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Engelmann I, Alidjinou EK, Ogiez J, Pagneux Q, Miloudi S, Benhalima I, Ouafi M, Sane F, Hober D, Roussel A, Cambillau C, Devos D, Boukherroub R, Szunerits S. Preanalytical Issues and Cycle Threshold Values in SARS-CoV-2 Real-Time RT-PCR Testing: Should Test Results Include These? ACS OMEGA 2021; 6:6528-6536. [PMID: 33748564 PMCID: PMC7970463 DOI: 10.1021/acsomega.1c00166] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 02/12/2021] [Indexed: 05/18/2023]
Abstract
Since the emergence of SARS-CoV-2 pandemic, clinical laboratories worldwide are overwhelmed with SARS-CoV-2 testing using the current gold standard: real-time reverse-transcription polymerase chain reaction (RT-PCR) assays. The large numbers of suspected cases led to shortages in numerous reagents such as specimen transport and RNA extraction buffers. We try to provide some answers on how strongly preanalytical issues affect RT-PCR results by reviewing the utility of different transport buffer media and virus inactivation procedures and comparing the literature data with our own recent findings. We show that various viral inactivation procedures and transport buffers are available and are less of a bottleneck for PCR-based methods. However, efficient alternative lysis buffers remain more difficult to find, and several fast RT-PCR assays are not compatible with guanidine-containing media, making this aspect more of a challenge in the current crisis. Furthermore, the availability of different SARS-CoV-2-specific RT-PCR kits with different sensitivities makes the definition of a general cutoff level for the cycle threshold (Ct) value challenging. Only a few studies have considered how Ct values relate to viral infectivity and how preanalytical issues might affect viral infectivity and RNA detection. We review the current data on the correlation between Ct values and viral infectivity. The presence of the SARS-CoV-2 viral genome in its own is not sufficient proof of infectivity and caution is needed in evaluation of the infectivity of samples. The correlation between Ct values and viral infectivity revealed an RT-PCR cutoff value of 34 cycles for SARS-CoV-2 infectivity using a laboratory-developed RT-PCR assay targeting the RdRp gene. While ideally each clinical laboratory should perform its own correlation, we believe this perspective article could be a reference point for others, in particular medical doctors and researchers interested in COVID-19 diagnostics, and a first step toward harmonization.
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Affiliation(s)
- Ilka Engelmann
- Univ.
Lille, CHU Lille, Laboratoire de Virologie ULR3610, F-59000 Lille, France
| | | | - Judith Ogiez
- Univ.
Lille, CHU Lille, Laboratoire de Virologie ULR3610, F-59000 Lille, France
| | - Quentin Pagneux
- Univ.
Lille, CNRS, Centrale Lille, University
Polytechnique Hauts-de-France, UMR 8520−IEMN, F-59000 Lille, France
| | - Sana Miloudi
- Univ.
Lille, CHU Lille, Laboratoire de Virologie ULR3610, F-59000 Lille, France
| | - Ilyes Benhalima
- Univ.
Lille, CHU Lille, Laboratoire de Virologie ULR3610, F-59000 Lille, France
| | - Mahdi Ouafi
- Univ.
Lille, CHU Lille, Laboratoire de Virologie ULR3610, F-59000 Lille, France
| | - Famara Sane
- Univ.
Lille, CHU Lille, Laboratoire de Virologie ULR3610, F-59000 Lille, France
| | - Didier Hober
- Univ.
Lille, CHU Lille, Laboratoire de Virologie ULR3610, F-59000 Lille, France
| | - Alain Roussel
- Architecture
et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, CEDEX 20, 13020 Marseille, France
- Architecture
et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, CEDEX 20, 13020 Marseille, France
| | - Christian Cambillau
- Architecture
et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, CEDEX 20, 13020 Marseille, France
- Architecture
et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, CEDEX 20, 13020 Marseille, France
| | - David Devos
- Univ.
Lille, CHU-Lille, Inserm, U1172, Lille Neuroscience & Cognition,
LICEND, F-59000 Lille, France
| | - Rabah Boukherroub
- Univ.
Lille, CNRS, Centrale Lille, University
Polytechnique Hauts-de-France, UMR 8520−IEMN, F-59000 Lille, France
| | - Sabine Szunerits
- Univ.
