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Mannonen L, Jokela P, Kragh Thomsen M, Yerly S, Cilla G, Jarem D, Canchola JA, Hopkins M. Performance of the cobas EBV and cobas BKV assays: multi-site comparison of standardized quantitation. J Clin Microbiol 2024; 62:e0026724. [PMID: 39046255 PMCID: PMC11323559 DOI: 10.1128/jcm.00267-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 06/21/2024] [Indexed: 07/25/2024] Open
Abstract
Guidelines recommend monitoring of Epstein-Barr virus (EBV) and BK virus (BKV) in solid organ and hematopoietic stem cell transplant patients. The majority of quantitative DNA testing for EBV and BKV employs unstandardized individual laboratory-developed testing solutions (LDTs), with implications for accuracy, reproducibility, and comparability between laboratories. The performance of the cobas EBV and cobas BKV assays was assessed across five laboratories, using the World Health Organization International Standards (WHO IS) for EBV and BKV, and the National Institute of Standards and Technology Quantitative Standard for BKV, and results were compared with the LDTs in use at the time. Methods were also compared using locally sourced clinical specimens. Variation was high when laboratories reported EBV or BKV DNA values using LDTs, where quantitative values were observed to differ by up to 1.5 log10 unit/mL between sites. Conversely, results from the cobas EBV and cobas BKV assays were accurate and reproducible across sites and on different testing days. Adjustment of LDTs using the international standards led to closer alignment between the assays; however, day-to-day reproducibility of LDTs remained high. In addition, BKV continued to show bias, indicating challenges with the commutability of the BKV International Standard. The cobas EBV and cobas BKV assays are automated, aligned to the WHO IS, and have the potential to reduce the variability in viral load testing introduced by differences in LDTs. Standardization of reporting values may eventually allow different centers to compare data to allow clinical decision thresholds to be established supporting improvements in patient management.IMPORTANCEThe application of center-specific cut-offs for clinical decisions and the variability of LDTs often hinder interpretation; thus, the findings reported here support the need for standardization in the field of post-transplant monitoring of EBV and BKV to improve patient management. Alongside the choice of assay, it is also important to consider which standard to use when deciding upon a testing methodology. This is a call to action for standardization, as treatment for EBV and BKV is driven by viral load test results, and the more accurate and comparable the test results are across institutions, the more informed and better the treatment decisions can be.
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Affiliation(s)
- Laura Mannonen
- Department of Clinical Microbiology, HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Pia Jokela
- Department of Clinical Microbiology, HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | | | - Sabine Yerly
- Laboratory of Virology, Diagnostic Department, Geneva University Hospitals, Geneva, Switzerland
| | - Gustavo Cilla
- Department of Microbiology, Donostia University Hospital and Biodonostia Health Research Institute, San Sebastián, Spain
| | - Daniel Jarem
- Clinical Development and Medical Affairs, Roche Molecular Systems, Inc., Pleasanton, California, USA
| | - Jesse A. Canchola
- CDMA Biometrics, Biostatistics Group, Roche Molecular Systems, Inc., Pleasanton, California, USA
| | - Mark Hopkins
- Department of Virology, Barts Health NHS Trust, London, United Kingdom
- Department of Infection and Immunity, Liverpool University Hospitals NHS Trust, Liverpool, United Kingdom
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2
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Nast CC. Polyomavirus nephropathy: diagnosis, histologic features, and differentiation from acute rejection. CLINICAL TRANSPLANTATION AND RESEARCH 2024; 38:71-89. [PMID: 38725187 PMCID: PMC11228385 DOI: 10.4285/ctr.24.0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/28/2024] [Accepted: 03/20/2024] [Indexed: 06/29/2024]
Abstract
Polyomaviruses, particularly BK virus, are ubiquitous latent infections that may reactivate with immunosuppression during kidney transplantation, resulting in polyomavirus nephropathy (PVN). The levels of viruria and viremia serve as tools for screening and making a presumptive diagnosis of PVN, respectively, while a definitive diagnosis requires a kidney biopsy. There are histologic classifications of PVN based on the extent of tubular cell viral infection, interstitial fibrosis, and interstitial inflammation. These classifications correlate to some degree with graft function and loss, aiding in determining treatment efficacy and prognostication. PVN has histologic overlap with acute cell-mediated rejection, making the differential diagnosis challenging, although there are suggestive features for these different causes of graft dysfunction. This article reviews the diagnosis, histologic findings, and classifications of PVN, and discusses how to differentiate viral nephropathy from acute rejection.
