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.

中文翻译：

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SARS-CoV-2 26340 位点的反复突变与商业双靶点诊断检测中使用的 E 基因定量逆转录 PCR 的失败有关。

控制正在进行的严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 大流行需要准确的实验室检测来识别感染者，同时确保必要的工作人员继续工作。目前，已经开发出多种定量实时 PCR (qRT-PCR) 检测方法来识别 SARS-CoV-2，针对病毒基因组中的多个位置。虽然 SARS-CoV-2 的突变率适中，但鉴于传播链数量众多，因此应谨慎监测循环病毒是否存在可能损害这些检测的变异体。在这里，我们报告了在 SARS-CoV-2 基因组第 26340 位处鉴定出 C 到 U 的转变，该转变与 8 名患者的 cobas SARS-CoV-2 E 基因 qRT-PCR 失败相关。由于 cobas SARS-CoV-2 检测针对的是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均携带密切相关的病毒。对存放在 GISAID 上的病毒基因组的检查表明，这种突变已经独立出现了至少四次。这项工作强调了监测 SARS-CoV-2 是否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，它还认为应该针对 SARS-CoV-2 中的两个区域以避免假阴性。