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.
Highlights
Mutation-specific PCR assays for the detection of specific mutations in known variants of SARS-CoV-2 virus were introduced as a fast, easy to implement and high-capacity method to help clinicians and authorities perform infection control measures [1]
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)
The results reported in a recent round of an external quality assessment (EQA) scheme for SARS-CoV-2 mutation-specific PCR were retrospectively analyzed
Summary
Mutation-specific PCR assays for the detection of specific mutations in known variants of SARS-CoV-2 virus were introduced as a fast, easy to implement and high-capacity method to help clinicians and authorities perform infection control measures [1]. Independent evaluations provide important information about the properties, performance and limitations of such assays and are essential for good laboratory operation by ensuring reliable results. Several such reports on assay evaluation and optimized panels for mutation-specific PCR have been published [2,3,4,5,6,7]; data are lacking on the performance of SARS-CoV-2 mutation and variant detection assays in routine use. Schemes for SARS-CoV-2 PCR have repeatedly proven their potential in this regard [8,9,10,11,12,13,14]
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