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Affiliation(s)
- Cynthia C Nast
- Department of Pathology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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3
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Lorant C, Zigmantaviciute J, Ali N, Bonnevier U, Tejde M, von Zur-Mühlen B, Eriksson BM, Bergqvist A, Westman G. The risk factors associated with post-transplantation BKPyV nephropathy and BKPyV DNAemia: a prospective study in kidney transplant recipients. BMC Infect Dis 2024; 24:245. [PMID: 38388351 PMCID: PMC10885533 DOI: 10.1186/s12879-024-09093-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/03/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND BK polyomavirus (BKPyV) infection after kidney transplantation can lead to serious complications such as BKPyV-associated nephropathy (BKPyVAN) and graft loss. The aim of this study was to investigate the incidence of BKPyVAN after implementing a BKPyV screening program, to map the distribution of BKPyV genotypes and subtypes in the Uppsala-Örebro region and to identify host and viral risk factors for clinically significant events. METHODS This single-center prospective cohort study included kidney transplant patients aged ≥ 18 years at the Uppsala University Hospital in Sweden between 2016 and 2018. BKPyV DNA was analyzed in plasma and urine every 3 months until 18 months after transplantation. Also genotype and subtype were determined. A logistic regression model was used to analyze selected risk factors including recipient sex and age, AB0 incompatibility and rejection treatment prior to BKPyVAN or high-level BKPyV DNAemia. RESULTS In total, 205 patients were included. Of these, 151 (73.7%) followed the screening protocol with 6 plasma samples, while184 (89.8%) were sampled at least 5 times. Ten (4.9%) patients developed biopsy confirmed BKPyVAN and 33 (16.1%) patients met criteria for high-level BKPyV DNAemia. Male sex (OR 2.85, p = 0.025) and age (OR 1.03 per year, p = 0.020) were identified as significant risk factors for developing BKPyVAN or high-level BKPyV DNAemia. BKPyVAN was associated with increased viral load at 3 months post transplantation (82,000 vs. < 400 copies/mL; p = 0.0029) and with transient, high-level DNAemia (n = 7 (27%); p < 0.0001). The most common genotypes were subtype Ib2 (n = 50 (65.8%)) and IVc2 (n = 20 (26.3%)). CONCLUSIONS Male sex and increasing age are related to an increased risk of BKPyVAN or high-level BKPyV DNAemia. BKPyVAN is associated with transient, high-level DNAemia but no differences related to viral genotype were detected.
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Affiliation(s)
- Camilla Lorant
- Department of Medical Sciences, Section of Infectious Diseases, Uppsala University, SE-751 85, Uppsala, Sweden.
