Microbiology Department, Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos State, Nigeria.
Department of Medical Microbiology and Parasitology, Centre for Human & Zoonotic Virology, College of Medicine, University of Lagos, Idi-Araba, Lagos State, Nigeria.
PLoS One. 2021 Feb 4;16(2):e0246637. doi: 10.1371/journal.pone.0246637. eCollection 2021.
A key element in containing the spread of the SARS-CoV-2 infection is quality diagnostics which is affected by several factors. We now report the comparative performance of five real-time diagnostic assays. Nasopharyngeal swab samples were obtained from persons seeking a diagnosis for SARS-CoV-2 infection in Lagos, Nigeria. The comparison was performed on the same negative, low, and high-positive sample set, with viral RNA extracted using the Qiagen Viral RNA Kit. All five assays are one-step reverse transcriptase real-time PCR assays. Testing was done according to each assay's manufacturer instructions for use using real-time PCR platforms. 63 samples were tested using the five qPCR assays, comprising of 15 negative samples, 15 positive samples (Ct = 16-30; one Ct = 35), and 33 samples with Tib MolBiol E-gene Ct value ranging from 36-41. All assays detected all high positive samples correctly. Three assays correctly identified all negative samples while two assays each failed to correctly identify one different negative sample. The consistent detection of positive samples at different Ct/Cq values gives an indication of when to repeat testing and/or establish more stringent in-house cut-off value. The varied performance of different diagnostic assays, mostly with emergency use approvals, for a novel virus is expected. Comparative assays' performance reported may guide laboratories to determine both their repeat testing Ct/Cq range and/or cut-off value.
控制 SARS-CoV-2 感染传播的一个关键因素是质量诊断，这受到几个因素的影响。我们现在报告五种实时诊断检测方法的比较性能。从尼日利亚拉各斯寻求 SARS-CoV-2 感染诊断的人获得鼻咽拭子样本。在相同的阴性、低和高阳性样本集中进行了比较，使用 Qiagen Viral RNA 试剂盒提取病毒 RNA。所有五种检测方法都是一步逆转录实时 PCR 检测方法。根据每个检测方法的使用说明书，使用实时 PCR 平台进行检测。使用五种 qPCR 检测方法对 63 个样本进行了测试，包括 15 个阴性样本、15 个阳性样本（Ct = 16-30；一个 Ct = 35）和 33 个样本，Tib MolBiol E 基因 Ct 值范围为 36-41。所有检测方法均正确检测到所有高阳性样本。三种检测方法正确识别了所有阴性样本，而两种检测方法均未能正确识别出一个不同的阴性样本。在不同的 Ct/Cq 值下一致检测到阳性样本表明何时需要重复检测和/或建立更严格的内部截止值。对一种新型病毒的不同诊断检测方法的性能差异，主要是具有紧急使用批准，是可以预期的。报告的比较检测方法的性能可能有助于实验室确定其重复测试的 Ct/Cq 范围和/或截止值。
