Inadequate design of mutation detection panels prevents interpretation of variants of concern: results of an external quality assessment for SARS-CoV-2 variant detection
Author:
Buchta Christoph1, Camp Jeremy V.2, Jovanovic Jovana1, Radler Ulla1, Benka Bernhard3, Puchhammer-Stöckl Elisabeth2, Müller Mathias M.1, Griesmacher Andrea1, Aberle Stephan W.2, Görzer Irene2
Affiliation:
1. Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests (ÖQUASTA) , Vienna , Austria 2. Center for Virology , Medical University of Vienna , Vienna , Austria 3. Division Public Health , AGES – Austrian Agency for Health and Food Safety , Vienna , Austria
Abstract
Abstract
Objectives
Mutation-specific PCR assays have quickly found their way into laboratory diagnostics due to their capacity to be a fast, easy to implement and high-throughput method for the detection of known SARS-CoV-2 variants of concern (VoCs). However, little is known about the performance of such assays in routine laboratory analysis.
Methods
The results reported in a recent round of an external quality assessment (EQA) scheme for SARS-CoV-2 mutation-specific PCR were retrospectively analyzed. For the determination of individual variant-specific sequences as well as for the interpretation results for certain virus variants, correct, incorrect, and unreported results were evaluated, and their possible causes were investigated.
Results
A total of 34 laboratories participated in this study. For five samples containing the VoC Alpha + E484K, Beta, Gamma, Delta, or B.1.1.318 (as a variant of interest), 848 results for SARS-2-CoV mutation detection were reported, 824 (97.2%, range per sample 88–100%) of which were correct. Melting curve assays gave 99% correct results, real-time RT-qPCR 94%, microarray-based assays 100%, and MALDI-TOF MS 96%. A total of 122/167 (73%) reported results for SARS-CoV-2 variant determination were correct. Of the 45 inconclusive or incorrect results, 33 (73%) were due to inadequate selection of targets that did not allow identification of contemporary VoC, 11 (24%) were due to incorrect results, and one (3%) was due to correct results of mutation-specific PCR.
Conclusions
Careful and up-to-date selection of the targets used in mutation-specific PCR is essential for successful detection of current SARS-CoV-2 variants.
Publisher
Walter de Gruyter GmbH
Subject
Biochemistry (medical),Clinical Biochemistry,General Medicine
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