Inadequate design of mutation detection panels prevents interpretation of variants of concern: results of an external quality assessment for SARS-CoV-2 variant detection
Inadequate design of mutation detection panels prevents interpretation of variants of concern: results of an external quality assessment for SARS-CoV-2 variant detection
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DOI：
10.1515/cclm-2021-0889
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发表时间：
2021-11-05
影响因子：
6.8
通讯作者：
Goerzer, Irene
中科院分区：
文献类型：
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作者：
Buchta, Christoph;Camp, Jeremy, V;Goerzer, Irene
突变特异性PCR检测由于能够快速、易于实施和高通量地检测已知的SARS-CoV-2关注变体（VoCs），已迅速进入实验室诊断领域。然而，在常规的实验室分析中，人们对这种检测方法的性能知之甚少。方法回顾性分析最近一轮SARS-CoV-2突变特异性PCR外部质量评价（EQA）方案报告的结果。为了确定单个变异特异性序列以及某些病毒变异的解释结果，对正确、不正确和未报告的结果进行了评估，并调查了其可能的原因。结果共有34家实验室参与本研究。对于含有VoC Alpha + E484K、Beta、Gamma、Delta或B.1.1.318（作为感兴趣的变体）的5个样本，报告了848个SARS-2-CoV突变检测结果，其中824个（97.2%，每个样本范围88-100%）是正确的。熔融曲线测定的准确度为99%，实时RT-qPCR为94%，基于微阵列的测定为100%，MALDI-TOF MS为96%。167例报告的SARS-CoV-2变异鉴定结果中，共有122例（73%）是正确的。在45个不确定或不正确的结果中，33个（73%）是由于目标选择不充分，无法识别当代VoC， 11个（24%）是由于不正确的结果，1个（3%）是由于突变特异性PCR的正确结果。结论：在突变特异性PCR中仔细选择最新的靶标对于成功检测当前的SARS-CoV-2变体至关重要。
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.