From Crisis to Routine - Standardization of SARS-CoV-2 Genome Detection by Enhanced EQA Schemes in a Scientific Pandemic Network

Published

May 24, 2025

Author(s)

Martin Kammel, Hans-Peter Grunert, Anika Zimmerman, Annemarie Martin, Vanessa Lindig, Samuel Samuleit, Ulf Duehring, Mechthild Adams-Bagusche, Dirk Sander, Hannah Zeichhardt, Christian Drosten, Victor Corman, Daniela Niemeyer, Sandra Ciesek, Holger Rabenau, Martin Obermeier, Robert Ehret, Rolf Kaiser, Jim Huggett, Denise O'Sullivan, Peter Vallone, Megan Cleveland, Samreen Falak, Andreas Kummrow, Esmeralda Valiente, Rainer Macdonald, Mojca Milavec, Sabine Goseberg, Silke Kappler, Natalie Weiss, Laura Vierbaum, Patricia Kaiser, Ingo Schellenberg, Heinz Zeichhardt

Abstract

The outbreak of the COVID-19 pandemic led to a crisis situation in which diagnostic methods for the genome detection of the emerging SARS-CoV-2 were urgently needed from the beginning of 2020 for patient diagnostics, detection of infection chains and epidemiological surveillance. Based on the very early publication of the basic principles for a diagnostic test for the detection of SARS-CoV-2, the first in-house tests (laboratory-developed tests = LDTs) and commercial tests were used in the laboratories, but with the major limitation that there was initially great uncertainty about the reliability of the handling of the tests in the laboratories and the performance of the individual tests. Under these conditions, INSTAND e.V. established EQA schemes for the genome detection of SARS-CoV-2 in April 2020, which were based on the experience of already implemented EQA schemes for other viruses. This study summarizes the results of a total of 13 EQA schemes for the detection of SARS-CoV-2, which were conducted between April 2020 and June 2023 and in which a total of 1 413 laboratories from 49 countries participated. In total 82 702 qualitative and 2 719 quantitative results of the all 13 EQA schemes were taken into account for the evaluation. This assessment focuses on analyzing the reported qualitative results in terms of the proficiency of the laboratories and the performance of the tests used. The success rates for both the SARS-CoV-2-positive samples from a 10-fold dilution series and the SARS-CoV-2-negative samples were satisfactory at 93.0% to 98.9% correct results in the first EQA scheme already in April 2020. This showed that, regardless of the virus variants tested, samples with a SARS-CoV-2 viral load of more than 100 000 copies/ml consistently had success rates of greater than 95% correct positive results. Over the entire period of the 13 EQA schemes, it was noticeable that the ct/cq values reported together with the qualitative results showed very large variations of 10 cycles or more, even when considering the individual ct/cq values reported by a single group of participants performing analyses with a single test system of one manufacturer for a specific target region. In order to provide the laboratories with an orientation to interpret the ct/cq values of a sample obtained with the test used with regard to its virus RNA load, revealed samples - some of which were quantitatively characterized with digital PCR (dPCR) - were used from the beginning. Of particular relevance was the introduction of independently applied reference materials to which quantitative SARS-CoV-2 RNA loads were assigned by dPCR in parallel with the EQA schemes. The introduction of revealed samples already during the very early EQA schemes and the provision of independent reference materials, each assigned with a quantitative value in copies/ml, were the main elements that expanded the EQA schemes and turned them into "enhanced EQA schemes". This enabled laboratories to monitor their tests for reliable routine diagnostics and, under certain conditions, even supported clinical decisions for patient management. Quantitative results accounted for less than 5% of the total number of results reported. While some of the reported quantitative results for the first 2 EQA schemes had unsatisfactory success rates (some of them below 85%), the success rates subsequently improved and were generally more than 90% correct quantitative results for the different SARS-CoV-2 variants used in different concentrations, which coincides with the introduction of the independent reference materials. This review shows that the described "enhanced EQA schemes" not only allowed monitoring the proficiency of the laboratories and the performance of the test systems used, but also led to an overall improvement in diagnostics even very early during the COVID-19 pandemic.

Citation

International Journal of Medical Microbiology

Pub Type

Journals

Download Paper

https://doi.org/10.1016/j.ijmm.2025.151656

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Keywords

virus, SARS-Cov-2, COVID-19

Citation

Kammel, M. , Grunert, H. , Zimmerman, A. , Martin, A. , Lindig, V. , Samuleit, S. , Duehring, U. , Adams-Bagusche, M. , Sander, D. , Zeichhardt, H. , Drosten, C. , Corman, V. , Niemeyer, D. , Ciesek, S. , Rabenau, H. , Obermeier, M. , Ehret, R. , Kaiser, R. , Huggett, J. , O'Sullivan, D. , Vallone, P. , Cleveland, M. , Falak, S. , Kummrow, A. , Valiente, E. , Macdonald, R. , Milavec, M. , Goseberg, S. , Kappler, S. , Weiss, N. , Vierbaum, L. , Kaiser, P. , Schellenberg, I. and Zeichhardt, H. (2025), From Crisis to Routine - Standardization of SARS-CoV-2 Genome Detection by Enhanced EQA Schemes in a Scientific Pandemic Network, International Journal of Medical Microbiology, [online], https://doi.org/10.1016/j.ijmm.2025.151656, https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=957919 (Accessed July 26, 2025)