| | - Justina Zigmantaviciute
- Department of Medical Sciences, Clinical Microbiology, Uppsala University, Uppsala, Sweden
- Clinical Microbiology and Infection Control, Uppsala University Hospital, Uppsala, Sweden
| | - Naima Ali
- Clinical Microbiology and Infection Control, Uppsala University Hospital, Uppsala, Sweden
| | | | - Mattias Tejde
- Department of Nephrology, Falun Hospital, Falun, Sweden
| | - Bengt von Zur-Mühlen
- Department of Surgical Sciences, Section of Transplantation Surgery, Uppsala University, Uppsala, Sweden
| | - Britt-Marie Eriksson
- Department of Medical Sciences, Section of Infectious Diseases, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Anders Bergqvist
- Department of Medical Sciences, Clinical Microbiology, Uppsala University, Uppsala, Sweden
- Clinical Microbiology and Infection Control, Uppsala University Hospital, Uppsala, Sweden
| | - Gabriel Westman
- Department of Medical Sciences, Section of Infectious Diseases, Uppsala University, SE-751 85, Uppsala, Sweden
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4
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Lowe CF, Lawson T, Young M, Jang W, Ritchie G, Romney MG, Matic N. Stability of BK polyomavirus DNA in urine over time and analytical evaluation of an automated BKV quantitative nucleic acid test. J Med Microbiol 2024; 73. [PMID: 38265290 DOI: 10.1099/jmm.0.001789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024] Open
Abstract
Introduction. BK polyomavirus (BKPyV) quantitative testing is an important screening tool post-transplantation, although interpretation can be challenging due to lack of standardization, assay heterogeneity and variability of BKPyV DNA over time (in urine).Methods. Remnant clinical EDTA plasma and urine samples were tested by the cobas BKV test and a validated laboratory-developed test (LDT). Accuracy [positive and negative percent agreement (PPA and NPA), Pearson's correlation, Bland-Altman analysis] and reproducibility were evaluated. To assess BKPyV DNA stability in urine, prospective urine samples were maintained at two different storage temperatures and tested in triplicate over 7 days.Results. Overall PPA was 95.6 % (43/45) and NPA was 94.4 % (170/180). For plasma, Pearson's correlation (0.950) and Bland-Altman analysis (0.113±0.22 log10 IU ml-1) showed high agreement. For neat urine, Pearson's correlation (0.842) and Bland-Altman analysis (0.326±0.80 log10 IU ml-1) showed somewhat higher variability. Reproducibility was high for the cobas BKV versus the LDT. BKPyV DNA levels in neat urine remained relatively stable over 7 days at both storage temperatures, although outlier results were intermittently detected.Conclusion. The cobas BKV test showed high agreement and reproducibility compared to the reference LDT. BKPyV viral load testing in urine has known limitations, but neat urine can be processed by the cobas BKV.
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Affiliation(s)
- Christopher F Lowe
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Tanya Lawson
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
| | - Matthew Young
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
| | - Willson Jang
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
| | - Gordon Ritchie
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Nancy Matic
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
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5
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Hoerres D, Dai Q, Elmore S, Sheth S, Gupta GP, Kumar S, Gulley ML. Calibration of cell-free DNA measurements by next-generation sequencing. Am J Clin Pathol 2023; 160:314-321. [PMID: 37244060 PMCID: PMC10472744 DOI: 10.1093/ajcp/aqad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/17/2023] [Indexed: 05/29/2023] Open
Abstract
OBJECTIVES Accurate monitoring of disease burden depends on accurate disease marker quantification. Although next-generation sequencing (NGS) is a promising technology for noninvasive monitoring, plasma cell-free DNA levels are often reported in misleading units that are confounded by non-disease-related factors. We proposed a novel strategy for calibrating NGS assays using spiked normalizers to improve precision and to promote standardization and harmonization of analyte concentrations. METHODS In this study, we refined our NGS protocol to calculate absolute analyte concentrations to (1) adjust for assay efficiency, as judged by recovery of spiked synthetic normalizer DNAs, and (2) calibrate NGS values against droplet digital polymerase chain reaction (ddPCR). As a model target, we chose the Epstein-Barr virus (EBV) genome. In patient (n = 12) and mock (n = 12) plasmas, NGS and 2 EBV ddPCR assays were used to report EBV load in copies per mL of plasma. RESULTS Next-generation sequencing was equally sensitive to ddPCR, with improved linearity when NGS values were normalized for spiked DNA read counts (R2 = 0.95 for normalized vs 0.91 for raw read concentrations). Linearity permitted NGS calibration to each ddPCR assay, achieving equivalent concentrations (copies/mL). CONCLUSIONS Our novel strategy for calibrating NGS assays suggests potential for a universal reference material to overcome biological and preanalytical variables hindering traditional NGS strategies for quantifying disease burden.
