Comparison of BKV quantification using a single automated nucleic acid extraction platform and 3 real-time PCR assays

Greer, Amy; Forman, Michael; Valsamakis, Alexandra

doi:10.1016/j.diagmicrobio.2015.04.006

Cited by 7 publications

(3 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To extend utility of our in silico qPCR evaluation strategy, we applied it to a substantial subset of BKPyV qPCRs described in literature. A database of 52 BKPyV-specific qPCRs taken from 32 papers ( Bárcena-Panero et al., 2012 ; Bergallo et al., 2018 ; Bressollette-Bodin et al., 2005 ; Dadhania et al., 2008 ; Delbue et al., 2015 ; Dumoulin and Hirsch, 2011 ; Funahashi et al., 2010 ; Gard et al., 2015 ; Greer et al., 2015 ; Gustafsson et al., 2013 ; Hammarin et al., 2011 ; Hasan et al., 2016 ; Hoffman et al., 2008 ; Kamminga et al., 2019 ; Keith et al., 2018 ; Ledesma et al., 2012 ; Marchetti et al., 2007 ; Marinelli et al., 2007 ; Mitui et al., 2013 ; Muldrew and Lovett, 2013 ; Pal et al., 2006 ; Pang et al., 2007 ; Pietilä et al., 2015 ; Priftakis et al., 2003 ; Ryschkewitsch et al., 2004 ; Şahiner et al., 2014 ; Sarmento et al., 2019 ; Signorini et al., 2014 ; Si-Mohamed et al., 2006 ; Stolt et al., 2005 ; Thomas et al., 2007 ; Yamamoto et al., 2015 ) was created by searching PubMed using a text-mining approach detailed in the STAR methods section. Each selected BKPyV qPCR is listed in Table S1 with its reference, original and adjusted Ta values, and degeneracy of its oligos.…”

Section: Resultsmentioning

confidence: 99%

Translating genomic exploration of the family Polyomaviridae into confident human polyomavirus detection

et al. 2022

View full text Add to dashboard Cite

Summary The Polyomaviridae is a family of ubiquitous dsDNA viruses that establish persistent infection early in life. Screening for human polyomaviruses (HPyVs), which comprise 14 diverse species, relies upon species-specific qPCRs whose validity may be challenged by accelerating genomic exploration of the virosphere. Using this reasoning, we tested 64 published HPyV qPCR assays in silico against the 1781 PyV genome sequences that were divided in targets and nontargets, based on anticipated species specificity of each qPCR. We identified several cases of problematic qPCR performance that were confirmed in vitro and corrected through using degenerate oligos. Furthermore, our study ranked 8 out of 52 tested BKPyV qPCRs as remaining of consistently high quality in the wake of recent PyV discoveries and showed how sensitivity of most other qPCRs could be rescued by annealing temperature adjustment. This study establishes an efficient framework for ensuring confidence in available HPyV qPCRs in the genomic era.

show abstract

Section: Resultsmentioning

confidence: 99%

Translating genomic exploration of the family Polyomaviridae into confident human polyomavirus detection

et al. 2022

View full text Add to dashboard Cite

show abstract

“…In this study, if PCR results showed more than 107 copies/ml in urine and more than 104 copies/ml in blood, the results were considered to be positive. [3,4]…”

Section: Experiments Methodsmentioning

confidence: 99%

Clinical study of different immune induction and BK virus infection after renal transplantation