Lille, CNRS, Centrale Lille, University
Polytechnique Hauts-de-France, UMR 8520−IEMN, F-59000 Lille, France
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Implementation and Validation of the Roche Light Cycler 480 96-Well Plate Platform as a Real-Time PCR Assay for the Quantitative Detection of Cytomegalovirus (CMV) in Clinical Specimens Using the Luminex MultiCode ASRs System. Med Sci (Basel) 2020; 8:medsci8010014. [PMID: 32168800 PMCID: PMC7151591 DOI: 10.3390/medsci8010014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/03/2020] [Accepted: 03/07/2020] [Indexed: 11/16/2022] Open
Abstract
Allogenic stem-cell therapies benefit patients in the treatment of multiple diseases; however, the side effects of stem-cell therapies (SCT) derived from the concomitant use of immune suppression agents often include triggering infection diseases. Thus, analysis is required to improve the detection of pathogen infections in SCT. We develop a polymerase chain reaction (PCR)-based methodology for the qualitative real-time DNA detection of cytomegalovirus (CMV), with reference to herpes simplex virus types 1 (HSVI), Epstein–Barr virus (EBV), and varicella-zoster virus (VZV) in blood, urine, solid tissues, and cerebrospinal fluid. This real-time PCR of 96-well plate format provides a rapid framework as required by the Food and Drug Administration (FDA) for clinical settings, including the processing of specimens, reagent handling, special safety precautions, quality control criteria and analytical accuracy, precisely reportable range (analyst measurement range), reference range, limit of detection (LOD), analytical specificity established by interference study, and analyte stability. Specifically, we determined the reportable range (analyst measurement range) with the following criteria: CMV copies ≥200 copies/mL; report copy/mL value; CMV copies ≤199 copies/mL; report detected but below quantitative range; CMV copies = 0 with report <200 copies/mL. That is, with reference range, copy numbers (CN) per milliliter (mL) of the LOD were determined by standard curves that correlated Ct value and calibrated standard DNA panels. The three repeats determined that the measuring range was 1E2~1E6 copies/mL. The standard curves show the slopes were within the range −2.99 to −3.65 with R2 ≥ 0.98. High copy (HC) controls were within 0.17–0.18 log differences of DNA copy numbers; (2) low copy (LC) controls were within 0.17–0.18 log differences; (3) LOD was within 0.14–0.15 log differences. As such, we set up a fast, simple, inexpensive, sensitive, and reliable molecular approach for the qualitative detection of CMV pathogens. Conclusion: This real-time PCR of the 96-well plate format provides a rapid framework as required by the FDA for clinical settings.
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Bontems S, Boreux R, Capraro V, Huynen P, Descy J, Melin P, Hayette MP, Meex C. Evaluation of the Abbott RealTime quantitative CMV and EBV assays using the maxCycle protocol in a laboratory automation context. J Virol Methods 2019; 270:137-145. [PMID: 31121188 DOI: 10.1016/j.jviromet.2019.05.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/14/2019] [Accepted: 05/17/2019] [Indexed: 01/08/2023]
Abstract
Real-time PCR are often used for the diagnosis and monitoring of Cytomegalovirus (CMV) and Epstein-Barr virus (EBV) infections in susceptible populations. In this context, we evaluated the analytical performances of the Abbott RealTime CMV/EBV maxCycle protocol automated on the m2000 platform (Abbott). It was compared to our routinely-used procedure consisting of a NucleoMag® DNA extraction automated on a STARlet platform followed by manually processed CMV and EBV quantitative real-time PCR (Diagenode). In this study, we showed that both EBV assays exhibited a similar sensitivity but with a better precision for the EBV Abbott RealTime assay. For the CMV performances, the Abbott assay was more sensitive and more precise than our routine method. The use of WHO International Standards also indicated a slight underestimation of the viral loads (-0.25 log10 IU/mL and -0.21 log10 IU/mL for CMV and EBV assays respectively) while these were rather overestimated with the Starlet/Diagenode method (0.48 log10 IU/mL and 0.19 log10 IU/mL for CMV and EBV assays respectively). These trends were confirmed using relevant whole-blood clinical samples and external quality controls. The workflows were also compared and we highlighted a significant technician hands-on time reduction (-63%) using the Abbott CMV/EBV maxCycle automated protocol.
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Affiliation(s)
- Sébastien Bontems
- Laboratory of Clinical Microbiology, Unilab-Lg, CHU of Liege, 1 avenue de l'hopital, 4000 Liege, Belgium.
| | - Raphaël Boreux
- Laboratory of Clinical Microbiology, Unilab-Lg, CHU of Liege, 1 avenue de l'hopital, 4000 Liege, Belgium.
| | - Valérie Capraro
- Molecular Biology Platform, Unilab-Lg, CHU of Liege, 1 avenue de l'hopital, 4000 Liege, Belgium.
| | - Pascale Huynen
- Laboratory of Clinical Microbiology, Unilab-Lg, CHU of Liege, 1 avenue de l'hopital, 4000 Liege, Belgium.
