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1. Reliable and Scalable SARS-CoV-2 qPCR Testing at a High Sample Throughput: Lessons Learned from the Belgian Initiative

Author

Steven Van Vooren, James Grayson, Marc Van Ranst, Elisabeth Dequeker, Lies Laenen, Reile Janssen, Laurent Gillet, Fabrice Bureau, Wouter Coppieters, Nathalie Devos, Benjamin Hengchen, Pierre Wattiau, Sibylle Méhauden, Yvan Verlinden, Kurt Van Baelen, Theresa Pattery, Jean-Pierre Valentin, Kris Janssen, Martine Geraerts, John Smeraglia, Jan Hellemans, Pieter Wytynck, Pieter Mestdagh, Nienke Besbrugge, René Höfer, Friedel Nollet, Jo Vandesompele, Pieter De Smet, John Lebon, Emmanuel Vandewynckele, Steven Verstrepen, Wouter Uten, Arnaud Capron, Hugues Malonne, Jeroen Poels, and Emmanuel André

Subjects
Ecology, Evolution, SARS-CoV-2, data analysis, Data analysis, qPCR, lab automation, qc monitoring, high-throughput testing, Paleontology, Genetics and Molecular Biology, Qc monitoring, General Biochemistry, Genetics and Molecular Biology, QPCR, Behavior and Systematics, Space and Planetary Science, General Biochemistry, Medicine and Health Sciences, Lab automation, High-throughput testing, Ecology, Evolution, Behavior and Systematics
Abstract

We present our approach to rapidly establishing a standardized, multi-site, nation-wide COVID-19 screening program in Belgium. Under auspices of a federal government Task Force responsible for upscaling the country's testing capacity, we were able to set up a national testing initiative with readily available resources, putting in place a robust, validated, high-throughput, and decentralized qPCR molecular testing platform with embedded proficiency testing. We demonstrate how during an acute scarcity of equipment, kits, reagents, personnel, protective equipment, and sterile plastic supplies, we introduced an approach to rapidly build a reliable, validated, high-volume, high-confidence workflow based on heterogeneous instrumentation and diverse assays, assay components, and protocols. The workflow was set up with continuous quality control monitoring, tied together through a clinical-grade information management platform for automated data analysis, real-time result reporting across different participating sites, qc monitoring, and making result data available to the requesting physician and the patient. In this overview, we address challenges in optimizing high-throughput cross-laboratory workflows with minimal manual intervention through software, instrument and assay validation and standardization, and a process for harmonized result reporting and nation-level infection statistics monitoring across the disparate testing methodologies and workflows, necessitated by a rapid scale-up as a response to the pandemic. ispartof: LIFE-BASEL vol:12 issue:2 ispartof: location:Switzerland status: published

Published
2022
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2. Nationwide Harmonization Effort for Semi-Quantitative Reporting of SARS-CoV-2 PCR Test Results in Belgium

