First results of a national external quality assessment scheme for the detection of SARS-CoV-2 genome sequences

•Implementation of SARS-CoV-2 genome testing by numerous laboratories in Austria.•Broad range of combinations of nucleic acid extraction and RT-PCR methods.•Variable analytical performance of different protocols.•Good performance of some analytical setups.•Potential for optimisation of pre-RT-PCR di...

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Bibliographic Details
Published in:	Journal of clinical virology Vol. 129; p. 104537
Main Authors:	Görzer, I., Buchta, Ch, Chiba, P., Benka, B., Camp, J.V., Holzmann, H., Puchhammer-Stöckl, E., Aberle, S.W.
Format:	Journal Article
Language:	English
Published:	Netherlands Elsevier B.V 01-08-2020 The Authors. Published by Elsevier B.V
Subjects:	Austria Betacoronavirus - isolation & purification Clinical Laboratory Techniques - methods Clinical Laboratory Techniques - standards Coronavirus Infections - diagnosis COVID-19 COVID-19 pandemic COVID-19 Testing COVID-19 Vaccines Diagnostic Errors - statistics & numerical data Evaluation External quality assessment Humans Laboratory Proficiency Testing - organization & administration Molecular Diagnostic Techniques - methods Molecular Diagnostic Techniques - standards Molecular test Pandemics Pneumonia, Viral - diagnosis Real-Time Polymerase Chain Reaction - methods Real-Time Polymerase Chain Reaction - standards SARS-CoV-2 Sensitivity and Specificity Standardisation Austria Standardisation COVID-19 pandemic Evaluation External quality assessment SARS-CoV-2 Molecular test
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Summary:	•Implementation of SARS-CoV-2 genome testing by numerous laboratories in Austria.•Broad range of combinations of nucleic acid extraction and RT-PCR methods.•Variable analytical performance of different protocols.•Good performance of some analytical setups.•Potential for optimisation of pre-RT-PCR dilution steps. Broad and decentralised testing of SARS-CoV-2 RNA genomes is a WHO-recommended strategy to contain the SARS-CoV-2 pandemic by identifying infected cases in order to minimize onward transmission. With the need to increase the test capacities in Austria, nation-wide numerous laboratories rapidly implemented assays for molecular detection of SARS-CoV-2 based on real-time RT-PCR assays. The objective of this study was to monitor reliability of the laboratory results for SARS-CoV-2 RNA detection through an external quality assessment (EQA) scheme. For this, the Center for Virology, Medical University of Vienna was tasked by the Federal Ministry of Social Affairs, Health, Care and Consumer Protection to perform the first Austrian EQA on SARS-CoV-2 which was organised in cooperation with the Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests (ÖQUASTA). Data were analysed on the basis of qualitative outcome of testing in relation to the nucleic acid (NA) extraction and detection methods used. A total of 52 laboratories participated, contributing results from 67 test panels comprising 42 distinct combinations of NA extraction and PCR reagents. By testing 3 positive (CT values: S1, 28.4; S2, 33.6; S3, 38.5) and 1 negative sample, no false-positive results were obtained by any of the laboratories. Otherwise, 40/67 tests (60 %) detected all positive samples correctly as positive, but 25/67 tests (37 %) did not detect the weakest positive sample (S3), and 3 % reported S2 and S3 as false-negative. Improvement in test sensitivity by focusing on NA extraction and/or PCR-based detection is recommended.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1386-6532 1873-5967
DOI:	10.1016/j.jcv.2020.104537