Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA.
J Appl Lab Med. 2021 Mar 1;6(2):421-428. doi: 10.1093/jalm/jfaa187.
Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by reverse transcription PCR is the primary method to diagnose coronavirus disease 2019 (COVID-19). However, the analytic sensitivity required is not well defined and it is unclear how available assays compare.
For the Abbott RealTime SARS-CoV-2 assay (m2000; Abbott Molecular), we determined that it could detect viral concentrations as low as 26 copies/mL, we defined the relationship between cycle number and viral concentrations, and we tested naso- and oropharyngeal swab specimens from 8538 consecutive individuals. Using the m2000 as a reference assay method, we described the distribution of viral concentrations in these patients. We then used selected clinical specimens to determine the positive percent agreement of 2 other assays with more rapid turnaround times [Cepheid Xpert Xpress (GeneXpert; Cepheid); n = 27] and a laboratory developed test on the Luminex ARIES system [ARIES LDT (Luminex); n = 50] as a function of virus concentrations, from which we projected their false-negative rates in our patient population.
SARS-CoV-2 was detected in 27% (95% CI: 26%-28%) of all specimens. Estimated viral concentrations were widely distributed, and 17% (95% CI: 16%-19%) of positive individuals had viral concentrations <845 copies/mL. Positive percent agreement was strongly related to viral concentration, and reliable detection (i.e., ≥95%) was observed at concentrations >100 copies/mL for the GeneXpert but not the ARIES LDT, corresponding to projected false-negative rates of 4% (95% CI: 0%-21%) and 27% (95% CI: 11%-46%), respectively.
Substantial proportions of clinical specimens have low to moderate viral concentrations and may be missed by methods with less analytic sensitivity.
逆转录聚合酶链反应（RT-PCR）检测严重急性呼吸综合征冠状病毒 2（SARS-CoV-2）是诊断 2019 年冠状病毒病（COVID-19）的主要方法。然而，目前尚不清楚所需的分析灵敏度是多少，也不清楚现有的检测方法如何进行比较。
对于 Abbott RealTime SARS-CoV-2 检测法（m2000；Abbott Molecular），我们确定它可以检测到低至 26 拷贝/ml 的病毒浓度，定义了循环数与病毒浓度之间的关系，并测试了 8538 例连续个体的鼻咽和口咽拭子标本。使用 m2000 作为参考检测方法，我们描述了这些患者中病毒浓度的分布。然后，我们使用选定的临床标本来确定另外两种具有更快周转时间的检测方法的阳性百分符合率[Cepheid Xpert Xpress（GeneXpert；Cepheid）；n=27]和 Luminex ARIES 系统上的实验室开发检测法[ARIES LDT（Luminex）；n=50]，作为病毒浓度的函数，由此我们预测了它们在我们患者人群中的假阴性率。
SARS-CoV-2 在所有标本中的检出率为 27%（95%CI：26%-28%）。估计的病毒浓度分布广泛，17%（95%CI：16%-19%）的阳性个体的病毒浓度<845 拷贝/ml。阳性百分符合率与病毒浓度密切相关，GeneXpert 可在浓度>100 拷贝/ml 时可靠检测（即≥95%），但 ARIES LDT 则不行，这分别对应于预测的假阴性率为 4%（95%CI：0%-21%）和 27%（95%CI：11%-46%）。
大量临床标本的病毒浓度较低或中等，可能会被分析灵敏度较低的方法所遗漏。