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Affiliation(s)
- Derek Hoerres
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
| | - Qunsheng Dai
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC, US
| | - Sandra Elmore
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC, US
| | - Siddharth Sheth
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC, US
- Division of Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
| | - Gaorav P Gupta
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC, US
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
| | - Sunil Kumar
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC, US
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
| | - Margaret L Gulley
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC, US
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6
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Govind S, Fritzsche M, Jenkins A, Cleveland MH, Vallone PM, Almond N, Morris C, Berry N. Deep Sequencing and Molecular Characterisation of BK Virus and JC Virus WHO International Reference Materials for Clinical Diagnostic Use. Viruses 2023; 15:1289. [PMID: 37376589 DOI: 10.3390/v15061289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/24/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Reactivation of JC and BK polyomaviruses during immunosuppression can lead to adverse clinical outcomes. In renal transplant recipients, BKV-associated nephropathy can result in graft loss, while in patients with autoimmune disorders, prolonged immunomodulatory drug use can cause rare onset of progressive multifocal leukoencephalopathy due to JCV reactivation. In such patients, accurate BK and JC viral load determinations by molecular technologies are important for diagnosis and clinical management; however, comparability across centres requires effective standardisation of diagnostic molecular detection systems. In October 2015, the WHO Expert Committee for Biological Standardisation (ECBS) established the 1st WHO International Standards (ISs) for use as primary-order calibrants for BKV and JCV nucleic acid detection. Two multi-centre collaborative studies confirmed their utility in harmonising agreement across the wide range of BKV and JCV assays, respectively. Previous Illumina-based deep sequence analysis of these standards, however, identified deletions in different regions, including the large T-antigen coding region. Hence, further detailed characterization was warranted. METHODS Comprehensive sequence characterisation of each preparation using short- and long-read next-generation sequencing technologies was performed with additional corroborative independent digital PCR (dPCR) determinations. Potential error rates associated with long-read sequencing were minimised by applying rolling circle amplification (RCA) protocols for viral DNA (circular dsDNA), generating a full validation of sequence identity and composition and delineating the integrity of full-length BK and JC genomes. RESULTS The analysed genomes displayed subpopulations frequently characterised by complex gene re-arrangements, duplications and deletions. CONCLUSIONS Despite the recognition of such polymorphisms using high-resolution sequencing methodologies, the ability of these reference materials to act to enhance assay harmonisation did not appear significantly impacted, based on data generated by the 2015 WHO collaborative studies, but highlights cautionary aspects of IS generation and commutability for clinical molecular diagnostic application.
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Affiliation(s)
- Sheila Govind
- Division of Infectious Disease Diagnostics, National Institute for Biological Standards and Control (NIBSC), South Mimms EN6 3QG, UK
| | - Martin Fritzsche
- Division of Analytical and Biological Sciences, National Institute for Biological Standards and Control (NIBSC), Medicines and Healthcare Product Regulatory Agency (MHRA), South Mimms EN6 3QG, UK
| | - Adrian Jenkins
- Division of Infectious Disease Diagnostics, National Institute for Biological Standards and Control (NIBSC), South Mimms EN6 3QG, UK
| | - Megan H Cleveland
- Applied Genetics Group, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Peter M Vallone
- Applied Genetics Group, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Neil Almond
- Division of Infectious Disease Diagnostics, National Institute for Biological Standards and Control (NIBSC), South Mimms EN6 3QG, UK
| | - Clare Morris
- Division of Infectious Disease Diagnostics, National Institute for Biological Standards and Control (NIBSC), South Mimms EN6 3QG, UK
| | - Neil Berry
- Division of Infectious Disease Diagnostics, National Institute for Biological Standards and Control (NIBSC), South Mimms EN6 3QG, UK
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7
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Palavecino EL, Ridley T, Hester L, Blosser SJ. Analytical evaluation of the cobas® 6800 system for the detection and quantification of BK Virus (BKV) and Epstein Barr Virus (EBV) at a US solid organ and hematopoietic stem cell transplant center. Diagn Microbiol Infect Dis 2023; 105:115884. [PMID: 36630742 DOI: 10.1016/j.diagmicrobio.2022.115884] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/08/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
The cobas® EBV and BKV assays are the first FDA-approved, quantitative assays for monitoring posttransplant reactivation of these viruses. In this study, we assessed performance of the fully-automated cobas® assays, compared with Diasorin Molecular ASR, our laboratory developed test, and demonstrated a strong interassay correlation for BK and EBV monitoring.
