De Pace Vanessa, Bruzzone Bianca, Orsi Andrea, Ricucci Valentina, Domnich Alexander, Guarona Giulia, Randazzo Nadia, Stefanelli Federica, Battolla Enrico, Dusi Pier Andrea, Lillo Flavia, Icardi Giancarlo
Hygiene Unit, Ospedale Policlinico San Martino-IRCCS, 16132 Genoa, Italy.
Department of Health Sciences (DISSAL), University of Genoa, 16132 Genoa, Italy.
Microorganisms. 2022 Jan 27;10(2):306. doi: 10.3390/microorganisms10020306.
The rapid and presumptive detection of SARS-CoV-2 variants may be performed using multiplex RT-PCR assays. The aim of this study was to evaluate the diagnostic performance of five qualitative RT-PCR tests as compared with next-generation sequencing (NGS). We retrospectively examined a multi-variant panel ( = 72) of SARS-CoV-2-positive nasopharyngeal swabs categorized as variants of concern (Alpha, Beta, Gamma and Delta), variants under monitoring (Iota and Kappa) and wild-type strains circulating in Liguria (Italy) from January to August 2021. First, NGS libraries of study samples were prepared and mapped to the reference genome. Then, specimens were screened for the detection of L452R, W152C, K417T, K417N, E484Q, E484K and N501Y mutations using the SARS-CoV-2 Variants II Assay Allplex, UltraGene Assay SARS-CoV-2 452R & 484K & 484Q Mutations V1, COVID-19 Ultra Variant Catcher, SARS-CoV-2 Extended ELITe MGB and Simplexa SARS-CoV-2 Variants Direct. The overall accuracy of these assays ranged from 96.9% to 100%. Specificity and sensitivity were 100% and 96-100%, respectively. We highly recommend the use of these assays as second-level tests in the routine workflow of SARS-CoV-2 laboratory diagnostics, as they are accurate, user friendly, low cost, may identify specific mutations in about 2-3 h and, therefore, optimize the surveillance of SARS-CoV-2 variants.
可使用多重逆转录聚合酶链式反应（RT-PCR）检测法对严重急性呼吸综合征冠状病毒2（SARS-CoV-2）变异株进行快速初步检测。本研究旨在评估五种定性RT-PCR检测法与下一代测序（NGS）相比的诊断性能。我们回顾性检查了2021年1月至8月在意大利利古里亚地区流行的72份SARS-CoV-2阳性鼻咽拭子多变异株样本，这些样本分为关注变异株（阿尔法、贝塔、伽马和德尔塔）、监测中的变异株（约塔和卡帕）以及野生型毒株。首先，制备研究样本的NGS文库并将其比对到参考基因组。然后，使用SARS-CoV-2变异株II全谱检测法、超基因检测法SARS-CoV-2 452R & 484K & 484Q变异V1、COVID-19超变异株捕获检测法、SARS-CoV-2扩展ELITe MGB检测法和Simplexa SARS-CoV-2变异株直接检测法对样本进行L452R、W152C、K417T、K417N、E484Q、E484K和N501Y突变检测。这些检测法的总体准确率在96.9%至100%之间。特异性和敏感性分别为100%和96%-100%。我们强烈建议将这些检测法用作SARS-CoV-2实验室诊断常规工作流程中的二级检测，因为它们准确、用户友好、成本低，可在约2-3小时内识别特定突变，从而优化对SARS-CoV-2变异株的监测。