Author

Lize Cuypers, Jannes Bode, Kurt Beuselinck, Lies Laenen, Klaas Dewaele, Reile Janssen, Arnaud Capron, Yves Lafort, Henry Paridaens, Bertrand Bearzatto, Mathieu Cauchie, Aline Huwart, Jonathan Degosserie, Olivier Fagnart, Yarah Overmeire, Arlette Rouffiange, Ilse Vandecandelaere, Marine Deffontaine, Thomas Pilate, Nicolas Yin, Isabel Micalessi, Sandrine Roisin, Veronique Moons, Marijke Reynders, Sophia Steyaert, Coralie Henin, Elena Lazarova, Dagmar Obbels, François E. Dufrasne, Hendri Pirenne, Raf Schepers, Anaëlle Collin, Bruno Verhasselt, Laurent Gillet, Stijn Jonckheere, Philippe Van Lint, Bea Van den Poel, Yolien Van der Beken, Violeta Stojkovic, Maria-Grazia Garrino, Hannah Segers, Kevin Vos, Maaike Godefroid, Valerie Pede, Friedel Nollet, Vincent Claes, Inge Verschraegen, Pierre Bogaerts, Marjan Van Gysel, Judith Leurs, Veroniek Saegeman, Oriane Soetens, Merijn Vanhee, Gilberte Schiettekatte, Evelyne Huyghe, Steven Martens, Ann Lemmens, Heleen Nailis, Kim Laffineur, Deborah Steensels, Elke Vanlaere, Jérémie Gras, Gatien Roussel, Koenraad Gijbels, Michael Boudewijns, Catherine Sion, Wim Achtergael, Wim Maurissen, Luc Iliano, Marianne Chantrenne, Geert Vanheule, Reinoud Flies, Nicolas Hougardy, Mario Berth, Vanessa Verbeke, Robin Morent, Anne Vankeerberghen, Sébastien Bontems, Kaat Kehoe, Anneleen Schallier, Giang Ho, Kristof Bafort, Marijke Raymaekers, Yolande Pypen, Amelie Heinrichs, Wim Schuermans, Dominique Cuigniez, Salah Eddine Lali, Stefanie Drieghe, Dieter Ory, Marie Le Mercier, Kristel Van Laethem, Inge Thoelen, Sarah Vandamme, Iqbal Mansoor, Carl Vael, Maxime De Sloovere, Katrien Declerck, Elisabeth Dequeker, Stefanie Desmet, Piet Maes, Katrien Lagrou, Emmanuel André, Dufrasne, Francois/0000-0001-6288-7936, Yin, Nicolas/0000-0003-1706-6869, Van Laethem, Kristel/0000-0001-6036-2271, Micalessi, Isabel, Ory , Dieter, Dequeker, Elisabeth, CLAES , Vincent, Verhasselt, Bruno, Moons, Veronique, Soetens, Oriane, Godefroid, Maaike, Verschraegen, Inge, Pirenne, Hendri, Gillet, Laurent, Heinrichs, Amelie, Huwart, Aline, Vanhee, Merijn, Vandamme, Sarah, Maurissen, Wim, Laenen , Lies, Reynders , Marijke, Thoelen, Inge, Gras, Jeremie, Berth, Mario, Obbels, Dagmar, Vanheule, Geert, Maes, Piet, Bafort, Kristof, Flies, Reinoud, Janssen, Reile, van den Poel, Bea, Bontems, Sebastien, Schepers , Raf, Overmeire, Yarah, Boudewijns, Michael, van der Beken, Yolien, Cuypers , Lize, Bode, Jannes, Vos, Kevin, Paridaens, Henry, Achtergael, Wim, Saegeman, Veroniek, Rouffiange, Arlette, Dewaele, Klaas, Pypen, Yolande, Yin, Nicolas, Drieghe, Stefanie, Nailis, Heleen, Kehoe, Kaat, DE SMET, Stefanie, Verbeke, Vanessa, Vanlaere, Elke, Vael, Carl, Van Laethem, Kristel, Segers, Hannah, Pede, Valerie, Deffontaine, Marine, Martens , Steven, Lemmens, Ann, Vankeerberghen, Anne, Lagrou, Katrien, Iliano, Luc, Chantrenne, Marianne, Laffineur, Kim, Bearzatto, Bertrand, Vandecandelaere, Ilse, Sion, Catherine, Andre, Emmanuel, Cuigniez, Dominique, Pilate, Thomas, Capron, Arnaud, Nollet, Friedel, Roisin, Sandrine, Gijbels, Koenraad, Van Lint, Philippe, Bogaerts, Pierre, Lafort, Yves, Henin, Coralie, Van Gysel, Marjan, Huyghe, Evelyne, Lali, Salah Eddine, Roussel, Gatien, Garrino, Maria-Grazia, Schuermans, Wim, Steyaert, Sophia, Le Mercier, Marie, De Sloovere, Maxime, Leurs, Judith, STEENSELS, Deborah, Declerck, Katrien, Dufrasne, Francois E., Fagnart, Olivier, Ho, Giang, Lazarova, Elena, Schallier, Anneleen, Beuselinck, Kurt, Morent, Robin, Hougardy, Nicolas, Raymaekers, Marijke, Jonckheere, Stijn, Stojkovic, Violeta, Degosserie, Jonathan, Cauchie, Mathieu, Schiettekatte, Gilberte, Collin, Anaelle, Mansoor, Iqbal, Faculty of Economic and Social Sciences and Solvay Business School, Faculty of Medicine and Pharmacy, Supporting clinical sciences, Microbiology and Infection Control, Clinical Biology, Experimental Pharmacology, Department of Clinical Microbiology, Faculty of Psychology and Educational Sciences, UCL - (MGD) Laboratoire de biologie clinique, and UCL - SSS/IREC/MONT - Pôle Mont Godinne

Subjects
SARS-CoV-2, PCR, semi-quantitative reporting, RNA copies/mL, infectivity, COVID-19/diagnosis, COVID-19, Real-Time Polymerase Chain Reaction, mL, Infectious Diseases, Belgium, SARS-CoV-2/genetics, Virology, Humans, RNA copies, Human medicine, Belgium/epidemiology, Pandemics
Abstract

From early 2020, a high demand for SARS-CoV-2 tests was driven by several testing indications, including asymptomatic cases, resulting in the massive roll-out of PCR assays to combat the pandemic. Considering the dynamic of viral shedding during the course of infection, the demand to report cycle threshold (Ct) values rapidly emerged. As Ct values can be affected by a number of factors, we considered that harmonization of semi-quantitative PCR results across laboratories would avoid potential divergent interpretations, particularly in the absence of clinical or serological information. A proposal to harmonize reporting of test results was drafted by the National Reference Centre (NRC) UZ/KU Leuven, distinguishing four categories of positivity based on RNA copies/mL. Pre-quantified control material was shipped to 124 laboratories with instructions to setup a standard curve to define thresholds per assay. For each assay, the mean Ct value and corresponding standard deviation was calculated per target gene, for the three concentrations (10(7), 10(5) and 10(3) copies/mL) that determine the classification. The results of 17 assays are summarized. This harmonization effort allowed to ensure that all Belgian laboratories would report positive PCR results in the same semi-quantitative manner to clinicians and to the national database which feeds contact tracing interventions. UZ/KU Leuven: as National Reference Center for Respiratory Pathogens, is supported by Sciensano, which is gratefully acknowledged. We would like to acknowledge additional staff members of the participating laboratories that contributed to this study: Jean-Luc Gala, Benoit Kabamba, Elsa Wiam, Valentin Coste, Paul Blanpain, Jean Ruelle, Ari Serbetciyan, Nicolas Pinte, Ophélie Simon and the entire UCLouvain federal testing platform COVID-19 team (all affiliation 4), Aurore Demars (affiliation 7), Laura Vanden Daele (affiliation 9), Hanne Valgaeren (affiliation 22), Guillaume Bayon-Vicente (affiliation 23), Fabrice Bureau, Claire Gourzonès and Joey Schyns (affiliation 28), Stéphanie Evrard (affiliation 42), Clara Ceyssens (affiliation 58), Jorn Hellemans (affiliation 77), Bram Slechten (affiliation 86) and the entire team of the laboratory of microbiology of UZA (affiliation 89) and of the UZA Federal testing platform COVID-19 (affiliation 85) for their boundless dedication.

Published
2022

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