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Affiliation(s)
- Elizabeth L Palavecino
- Department of Pathology, Wake Forest School of Medicine, Winston Salem, NC, USA; Department of Pathology, Atrium Health -Wake Forest Baptist, Winston Salem, NC, USA.
| | - Tonika Ridley
- Department of Pathology, Atrium Health -Wake Forest Baptist, Winston Salem, NC, USA
| | - Louise Hester
- Department of Pathology, Atrium Health -Wake Forest Baptist, Winston Salem, NC, USA
| | - Sara J Blosser
- Medical and Scientific Affairs, Roche Diagnostics Corporation, Indianapolis, IN, USA
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8
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Hayden RT, Su Y, Boonyaratanakornkit J, Cook L, Gu Z, Jerome KR, Pinsky BA, Sam SS, Tan SK, Zhu H, Tang L, Caliendo AM. Matrix Matters: Assessment of Commutability among BK Virus Assays and Standards. J Clin Microbiol 2022; 60:e0055522. [PMID: 35997500 PMCID: PMC9491175 DOI: 10.1128/jcm.00555-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/18/2022] [Indexed: 11/20/2022] Open
Abstract
Quantitative testing of BK virus (BKPyV) nucleic acid has become the standard of care in transplant patients. While the relationship between interassay harmonization and commutability has been well characterized for other transplant-related viruses, it has been less well studied for BKPyV, particularly regarding differences in commutability between matrices. Here, interassay agreement was evaluated among six real-time nucleic acid amplification tests (NAATs) and one digital PCR (dPCR) BKPyV assay. Differences in the commutability of three quantitative standards was examined across all assays using a variety of statistical approaches. Panels, including 40 samples each of plasma and urine samples previously positive for BKPyV, together with one previously negative plasma sample and four previously negative urine samples, were tested using all assays, with each real-time NAAT utilizing its usual quantitative calibrators. Serial dilutions of WHO, National Institute for Standards and Technology (NIST), and commercially produced (Exact/Bio-Rad) reference materials were also run by each assay as unknowns. The agreement of the clinical sample values was assessed as a group and in a pairwise manner. The commutability was estimated using both relativistic and quantitative means. The quantitative agreement across assays in the urine samples was within a single log10 unit across all assays, while the results from the plasma samples varied by 2 to 3 log10 IU/mL. The commutability showed a similar disparity between the matrices. Recalibration using international standards diminished the resulting discrepancies in some but not all cases. Differences in the sample matrix can affect the commutability and interassay agreement of quantitative BKPyV assays. Differences in commutability between matrices may largely be due to factors other than those such as amplicon size, previously described as important in the case of cytomegalovirus. Continued efforts to standardize viral load measurements must address multiple sources of variability and account for differences in assay systems, quantitative standards, and sample matrices.
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Affiliation(s)
- R. T. Hayden
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Y. Su
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | | | - L. Cook
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Z. Gu
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - K. R. Jerome
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseaese Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - B. A. Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - S. S. Sam
- Division of Infectious Diseases, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - S. K. Tan
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - H. Zhu
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - L. Tang
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - A. M. Caliendo
- Division of Infectious Diseases, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
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9
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BK Virus Nephropathy in Kidney Transplantation: A State-of-the-Art Review. Viruses 2022; 14:v14081616. [PMID: 35893681 PMCID: PMC9330039 DOI: 10.3390/v14081616] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/10/2022] [Accepted: 07/22/2022] [Indexed: 11/16/2022] Open
Abstract
BK virus maintains a latent infection that is ubiquitous in humans. It has a propensity for reactivation in the setting of a dysfunctional cellular immune response and is frequently encountered in kidney transplant recipients. Screening for the virus has been effective in preventing progression to nephropathy and graft loss. However, it can be a diagnostic and therapeutic challenge. In this in-depth state-of-the-art review, we will discuss the history of the virus, virology, epidemiology, cellular response, pathogenesis, methods of screening and diagnosis, evidence-based treatment strategies, and upcoming therapeutics, along with the issue of re-transplantation in patients.
