External quality assessment of molecular detection and variant typing of SARS-CoV-2 in European expert laboratories in 2023

The COVID-19 pandemic highlighted the importance of laboratory preparedness. Regular monitoring of diagnostic tools via external quality assessments (EQAs) is key to maintaining robust public health response service. We hereby conducted a third SARS-CoV-2 EQA assessing the diagnostic capabilities of European expert public health laboratories. A 10 samples panel containing Alpha (used in previous EQA), BA.4, BA.5, and BQ.1.18 variants along with human seasonal coronaviruses and negative controls was produced and validated. Participants were invited by the European Centre for Disease Prevention and Control (ECDC) and asked to submit results and assay details via electronic forms. Thirty-eight laboratories from 31 European countries participated. Most (<i>n</i> = 32, 84%) identified all panel samples correctly and used in-house (11, 29%), commercial assays (22, 58%), or both (5, 13%). Compared to previous EQAs, correct detection of the SARS-CoV-2 samples in the panels increased: 8 (12%) in 2020, 45 (75%) in 2021, and 34 (90%) laboratories in 2023, respectively. The number of participants decreased to an average of one laboratory per country (range 1-3) compared to two (1-7) laboratories in both previous EQAs. The usage of commercial assays gradually increased in contrast to the usage of in-house or both approaches. The capacity for SARS-CoV-2 molecular diagnostics has markedly improved in Europe as evidenced by three consecutive EQAs carried out by expert public health laboratories. Routine monitoring of diagnostic and surveillance assays via EQAs remains key to maintaining rapid public health laboratory response systems.IMPORTANCEExternal quality assessments (EQAs) are crucial to ensure the reliability and consistency of diagnostic laboratories. They provide an objective framework for evaluating the performance of testing systems, enabling laboratories to identify weaknesses and implement improvements promptly. In the context of SARS-CoV-2, EQAs have become even more critical due to the high demand for accurate molecular diagnostics and the emergence of new variants. Accurate detection and typing of variants are especially essential for monitoring viral evolution. EQAs help standardize methodologies, ensuring that results across laboratories remain comparable and trustworthy. Moreover, they play a pivotal role in minimizing errors such as false positives or negatives. In this rapidly evolving landscape, regular EQAs are indispensable for maintaining high-quality standards in molecular diagnostics and variant surveillance. We demonstrate here that regular EQAs improve the molecular detection of SARS-CoV-2 in European laboratories.