Scott Lesley Erica, Hsiao Nei-Yuan, Dor Graeme, Hans Lucia, Marokane Puleng, da Silva Manuel Pedro, Preiser Wolfgang, Vreede Helena, Tsoka Jonathan, Mlisana Koleka, Stevens Wendy Susan
Wits Diagnostic Innovation Hub, Faculty of Health Science, University of the Witwatersrand, Johannesburg 2093, South Africa.
Division of Medical Virology, Faculty of Heath Sciences, University of Cape Town, Cape Town 7700, South Africa.
Diagnostics (Basel). 2023 Aug 1;13(15):2554. doi: 10.3390/diagnostics13152554.
The high demand for SARS-CoV-2 tests but limited supply to South African laboratories early in the COVID-19 pandemic resulted in a heterogenous diagnostic footprint of open and closed molecular testing platforms being implemented. Ongoing monitoring of the performance of these multiple and varied systems required novel approaches, especially during the circulation of variants. The National Health Laboratory Service centrally collected cycle threshold (Ct) values from 1,497,669 test results reported from 6 commonly used PCR assays in 36 months, and visually monitored changes in their median Ct within a 28-day centered moving average for each assays' gene targets. This continuous quality monitoring rapidly identified delayed hybridization of in the Allplex™ SARS-CoV-2 assay due to the Delta (B.1.617.2) variant; -gene target failure in the TaqPath™ COVID-19 assay due to B.1.1.7 (Alpha) and the B.1.1.529 (Omicron); and recently -gene delayed hybridization in the Xpert Xpress SARS-CoV-2 due to XBB.1.5. This near "real-time" monitoring helped inform the need for sequencing and the importance of multiplex molecular nucleic acid amplification technology designs used in diagnostics for patient care. This continuous quality monitoring approach at the granularity of Ct values should be included in ongoing surveillance and with application to other disease use cases that rely on molecular diagnostics.
在新冠疫情初期，南非实验室对新冠病毒检测的需求很高，但供应有限，导致开放和封闭分子检测平台的诊断格局参差不齐。对这些多样的系统的性能进行持续监测需要新的方法，尤其是在变异株传播期间。国家卫生实验室服务中心在36个月内集中收集了来自36个常用PCR检测方法报告的1,497,669份检测结果的循环阈值（Ct）值，并直观地监测了每个检测方法的基因靶点在以28天为中心的移动平均值内的中位数Ct变化。这种持续的质量监测迅速发现，由于德尔塔（B.1.617.2）变异株，Allplex™新冠病毒检测中出现杂交延迟；由于B.1.1.7（阿尔法）和B.1.1.529（奥密克戎）变异株，TaqPath™新冠检测中出现基因靶点失败；最近，由于XBB.1.5变异株，Xpert Xpress新冠病毒检测中出现基因杂交延迟。这种近乎“实时”的监测有助于了解测序的必要性以及诊断中用于患者护理的多重分子核酸扩增技术设计的重要性。这种以Ct值为粒度的持续质量监测方法应纳入正在进行监测中，并应用于其他依赖分子诊断的疾病用例。