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10
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Le Duff Y, Gärtner K, Busby EJ, Dalzini A, Danaviah S, Fuentes JLJ, Giaquinto C, Huggett JF, Hurley M, Marcellin AG, Muñoz-Fernández MÁ, O’Sullivan DM, Persaud D, Powell L, Rigsby P, Rossi P, de Rossi A, Siems L, Smit T, Watters SA, Almond N, Nastouli E. Assessing the Variability of Cell-Associated HIV DNA Quantification through a Multicenter Collaborative Study. Microbiol Spectr 2022; 10:e0024322. [PMID: 35658711 PMCID: PMC9241949 DOI: 10.1128/spectrum.00243-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/20/2022] [Indexed: 11/20/2022] Open
Abstract
Reliable and accurate quantification of cell-associated HIV DNA (CA HIV DNA) is critical for early infant diagnosis, clinical management of patients under therapy, and to inform new therapeutics efficacy. The present study assessed the variability of CA HIV DNA quantification obtained from various assays and the value of using reference materials to help harmonize the measurements. Using a common set of reagents, our multicenter collaborative study highlights significant variability of CA HIV DNA quantification and lower limit of quantification across assays. The quantification of CA HIV DNA from a panel of infected PBMCs can be harmonized through cross-subtype normalization but assay calibration with the commonly used 8E5 cell line failed to reduce quantification variability between assays, demonstrating the requirement to thoroughly evaluate reference material candidates to help improve the comparability of CA HIV DNA diagnostic assay performance. IMPORTANCE Despite a global effort, HIV remains a major public health burden with an estimated 1.5 million new infections occurring in 2020. HIV DNA is an important viral marker, and its monitoring plays a critical role in the fight against HIV: supporting diagnosis in infants and underpinning clinical management of patients under therapy. Our study demonstrates that HIV DNA measurement of the same samples can vary significantly from one laboratory to another, due to heterogeneity in the assay, protocol, and reagents used. We show that when carefully selected, reference materials can reduce measurement variability and harmonize HIV DNA quantification across laboratories, which will help contribute to improved diagnosis and clinical management of patients living with HIV.
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Affiliation(s)
- Yann Le Duff
- Division of Infectious Disease Diagnostics, Centre for AIDS Reagent, National Institute for Biological Standards and Control, South Mimms, United Kingdom
| | - Kathleen Gärtner
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Eloise J. Busby
- National Measurement Laboratory, LGC group Teddington, Middlesex, United Kingdom
| | - Annalisa Dalzini
- Section of Oncology and Immunology, Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | | | - José Luis Jiménez Fuentes
- Instituto Investigación Sanitaria Gregorio Marañón, Laboratorio InmunoBiología Molecular and Spanish HIV HGM BioBank, Madrid, Spain
| | - Carlo Giaquinto
- Department for Woman’s and Child’s Health, University of Padova, Padua, Italy
| | - Jim F. Huggett
- National Measurement Laboratory, LGC group Teddington, Middlesex, United Kingdom
| | - Matthew Hurley
- Division of Infectious Disease Diagnostics, Centre for AIDS Reagent, National Institute for Biological Standards and Control, South Mimms, United Kingdom
| | - Anne-Geneviève Marcellin
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (IPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - María Ángeles Muñoz-Fernández
- Instituto Investigación Sanitaria Gregorio Marañón, Laboratorio InmunoBiología Molecular and Spanish HIV HGM BioBank, Madrid, Spain
| | - Denise M. O’Sullivan
- National Measurement Laboratory, LGC group Teddington, Middlesex, United Kingdom
| | - Deborah Persaud
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Laura Powell
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Peter Rigsby
- Division of Analytical Biological Sciences, National Institute for Biological Standards and Control, South Mimms, United Kingdom
| | - Paolo Rossi
- Department of Pediatrics, University of Rome Tor Vergata, Rome, Italy
| | - Anita de Rossi
- Section of Oncology and Immunology, Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Lilly Siems
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Theresa Smit
- Africa Health Research Institute, Durban, South Africa
| | - Sarah A. Watters
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Neil Almond
- Division of Infectious Disease Diagnostics, Centre for AIDS Reagent, National Institute for Biological Standards and Control, South Mimms, United Kingdom
| | - Eleni Nastouli