| | - Julie Descy
- Laboratory of Clinical Microbiology, Unilab-Lg, CHU of Liege, 1 avenue de l'hopital, 4000 Liege, Belgium.
| | - Pierrette Melin
- Laboratory of Clinical Microbiology, Unilab-Lg, CHU of Liege, 1 avenue de l'hopital, 4000 Liege, Belgium.
| | - Marie-Pierre Hayette
- Laboratory of Clinical Microbiology, Unilab-Lg, CHU of Liege, 1 avenue de l'hopital, 4000 Liege, Belgium.
| | - Cécile Meex
- Laboratory of Clinical Microbiology, Unilab-Lg, CHU of Liege, 1 avenue de l'hopital, 4000 Liege, Belgium.
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Baron A, Gicquel A, Plantier JC, Gueudin M. Evaluation of four commercial extraction-quantification systems to monitor EBV or CMV viral load in whole blood. J Clin Virol 2019; 113:39-44. [PMID: 30870646 DOI: 10.1016/j.jcv.2019.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/24/2018] [Accepted: 03/01/2019] [Indexed: 12/26/2022]
Abstract
BACKGROUND Measurement of cytomegalovirus (CMV) and Epstein-Barr virus (EBV) viral loads is commonly used to monitor posttransplant patients. Two new systems (eMAG/eSTREAM and Versant/kPCR) have been recently commercialized. OBJECTIVES To evaluate the performance of four systems to quantify CMV and EBV in whole blood. STUDY DESIGN Three extraction and real-time PCR amplification systems: m2000SP/RT (M2000), eMAG/eSTREAM (EMAG), and Versant/kPCR (KPCR) were compared with our routine system Qiasymphony/RGQ (QS/RGQ). The 4 systems were tested using 3 dilutions in triplicate according to the WHO international standard (WHO-IS) for intra-assay reproducibility; 56 whole blood samples (24 patients, 4 follow-ups) for CMV and 45 samples (27 patients, 3 follow-ups) for EBV. RESULTS For CMV, the mean of the WHO-IS (expected value: 4.7 Log IU/ml) was: QS/RGQ=4.84, M2000=4.61, EMAG=4.33, and KPCR=4.79. One patient (10 samples) presented a major underquantification by QS/RGQ. Of the 46 remaining samples, 41 were quantified with QS/RGQ, 43 with M2000, 33 with EMAG and 24 with KPCR. For EBV, the mean of the WHO-IS was: QS/RGQ=4.70, M2000=4.61, EMAG=4.62, and KPCR=4.57. Among the 45 samples, 43 were quantified with QS/RGQ, 39 with M2000, 40 with EMAG and 32 with KPCR. CONCLUSION The results obtained with the WHO-IS were very good. The results of patients' samples were well correlated with the announced sensitivity of each system. The elevated threshold of the KPCR CMV assay may be problematic for the follow-up of highly immunocompromised patients who require early introduction of treatment.
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Affiliation(s)
- Adeline Baron
- CHU de Rouen, Laboratoire de Virologie, F-76000 Rouen, France
| | - Albane Gicquel
- CHU de Rouen, Laboratoire de Virologie, F-76000 Rouen, France
| | | | - Marie Gueudin
- CHU de Rouen, Laboratoire de Virologie, F-76000 Rouen, France
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Engelmann I, Alidjinou EK, Lazrek M, Pouillaude JM, Ogiez J, Rose F, Duhamel A, Dewilde A, Hober D. Comparison of two commercial quantitative PCR assays for EBV DNA detection and their correlation with the first WHO International Standard for EBV. J Med Microbiol 2018; 67:529-536. [DOI: 10.1099/jmm.0.000702] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Ilka Engelmann
- Université de Lille, Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, F-59000 Lille, France
| | - Enagnon Kazali Alidjinou
- Université de Lille, Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, F-59000 Lille, France
| | - Mouna Lazrek
- Université de Lille, Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, F-59000 Lille, France
| | - Jean-Marie Pouillaude
- Université de Lille, Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, F-59000 Lille, France
| | - Judith Ogiez
- Université de Lille, Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, F-59000 Lille, France
| | - François Rose
- Université de Lille, Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, F-59000 Lille, France
| | - Alain Duhamel
- Université de Lille, CHU Lille, EA 2694 - Santé publique : épidémiologie et qualité des soins, F-59000 Lille, France
| | - Anny Dewilde
- Université de Lille, Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, F-59000 Lille, France
| | - Didier Hober
- Université de Lille, Faculté de Médecine, CHU Lille, Laboratoire de Virologie EA3610, F-59000 Lille, France
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