Introduction

Following the emergence of SARS-CoV-2 variants of concern (VOCs) worldwide, it is important to monitor local epidemiology to better understand the occurrence of clusters, reinfections, or infection after vaccination. Detecting mutations by specific RT-qPCR is a rapid and affordable alternative to sequencing. However, care must be taken to ensure that the techniques used are up-to-date and adapted to the variants circulating in the studied population.

Material and methods

All samples tested positive for SARS-CoV-2 were screened for detection of mutations of the spike protein using the Novaplex™ SARS-CoV-2 Variants I Assay from week 11 of 2021. Target sought were deletion H69/V70 and mutations N501Y and E484 K. From week 18 we used in addition the new Novaplex™ SARS-CoV-2 Variants II Assay for samples with no targets found with the Variants I assay or with the mutation E484 K alone, in order to screen the mutations L452R, K417 N/T and W152C.

Results

Between weeks 11 and 25, 2239 positive samples out of 54,317 were tested with the Variants I Assay. Between weeks 18 and 25, 94 samples met the criteria for being tested with the Variants II Assay. Of these, 47 had the L452R mutation without the W152C mutation, typical in the B.1.617 variant. At week 25, this profile was found in 45.5 % of the samples and was the most frequent.

Conclusion

According to our observations, variant B.1.617 has become predominant in our institution and most probably in our region. In the absence of the use of the Variants II Assay, they would have been considered wild.

中文翻译：

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使用 RT-qPCR 筛查 SARS-CoV-2 相关变体的挑战：一个变体可以隐藏另一个

介绍

随着 SARS-CoV-2 关注变体 (VOC) 在全球范围内的出现，监测当地流行病学以更好地了解集群、再感染或接种后感染的发生情况非常重要。通过特异性 RT-qPCR 检测突变是一种快速且经济实惠的测序替代方法。然而，必须注意确保所使用的技术是最新的并适应在研究人群中传播的变体。

材料与方法

从 2021 年第 11 周开始，使用 Novaplex™ SARS-CoV-2 Variants I Assay 筛选所有 SARS-CoV-2 检测呈阳性的样本以检测刺突蛋白的突变。寻找的目标是缺失 H69/V70 以及突变 N501Y 和 E484 K. 从第 18 周开始，我们还使用了新的 Novaplex™ SARS-CoV-2 Variants II Assay，用于在 Variants I 测定中未发现目标或仅具有突变 E484 K 的样本，以筛选突变 L452R、K417 N /T 和 W152C。

结果

在第 11 周和第 25 周之间，对 54,317 个阳性样本中的 2239 个样本进行了 Variants I Assay 检测。在第 18 周和第 25 周之间，94 个样本符合使用 Variants II Assay 进行测试的标准。其中，47 个具有 L452R 突变而没有 W152C 突变，这在 B.1.617 变体中很典型。在第 25 周，此配置文件出现在 45.5% 的样本中并且出现频率最高。

结论

根据我们的观察，变体 B.1.617 已在我们的机构中​​占据主导地位，而且很可能在我们的地区。如果不使用 Variants II Assay，它们将被认为是野生的。