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
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11
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Maung Myint T, Chong CH, von Huben A, Attia J, Webster AC, Blosser CD, Craig JC, Teixeira-Pinto A, Wong G. Serum and urine nucleic acid screening tests for polyomavirus-associated nephropathy in kidney and kidney-pancreas transplant recipients. Hippokratia 2022. [DOI: 10.1002/14651858.cd014839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Thida Maung Myint
- John Hunter Hospital; Newcastle Australia
- Sydney School of Public Health; University of Sydney; Sydney Australia
| | - Chanel H Chong
- Sydney School of Public Health; University of Sydney; Sydney Australia
| | - Amy von Huben
- Sydney School of Public Health; University of Sydney; Sydney Australia
| | - John Attia
- University of Newcastle; Newcastle Australia
| | - Angela C Webster
- Sydney School of Public Health; University of Sydney; Sydney Australia
- Centre for Transplant and Renal Research; Westmead Hospital; Westmead Australia
| | - Christopher D Blosser
- Department of Medicine, Nephrology; University of Washington & Seattle Children’s Hospital; Seattle WA USA
| | - Jonathan C Craig
- College of Medicine and Public Health; Flinders University; Adelaide Australia
- Cochrane Kidney and Transplant, Centre for Kidney Research; The Children's Hospital at Westmead; Westmead Australia
| | | | - Germaine Wong
- Sydney School of Public Health; University of Sydney; Sydney Australia
- Centre for Transplant and Renal Research; Westmead Hospital; Westmead Australia
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12
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Myint TM, Chong CHY, Wyld M, Nankivell B, Kable K, Wong G. Polyoma BK Virus in Kidney Transplant Recipients: Screening, Monitoring, and Management. Transplantation 2022; 106:e76-e89. [PMID: 33908382 DOI: 10.1097/tp.0000000000003801] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Polyomavirus BK virus (BKPyV) infection is an important complication of kidney transplantation and allograft failure. The prevalence of viremia is 10%-15%, compared with BK-associated nephropathy (BKPyVAN) at 3%-5%. Given that there are no effective antiviral prophylaxis or treatment strategies for BKPyVAN, active screening to detect BKPyV viremia is recommended, particularly during the early posttransplant period. Immunosuppression reduction to allow viral clearance may avoid progression to severe and irreversible allograft damage. The frequency and duration of screening are highly variable between transplant centers because the evidence is reliant largely on observational data. While the primary treatment goals center on achieving viral clearance through immunosuppression reduction, prevention of subsequent acute rejection, premature graft loss, and return to dialysis remain as major challenges. Treatment strategies for BKPyV infection should be individualized to the recipient's underlying immunological risk and severity of the allograft infection. Efficacy data for adjuvant therapies including intravenous immunoglobulin and cidofovir are sparse. Future well-powered and high-quality randomized controlled trials are needed to inform evidence-based clinical practice for the management of BKPy infection.
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Affiliation(s)
- Thida Maung Myint
- Sydney School of Public Health, University of Sydney, Sydney, NSW, Australia
- Newcastle Transplant Unit, John Hunter Hospital, Newcastle, NSW, Australia
| | - Chanel H Y Chong
- Sydney School of Public Health, University of Sydney, Sydney, NSW, Australia
| | - Melanie Wyld
- Department of Renal Medicine, Centre for Transplant and Renal Research, Westmead Hospital, Westmead, NSW, Australia
| | - Brian Nankivell
- Department of Renal Medicine, Centre for Transplant and Renal Research, Westmead Hospital, Westmead, NSW, Australia
| | - Kathy Kable
- Department of Renal Medicine, Centre for Transplant and Renal Research, Westmead Hospital, Westmead, NSW, Australia
| | - Germaine Wong
- Sydney School of Public Health, University of Sydney, Sydney, NSW, Australia
- Department of Renal Medicine, Centre for Transplant and Renal Research, Westmead Hospital, Westmead, NSW, Australia
- Centre for Kidney Research, The Children's Hospital at Westmead, Westmead, NSW, Australia
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13
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Yazısız H, Uygun V, Çolak D, Mutlu D, Hazar V, Öğünç D, Öngüt G, Küpesiz FT. Incidence of BKV in the urine and blood samples of pediatric patients undergoing HSCT. Pediatr Transplant 2021; 25:e13894. [PMID: 33136312 DOI: 10.1111/petr.13894] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/20/2020] [Accepted: 09/28/2020] [Indexed: 11/27/2022]
