20.500.12556/DiRROS-22722 From crisis to routine – standardization of SARS-CoV-2 genome detection by enhanced EQA schemes in a scientific pandemic network From crisis to routine In the beginning of 2020, the outbreak of the COVID-19 pandemic led to a crisis in which diagnostic methods for the genome detection of SARS-CoV-2 were urgently needed. Based on the very early publication of the basic principles for a diagnostic test for the genome detection of SARS-CoV-2, the first noncommercial laboratory-developed tests (LDTs) and commercial tests were introduced. As there was considerable uncertainty about the reliability and performance of different tests and different laboratories, INSTAND established external quality assessment (EQA) schemes for the detection of SARS-CoV-2 starting in April 2020. In close partnership in a scientific network, the EQA schemes were enhanced, especially the April, June and November 2020 terms. The enhancement included: (i) immediate provision of suitable virus including variants of concern at the beginning of the pandemic outbreak, (ii) short frequency of EQA schemes, (iii) concentration dependency of the testing and sensitivity check, achieved by using SARS-CoV-2-positive samples from a 10-fold dilution series of the same starting material, (iv) specificity check of the testing, achieved by using SARS-CoV-2-negative samples containing human coronaviruses or MERS CoV, (v) revealed samples for orientation on test performance during an ongoing or at the start of an EQA scheme using a pre-quantified SARS-CoV-2-positive EQA sample with a low viral RNA load of only 1 570 copies/mL assigned by digital PCR (dPCR) in June 2020 and (vi) quantified reference materials based on the experiences of the first two EQA schemes with dPCR-assigned values in copies/mL beginning in November 2020 for self-evaluation of the applied test system. This manuscript summarizes the results of a total of 13 EQA schemes for the detection of SARS-CoV-2 between April 2020 and June 2023 in which a total of 1 413 laboratories from 49 countries participated. The qualitative results for the detection of SARS-CoV-2-positive samples were between 95.8 % and 99.7 % correct positive, excluding extremely low concentration samples. For all SARS-CoV-2-negative EQA samples, the qualitative success rates ranged from 95.1 % to 99.4 % correct negative results. The widely varying values for the cycle threshold (Ct)/crossing point (Cq) reported for the different target genes and test systems were striking. A few laboratories reported quantitative results in copies/mL for several VOCs with an acceptable rate of over 93 % correct positive results in the majority of cases. The description of the enhanced EQA schemes for SARS-CoV-2 detection in terms of timing and scope can serve as a blueprint for the rapid development of a quality assessment of diagnostics for an emerging pathogen. COVID-19 pandemic SARS-CoV-2 virus genome detection tests reference materials external quality assessment laboratory medicine epidemiology pandemija COVID-19 SARS-CoV-2 testi za odkrivanje genoma virusa referenčni materiali zunanja ocena kakovosti laboratorijska medicina epidemiologija true false true Angleški jezik Slovenski jezik Neznano 2025-06-18 14:02:37 2025-06-18 14:02:38 2025-10-24 03:52:03 0000-00-00 00:00:00 2025 0 0 Soavtorica iz Slovenije: Mojca Milavec; str. 1-24 [art. no.] ǂ151656 Vol. 319 Jun. 2025 0000-00-00 Zaloznikova Objavljeno NiDoloceno 0000-00-00 0000-00-00 2025-06-01 578 1438-4221 10.1016/j.ijmm.2025.151656 239799299 https://doi.org/10.1016/j.ijmm.2025.151656 1 60bb1ee6-4c2b-11f0-bf0a-001a4af901a5 https://dirros.openscience.si/Dokument.php?lang=slv&id=32962 RAZ_Kammel_Martin_2025.pdf RAZ_Kammel_Martin_2025.pdf 1 35244153C26B6E70E6037E6D16E6DEE7 d894f9ecf9aee61244fe5fe8461a4987d879115c1617e54f74d65240da157f47 95768960-4c2b-11f0-bf0a-001a4af901a5 https://dirros.openscience.si/Dokument.php?lang=slv&id=32963 ScienceDirect_files_20Jun2025_11-43-43.315.zip ScienceDirect_files_20Jun2025_11-43-43.315.zip Dopolnilne informacije Supplementary material 1 B3E3EBDE61ED2AEBBDACA7AC724633B4 10fef4e9e41660c95f75bf419410001ced25718b8c8c4f3d1a48e7d5161627b6 18e66b8d-4dbd-11f0-bf0a-001a4af901a5 https://dirros.openscience.si/Dokument.php?lang=slv&id=33034 Nacionalni inštitut za biologijo 0 0 0