Han¹,

Liu²,

Feng³

et al. 2023

DCC

View full text Add to dashboard Cite

Objective: To monitor the incidence of BK virus infection in hematuria of renal transplant recipients induced by different immunizations.Methods: A total of 109 patients who underwent renal transplantation in Baogang Hospital of Inner Mongolia from January 2019 to December 2022 were analyzed retrospectively. The results of BK virus DNA detection in urine and blood were observed after operation. They were divided into three groups according to different immunosuppressive induction regimens; 35 patients in group A, 42 patients in group B, and 32 patients in group C (basiliximab). To explore the effect of different immune induction regimens on BK virus infection in renal transplant recipients.Results: The positive rate of urine BK virus in all patients in 1 month after operation was 10.09% (11/109), which was significantly higher than that of blood BK virus 0% (0/109), and the difference had a statistical significance (p < .05). The positive rate of urine BK virus in all patients in 6 months after operation was 31.19% (34/109), which was significantly higher than that of blood BK virus 3.67% (4/109), and the difference had a statistical significance (p < .05). The positive rate of urine BK virus in all patients in 12 months after operation was 35.79% (39/109), which was significantly higher than that of blood BK virus 5.50% (6/109), and the difference had a statistical significance (p < .05). The urinary BK virus infection rate was increased significantly from 1 month to 6 months after operation, but was not increased significantly from 6 months to 12 months after operation. There was a statistically significant difference between the two groups (p < .05). The BK virus infection rate in renal transplant recipients induced by basiliximab within the first month was significantly lower than that in patients using polyclonal antibodies, but the urinary BK virus infection rate after one year was not significantly different from that in patients using polyclonal antibodies.Conclusions: There are slight differences in BK virus infection after early renal transplantation with different immune induction therapies, but there is no significant difference in the long-term. It is recommended to strengthen the early monitoring of BK virus after renal transplantation, timely adjust immunosuppressive regimens to achieve the early detection and early treatment.

show abstract

“…Such variability has been well described with negative impact on patient care, particularly when two laboratories report discrepant viral loads and management is initiated or delayed based on inaccurate or discordant quantitative results (6)(7)(8)(9)(10). Among the most cited factors contributing to this variability are the use of different standards for quantitation and primer and probe designs that do not account for BKV genotypic variation (7)(8)(9)11).…”

mentioning

confidence: 99%

Calibration of BK Virus Nucleic Acid Amplification Testing to the 1st WHO International Standard for BK Virus

et al. 2017

View full text Add to dashboard Cite

Significant interassay variability in the quantification of BK virus (BKV) DNA precludes establishing broadly applicable thresholds for the management of BKV infection in transplantation. The 1st WHO International Standard for BKV (primary standard) was introduced in 2016 as a common calibrator for improving the harmonization of BKV nucleic acid amplification testing (NAAT) and enabling comparisons of biological measurements worldwide. Here, we evaluated the Altona RealStar BKV assay (Altona) and calibrated the results to the international unit (IU) using the Exact Diagnostics BKV verification panel, a secondary standard traceable to the primary standard. The primary and secondary standards on Altona had nearly identical linear regression equations (primary standard, Y ϭ 1.05X Ϫ 0.28, R 2 ϭ 0.99; secondary standard, Y ϭ 1.04X Ϫ 0.26, R 2 ϭ 0.99) and conversion factors (primary standard, 1.11 IU/copy; secondary standard, 1.09 IU/copy). A comparison of Altona with a laboratory-developed BKV NAAT assay in IU/ml versus copies/ml using PassingBablok regression revealed similar regression lines, no proportional bias, and improvement in the systematic bias (95% confidence interval of intercepts: copies/ml, Ϫ0.52 to Ϫ1.01; IU/ml, 0.07 to Ϫ0.36). Additionally, Bland-Altman analyses revealed a clinically significant reduction of bias when results were reported in IU/ml (IU/ml, Ϫ0.10 log 10 ; copies/ml, Ϫ0.70 log 10 ). These results indicate that the use of a common calibrator improved the agreement between the two assays. As clinical laboratories worldwide use calibrators traceable to the primary standard to harmonize BKV NAAT results, we anticipate improved interassay comparisons with a potential for establishing broadly applicable quantitative BKV DNA load cutoffs for clinical practice.

show abstract

Comparison of BKV quantification using a single automated nucleic acid extraction platform and 3 real-time PCR assays

Cited by 7 publications

References 19 publications

Translating genomic exploration of the family Polyomaviridae into confident human polyomavirus detection

Translating genomic exploration of the family Polyomaviridae into confident human polyomavirus detection

Clinical study of different immune induction and BK virus infection after renal transplantation

Calibration of BK Virus Nucleic Acid Amplification Testing to the 1st WHO International Standard for BK Virus

Contact Info

Product

Resources

About