Abstract
The aims were to investigate the incidence of BKV infection and the presence of HC in pediatric patients undergoing HSCT. Twenty-four children patients (M/F: 17/7) undergoing HSCT in a single center over a period of 1 year were included in the study. The presence of BKV DNA was determined by quantitative real-time PCR in plasma and urine samples at the following times: before transplantation, twice a week until engraftment time, and weekly for + 100 days. The mean age of the patients was 7.79 ± 5.03 years, the mean follow-up time was 95.6 ± 25.9 days, and the average number of samples per patient was 15.8 ± 3.2. BKV DNA was detected in at least one urine sample in 91.6% (n: 22) and at least one plasma sample in 75% (n:18) of the patients. The median time to the first BKV DNA positivity in urine and plasma samples was 11 (range: 1-80) and 32 days (range: 2-79), respectively. The median value of BKV DNA copies in urine and plasma were 1.7 × 106 (range: 2.8 × 101 -1.2 × 1014 ) and 1.9 × 103 copies/mL (range: 3-2.1 × 106 ), respectively. Thirteen patients (54.2%) had hematuria with BKV viruria; 8 (33.3%) patients had viremia. The median value of the BKV DNA copies in urine and plasma was 4.4 × 107 (range: 65-1 × 1011 ) and 2.9 × 103 (range: 7-7.8 × 104 ) copies/mL in these patients. Two (15.4%) of the 13 patients with BKV viruria and hematuria were diagnosed with BKV-related HC. BKV DNA viral load monitoring of urine and plasma in pediatric HSCT patients with a high risk for viral infections is valuable for understanding the development of BKV-related HC.
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Affiliation(s)
- Hatice Yazısız
- Department of Medical Microbiology, Akdeniz University Medical Faculty, Antalya, Turkey
| | - Vedat Uygun
- Department of Pediatric Hematology & Oncology, Medical Park Antalya Hospital, Antalya, Turkey
| | - Dilek Çolak
- Department of Medical Microbiology, Akdeniz University Medical Faculty, Antalya, Turkey
| | - Derya Mutlu
- Department of Medical Microbiology, Akdeniz University Medical Faculty, Antalya, Turkey
| | - Volkan Hazar
- Department of Pediatric Hematology & Oncology, MSG Medstar Yıldız Hospital, Antalya, Turkey
| | - Dilara Öğünç
- Department of Medical Microbiology, Akdeniz University Medical Faculty, Antalya, Turkey
| | - Gözde Öngüt
- Department of Medical Microbiology, Akdeniz University Medical Faculty, Antalya, Turkey
| | - Funda Tayfun Küpesiz
- Department of Pediatric Hematology & Oncology, Akdeniz University Medical Faculty, Antalya, Turkey
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14
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Leuzinger K, Naegele K, Schaub S, Hirsch HH. Quantification of plasma BK polyomavirus loads is affected by sequence variability, amplicon length, and non-encapsidated viral DNA genome fragments. J Clin Virol 2019; 121:104210. [PMID: 31759262 DOI: 10.1016/j.jcv.2019.104210] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/31/2019] [Accepted: 11/03/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Karoline Leuzinger
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Klaudia Naegele
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Stefan Schaub
- Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland; Transplantation Immunology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Hans H Hirsch
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland; Transplantation & Clinical Virology, Department Biomedicine, University of Basel, Basel, Switzerland; Infectious Diseases & Hospital Epidemiology, University Hospital Basel, Basel, Switzerland.
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15
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Complete Genome Sequence of Original Material Used To Derive the WHO International Standard for Human Polyomavirus BK DNA. Microbiol Resour Announc 2019; 8:8/43/e00911-19. [PMID: 31649077 PMCID: PMC6813389 DOI: 10.1128/mra.00911-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The complete genomic sequence was determined for the original biological material used to derive the WHO international standard for BK polyomavirus (BKV) DNA. The entire coding sequence and noncoding regions were assigned BKV subtype 1, subgroup 1b-1. This information will aid development and evaluation of human BKV DNA amplification assays. The complete genomic sequence was determined for the original biological material used to derive the WHO international standard for BK polyomavirus (BKV) DNA. The entire coding sequence and noncoding regions were assigned BKV subtype 1, subgroup 1b-1. This information will aid development and evaluation of human BKV DNA amplification assays.
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