与牛津纳米孔技术的下一代测序相比，多重实时 PCR 技术在鉴定 SARS-CoV-2 关注变异株方面的比较。
Comparison of a Multiplex Real-Time PCR Technique with Oxford Nanopore Technologies Next-Generation Sequencing for Identification of SARS-CoV-2 Variants of Concern.
机构信息
COVID-19 National Reference Laboratory, Pasteur Institute of Iran, Tehran, Iran,
COVID-19 National Reference Laboratory, Pasteur Institute of Iran, Tehran, Iran.
出版信息
Intervirology. 2023;66(1):136-141. doi: 10.1159/000534067. Epub 2023 Oct 9.
INTRODUCTION
The rapid emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and their potential to endangering the global health has increased the demand for a fast-tracking method in comparison to the next-generation sequencing (NGS) as a gold standard assay, particularly in developing countries. This study was designed to evaluate the performance of a commercial multiplex real-time PCR technique (GA SARS-CoV-2 OneStep RT-PCR Kit, Iran) for identification of SARS-CoV-2 variants of concern (VOCs) compared to the Oxford Nanopore NGS assay.
METHODS
A total of 238 SARS-CoV-2-positive respiratory samples from different waves of COVID-19 in Iran were randomly selected in this study. To determine the SARS-CoV-2 VOC, the samples were analyzed via the commercial triple target assay, GA SARS-CoV-2 OneStep RT-PCR Kit, and NGS as well.
RESULTS
The results revealed good concordance between GA SARS-CoV-2 OneStep RT-PCR Kit and NGS for identification of SARS-CoV-2 VOCs. GA SARS-CoV-2 OneStep RT-PCR Kit identified Wuhan, Alpha, and Delta variants with 100% relative sensitivity and specificity. Regarding Omicron subvariants of BA.1, BA.2, and BA.4/5, the relative sensitivity of 100%, 100%, and 81.5% and the relative specificity of 95.3%, 93.5%, and 100% were observed.
CONCLUSION
Overall, GA SARS-CoV-2 OneStep RT-PCR Kit can be used as a rapid and cost-effective alternative to NGS for identification of SARS-CoV-2 VOCs.
简介
严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 变体的迅速出现及其对全球健康的潜在威胁增加了对快速跟踪方法的需求，与下一代测序 (NGS) 作为金标准检测相比，尤其是在发展中国家。本研究旨在评估一种商业多重实时 PCR 技术 (GA SARS-CoV-2 OneStep RT-PCR Kit，伊朗) 与牛津纳米孔 NGS 检测相比，用于鉴定 SARS-CoV-2 关注变体 (VOCs) 的性能。
方法
本研究随机选择了来自伊朗不同 COVID-19 浪潮的 238 份 SARS-CoV-2 阳性呼吸道样本。为了确定 SARS-CoV-2 VOC，通过商业三靶标检测、GA SARS-CoV-2 OneStep RT-PCR Kit 和 NGS 对样本进行分析。
结果
GA SARS-CoV-2 OneStep RT-PCR Kit 与 NGS 对 SARS-CoV-2 VOC 的鉴定具有良好的一致性。GA SARS-CoV-2 OneStep RT-PCR Kit 对武汉、阿尔法和德尔塔变体的鉴定具有 100%的相对灵敏度和特异性。关于奥密克戎 BA.1、BA.2 和 BA.4/5 的亚变体，相对灵敏度为 100%、100%和 81.5%，相对特异性为 95.3%、93.5%和 100%。
结论
总体而言，GA SARS-CoV-2 OneStep RT-PCR Kit 可作为 NGS 的快速、经济有效的替代方法，用于鉴定 SARS-CoV-2 VOCs。
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