Multiple assays in a real-time RT-PCR SARS-CoV-2 panel can mitigate the risk of loss of sensitivity by new genomic variants during the COVID-19 outbreak
Multiple assays in a real-time RT-PCR SARS-CoV-2 panel can mitigate the risk of loss of sensitivity by new genomic variants during the COVID-19 outbreak
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DOI：
10.1016/j.ijid.2020.06.027
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发表时间：
2020-08-01
影响因子：
8.4
通讯作者：
Pareja, Josep
中科院分区：
文献类型：
--
作者：
Penarrubia, Luis;Ruiz, Maria;Pareja, Josep
目的：在这项研究中，针对病毒的累积遗传变异性评估了五个SARS-CoV-2 PCR检测面板，以评估对单个检测灵敏度的影响。设计或方法：截至2020年第21周，本研究使用了GISAID和GenBank数据库中的完整SARS-CoV-2基因组。SARS-CoV-2引物序列来自公共可用的面板（WHO，CDC，NMDC，和香港大学）和QIAstat-Dx的比对，并注释了影响任何寡核苷酸退火的累积遗传变异。8，773（25.94%）个基因组的变异被认为是高风险，而另外2，854（8.43%）个基因组呈现低频率的单突变，预计不会对敏感性产生影响。在QIAstat-Dx SARS-CoV-2 Panel的情况下，99.11%的基因组匹配，100%覆盖所有寡核苷酸，并且在体外测试了关键变异，证实灵敏度没有损失。这项分析强调了针对SARS-CoV病毒基因组中一个以上区域的重要性，2检测，以减轻在这次SARS-CoV-2爆发期间由于未知突变率而丧失灵敏度的风险。(C)2020作者（S）由爱思唯尔有限公司代表国际传染病学会出版。这是一个在CC BY-NC-ND许可证下的开放获取文章（http：//creativecommons.org/licenses/by-ncnd/4.0/）。
Objectives: In this study, five SARS-CoV-2 PCR assay panels were evaluated against the accumulated genetic variability of the virus to assess the effect on sensitivity of the individual assays.Design or methods: As of week 21, 2020, the complete set of available SARS-CoV-2 genomes from GISAID and GenBank databases were used in this study. SARS-CoV-2 primer sequences from publicly available panels (WHO, CDC, NMDC, and HKU) and QIAstat-Dx were included in the alignment, and accumulated genetic variability affecting any oligonucleotide annealing was annotated.Results: A total of 11,627 (34.38%) genomes included single mutations affecting annealing of any PCR assay. Variations in 8,773 (25.94%) genomes were considered as high risk, whereas additional 2,854 (8.43%) genomes presented low frequent single mutations and were predicted to yield no impact on sensitivity. In case of the QIAstat-Dx SARS-CoV-2 Panel, 99.11% of the genomes matched with a 100% coverage all oligonucleotides, and critical variations were tested in vitro corroborating no loss of sensitivity.Conclusions: This analysis stresses the importance of targeting more than one region in the viral genome for SARS-CoV-2 detection to mitigate the risk of loss of sensitivity due to the unknown mutation rate during this SARS-CoV-2 outbreak. (C) 2020 The Author(s). Published by Elsevier Ltd on behalf of International Society for Infectious Diseases. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-ncnd/4.0/).