A Recurrent Mutation at Position 26340 of SARS-CoV-2 Is Associated with Failure of the E Gene Quantitative Reverse Transcription-PCR Utilized in a Commercial Dual-Target Diagnostic Assay.
A Recurrent Mutation at Position 26340 of SARS-CoV-2 Is Associated with Failure of the E Gene Quantitative Reverse Transcription-PCR Utilized in a Commercial Dual-Target Diagnostic Assay.
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DOI：
10.1128/jcm.01598-20
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发表时间：
2020-09-22
影响因子：
9.4
通讯作者：
Durkin K
中科院分区：
文献类型：
--
作者：
Artesi M;Bontems S;Göbbels P;Franckh M;Maes P;Boreux R;Meex C;Melin P;Hayette MP;Bours V;Durkin K
控制正在进行的严重急性呼吸系统综合征冠状病毒2（SARS-CoV-2）大流行需要准确的实验室检测，以确定感染者，同时也清除必要的工作人员继续工作。目前，已经开发了许多定量实时PCR（qRT-PCR）检测方法来鉴定SARS-CoV-2，靶向病毒基因组中的多个位置。虽然SARS-CoV-2的突变率是中等的，但考虑到大量的传播链，监测可能损害这些检测的变异的循环病毒是谨慎的。控制正在进行的严重急性呼吸系统综合征冠状病毒2（SARS-CoV-2）大流行需要准确的实验室检测，以确定感染者，同时也清除必要的工作人员继续工作。目前，已经开发了许多定量实时PCR（qRT-PCR）检测方法来鉴定SARS-CoV-2，靶向病毒基因组中的多个位置。虽然SARS-CoV-2的突变率是中等的，但考虑到大量的传播链，监测可能损害这些检测的变异的循环病毒是谨慎的。在这里，我们报告了在SARS-CoV-2基因组的26340位置处的C到U转换的鉴定，该转换与8名患者中cobas SARS-CoV-2 E基因qRT-PCR的失败有关。由于cobas SARS-CoV-2检测针对基因组中的两个位置，因此携带该变体的个体仍被称为SARS-CoV-2阳性。SARS-CoV-2的全基因组测序显示，所有病毒都携带密切相关的病毒。对保存在GISAID上的病毒基因组的检查表明，这种突变至少独立出现了四次。这项工作强调了监测SARS-CoV-2出现单核苷酸多态性的必要性，这些多态性可能会对诊断中使用的RT-PCR产生不利影响。此外，它认为SARS-CoV-2中的两个区域应该被靶向以避免假阴性。
Control of the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic requires accurate laboratory testing to identify infected individuals while also clearing essential staff to continue to work. At the current time, a number of quantitative real-time PCR (qRT-PCR) assays have been developed to identify SARS-CoV-2, targeting multiple positions in the viral genome. While the mutation rate of SARS-CoV-2 is moderate, given the large number of transmission chains, it is prudent to monitor circulating viruses for variants that might compromise these assays. Control of the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic requires accurate laboratory testing to identify infected individuals while also clearing essential staff to continue to work. At the current time, a number of quantitative real-time PCR (qRT-PCR) assays have been developed to identify SARS-CoV-2, targeting multiple positions in the viral genome. While the mutation rate of SARS-CoV-2 is moderate, given the large number of transmission chains, it is prudent to monitor circulating viruses for variants that might compromise these assays. Here, we report the identification of a C-to-U transition at position 26340 of the SARS-CoV-2 genome that is associated with failure of the cobas SARS-CoV-2 E gene qRT-PCR in eight patients. As the cobas SARS-CoV-2 assay targets two positions in the genome, the individuals carrying this variant were still called SARS-CoV-2 positive. Whole-genome sequencing of SARS-CoV-2 showed all to carry closely related viruses. Examination of viral genomes deposited on GISAID showed this mutation has arisen independently at least four times. This work highlights the necessity of monitoring SARS-CoV-2 for the emergence of single-nucleotide polymorphisms that might adversely affect RT-PCRs used in diagnostics. Additionally, it argues that two regions in SARS-CoV-2 should be targeted to avoid false negatives.