effects models were used to calculate the overall pooled prevalence. Visual inspection of a funnel plot plotting the log-transformed OR and its associated standard error of the log (OR) was combined with the Begg and Egger test to examine the presence and influence of publication bias. Analyzes were performed using Stata software v.14.1., Results: 23 articles (33 datasets) were included in the meta-analysis, of which 14 datasets were case/control and the rest were cross-sectional studies. The pooled polyomavirus infection rate in lung cancer patients was 0.06 % (0.02-0.11 %). In subgroup analysis, the pooled prevalence of JCV, MCPyV, KI, SV40, BKV, WU, MU, and STL was 21 %, 7 %, 6 %, 2 %, 0 %, 0 %, 0 %, and 0 % respectively. An association has been found between polyomavirus infection and lung cancer [summary OR 6.33 (95 % CI (1.76-22.77); I2=67.45 %)]. The subgroup analysis, based on the virus type, showed a strong association between MCPyV and lung cancer [summary OR 13.61 (95 % CI 2.41-76.59; I2=40.0 %)]. despite the high prevalence of JCV DNA in lung cancer tissue, analysis of case-control studies showed that JCV is not associated with lung cancer and does not increase the risk of lung cancer., Conclusion: This study showed a significant association between polyomaviruses infection with lung cancer. The results also revealed a pooled prevalence of 6 % for polyomaviruses in lung tumor patients. Altogether, the findings of the present work suggest that Merkel cell polyomavirus infection is a potential risk factor for lung cancer., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier GmbH. All rights reserved.)

Background: The Banff Working Group has updated the histological classification of BK virus nephropathy (BKVN), highlighting the importance of early detection. However, an early detection strategy for BKVN using biopsy has not yet been established. Our investigation aimed to assess the efficacy of protocol biopsy for the diagnosis of BKVN., Methods: We performed a retrospective cohort study of 314 patients who had undergone kidney transplantation between 2006 and 2021. Kidney allograft biopsies were performed as part of a protocol biopsy at 3 months and 1 year post-transplantation. Following the diagnosis of BKVN, the immunosuppressant dose was reduced., Results: Twelve patients (3.8%) were diagnosed with BKVN by biopsy. Most diagnoses are established during the early stages of BKVN (polyomavirus nephropathy class 1 in six, class 2 in five, and class 3 in one). Following the reduction in immunosuppressant dose, kidney allograft function did not deteriorate in any patients. Additionally, test for BK virus DNA in the blood was negative. All but one patient demonstrated histological resolution of BKVN, and the other had a very slight positivity for the simian virus 40 large T antigen. The median follow-up time after BKVN diagnosis was 6 years. One patient developed de novo donor-specific antibody and subclinical acute antibody-mediated rejection that was successfully cured., Conclusions: Our analysis indicates that protocol biopsy may enable the early detection of BKVN, resulting in the preservation of kidney function., (© 2024 Wiley Periodicals LLC.)

Background: The effect of belatacept on BK polyomavirus (BKPyV) control remains largely unknown., Methods: This is a propensity matched retrospective cohort study in adult kidney transplant recipients (KTR) transplanted between 2016-2020 who received a belatacept- versus tacrolimus-based immunosuppression regimen. A continuous time multi-state Markov model was used to evaluate BKPyV replication dynamics (BKPyV-dyn). Three BKPyV-dyn states were defined: BKPyV-dyn1 (viral load <3 log 10 ), BKPyV-dyn2 (viral load ≥ 3 log 10 and ≤4 log 10 ), and BKPyV-dyn3 (viral load >4 log 10 )., Results: Two hundred eighty KTR on belatacept- and 280 KTR on tacrolimus-based regimens were compared. The probability of transitioning between BKPyV-dyn states and time spent in each state in both groups was comparable. Total duration in BKPyV-dyn-1 was 632.1 days (95% CI 612.1, 648.5) for belatacept versus 615.2 days (95% CI 592.5, 635.8) for tacrolimus, BKPyV-dyn-2 was 49.2 days (95% CI 41.3, 58.4) for belatacept versus 55.6 days (95% CI 46.5, 66.8) for tacrolimus, and BKPyV-dyn-3 was 48.7 days (95% CI 37.1, 363.1) for belatacept versus 59.2 days (95% CI 45.8, 73.5) for tacrolimus. BKPyV associated nephropathy (PyVAN) occurred in 3.9% in belatacept- and 3.9% tacrolimus-treated KRT (P > .9)., Conclusions: Compared with tacrolimus-based immunosuppression, belatacept based immunosuppression was not associated with increased risk of BKPyV-DNAemia or nephropathy., (© 2024 Wiley Periodicals LLC.)

BK polyomavirus infection is an important cause of graft loss in transplant patients, however, currently available therapies lack effectiveness against this pathogen. Identification of immunological targets for potential treatments is therefore necessary. The aim of this study was to predict candidates of immunodominant epitopes within four BK virus proteins (VP1, VP2, VP3 and LTA) using PBMCs from 44 healthy donors. We used the ELISpot epitope mapping method to evaluate the T-cell response, and HLA-peptide binding was predicted using the NetMHCpan algorithm. A total of 11 potential peptides were selected for VP1, 3 for VP2/VP3 and 13 for LTA. Greater reactivity was observed for VP1 and LTA proteins compared with VP2/VP3. Most of the peptides selected as potential immunodominant candidates were restricted towards several HLA class I and II alleles, with predominant HLA class I binding by computational predictions. Based on these findings, the sequences of the selected immunodominant epitopes candidates and their corresponding HLA restrictions could contribute to the optimisation of functional assays and aid in the design and improvement of immunotherapy strategies against BK virus infections., (© 2024 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

Background: In kidney transplantation, concerns have been raised regarding increased incidence of viral opportunistic infections in hepatitis C virus (HCV) nucleic acid test (NAT)-negative (-) recipients who received HCV NAT-positive (+) donor kidneys, specifically BK polyomavirus (BKPyV), cytomegalovirus (CMV), and Epstein-Barr virus (EBV). The purpose of this study was to determine the incidence of these three viral opportunistic infections in HCV NAT- recipients who have undergone kidney transplantation with HCV NAT+ donor kidneys at our institution., Methods: This was an Institutional Review Board-approved, single-center, retrospective case-control study of HCV NAT- kidney transplant recipients with HCV NAT+ donors from 2018 to 2021. The primary outcome was the cumulative incidence of viral infections of BKPyV, CMV, and/or EBV within 1 year following kidney transplantation., Results: A total of 231 patients were included, 77 in the exposed (donor HCV NAT+) group and 154 in the control (donor HCV NAT-) group. The adjusted cumulative incidence of viremia within 1 year did not statistically differ between groups (77% exposed group versus 66% for the control group, hazard ratio 1.34, 95% confidence interval 0.95-1.89). In addition, no statistically significant differences were observed for secondary outcomes with the exception of CMV viremia (62% exposed versus 49% control, p = 0.021). However, there were more patients in the exposed group at high risk for CMV viremia based on serostatus (CMV Donor+/Recipient-, D+/R-)., Conclusion: Among patients who received HCV NAT+ donor kidneys, no clear association was observed between exposure to HCV NAT+ donor kidneys and viral infections of BKPyV, CMV, or EBV., (© 2024 Wiley Periodicals LLC.)