Evaluating the Efficiency of the Cobas 6800 System for BK Virus Detection in Plasma and Urine Samples

Song, Junhyup; Kim, Sinyoung; Kwak, Eunmin; Park, Younhee

doi:10.3390/diagnostics13172860

Cited by 3 publications

(2 citation statements)

References 48 publications

(53 reference statements)

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“…Furthermore, the use of guanidine hydrochloride has additional biosafety handling precautions and precludes the ability to perform viral culture. One study directly comparing neat urine to urine within cobas PCR media tested at a single time point demonstrated no significant impact on the performance of the cobas BKV test [10]. Our assessment of the stability of viral load in urine samples without stabilizing media at RT and at 4 °C for 7 days showed limited deterioration of the viral load.…”

Section: Discussionmentioning

confidence: 70%

Stability of BK polyomavirus DNA in urine over time and analytical evaluation of an automated BKV quantitative nucleic acid test

Lowe,

Lawson,

Young

et al. 2024

Journal of Medical Microbiology

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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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Section: Discussionmentioning

confidence: 70%

Stability of BK polyomavirus DNA in urine over time and analytical evaluation of an automated BKV quantitative nucleic acid test

Lowe,

Lawson,

Young

et al. 2024

Journal of Medical Microbiology

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“…The sample processing time was shorter than ELITech BKV LDT run on the m 2000, a batch analyzer with separate sample extraction and amplification step with a total processing time of approximately 7 hours (personal communication) which was within the range observed by Galindo et al ( 20 ) for the Abbott RealTime HIV-1, HBV, HCV, STI, and HPV assays run on m 2000. The sample processing time of 1 hour and 54 minutes for Alinity m BKV IUO is also shorter than the Roche cobas BKV sample processing time of approximately 3 hours ( 21 ). The fully automated, random-access feature of the Alinity m system is predicated on all assays requiring the same amount of time to process a sample, regardless of the assay being tested.…”

Section: Discussionmentioning

confidence: 98%

Performance evaluation of the high-throughput quantitative Alinity m BK virus assay

Hirschhorn,

Sasaki,

Kegl

et al. 2024

J Clin Microbiol

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BK virus (BKV) infection or reactivation in immunocompromised individuals can lead to adverse health consequences including BKV-associated nephropathy (BKVAN) in kidney transplant patients and BKV-associated hemorrhagic cystitis (BKV-HC) in allogeneic hematopoietic stem cell transplant recipients. Monitoring BKV viral load plays an important role in post-transplant patient care. This study evaluates the performance of the Alinity m BKV Investigational Use Only (IUO) assay. The linearity of the Alinity m BKV IUO assay had a correlation coefficient of 1.000 and precision of SD ≤ 0.25 Log IU/mL for all panel members tested (2.0–7.3 Log IU/mL). Detection rate at 50 IU/mL was 100%. Clinical plasma specimens tested comparing Alinity m BKV IUO to ELITech MGB Alert BKV lab-developed test (LDT) on the Abbott m 2000 platform using specimen extraction protocols for DNA or total nucleic acid (TNA) resulted in coefficient of correlation of 0.900 and 0.963, respectively, and mean bias of 0.03 and −0.54 Log IU/mL, respectively. Alinity m BKV IUO compared with Altona RealStar BKV and Roche cobas BKV assays demonstrated coefficient of correlation of 0.941 and 0.980, respectively, and mean bias of −0.47 and −0.31 Log IU/mL, respectively. Urine specimens tested on Alintiy m BKV IUO and ELITech BKV LDT using TNA specimen extraction had a coefficient of correlation of 0.917 and mean bias of 0.29 Log IU/mL. The Alinity m BKV IUO assay was performed with high precision across the dynamic range and correlated well with other available BKV assays. IMPORTANCE BK virus (BKV) in transplant patients can lead to adverse health consequences. Viral load monitoring is important in post-transplant patient care. This study evaluates the Alinity m BKV assay with currently available assays.

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T‐cell Mediated Rejection Associated Microvascular Inflammation in the Allograft Kidney: RNAseq Analysis Using the Banff Human Organ Transplant Gene Panel

Barwad,

Huang,

Randhawa

2024

Clinical Transplantation

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BackgroundMicrovascular inflammation (MVI) can occur in biopsies showing T‐cell mediated rejection (TCMR), but it is not well established that T‐cells can directly mediate microvascular injury (TCMR‐MVI).MethodsThis was a cross sectional RNAseq based Banff Human Organ Transplant (BHOT) gene expression (GE) analysis. The objective of this study was to probe the molecular signature of TCMR‐MVI in comparison with C4d+, DSA+ antibody mediated rejection (ABMR), stable renal function (STA), and TCMR without MVI. Transcriptome analysis utilized CLC genomic workbench and R‐studio software.ResultsNo gene set was specific for any diagnostic category, and all were expressed at low levels in STA biopsies. BHOT gene set scores could differentiate ABMR from TCMR and TCMR‐MVI, but not TCMR from TCMR‐MVI. TCMR‐MVI underexpressed several genes associated with ABMR including DSATs, ENDAT, immunoglobulin genes, ADAMDEC1, PECAM1 and NK cell transcripts (MYBL1, GNLY), but overexpressed C3, NKBBIZ, and LTF. On the other hand, there was no significant difference in the expression of these genes in TCMR‐MVI versus TCMR. This indicates that the GE profile of TCMR MVI aligns more closely with TCMR than ABMR. The limitations of classifying biopsies using the binary ABMR‐TCMR algorithm, and the occurrence of common pathogenesis mechanisms amongst different rejection phenotype was highlighted by the frequent presence of molecular mixed rejection.ConclusionsT‐cell mediated mechanisms play a significant role in the pathogenesis of MVI. GE was broadly different between rejection phenotypes, but molecular scores varied substantially between biopsies with the same Banff grade. It was not always possible to achieve precise molecular score‐based diagnostic categorization of individual patients.

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Evaluating the Efficiency of the Cobas 6800 System for BK Virus Detection in Plasma and Urine Samples

Cited by 3 publications

References 48 publications

Stability of BK polyomavirus DNA in urine over time and analytical evaluation of an automated BKV quantitative nucleic acid test

Stability of BK polyomavirus DNA in urine over time and analytical evaluation of an automated BKV quantitative nucleic acid test

Performance evaluation of the high-throughput quantitative Alinity m BK virus assay

T‐cell Mediated Rejection Associated Microvascular Inflammation in the Allograft Kidney: RNAseq Analysis Using the Banff Human Organ Transplant Gene Panel

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