Diagnostic accuracy of nasopharyngeal swab, nasal swab and saliva swab samples for the detection of SARS-CoV-2 using RT-PCR

The current gold standard in coronavirus disease (COVID-19) diagnostics is the real-time reverse transcription–polymerase chain reaction (RT-PCR) assay for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in nasopharyngeal swab (NPS) samples. Alternatively, nasal swab (NS) or saliva swab (SS) specimens are used, although available data on test accuracy are limited. We examined the diagnostic accuracy of NPS/NS/SS samples for this purpose. Ten patients were included after being tested positive for SARS-CoV-2 RT-PCR in NPS samples according to the National Institute of Infectious Disease guidelines. In comparison with this conventional diagnostic method, NPS/NS/SS samples were tested using the cobas 6800 systems RT-PCR device. To investigate the usefulness of the cobas method and the difference among sample types, the agreement and sensitivity were calculated. Five to six samples were collected over a total period of 5–6 d from each patient. Fifty-seven sets of NPS/NS/SS samples were collected, of which 40 tested positive for COVID-19 by the conventional method. Overall, the concordance rates using the conventional method were 86.0%/70.2%/54.4% for NPS/NS/SS samples (cobas); however, for samples collected up to and including on Day 9 after disease onset (22 negative and one positive specimens), the corresponding rates were 95.7%/87.0%/65.2%. The overall sensitivity estimates were 100.0%/67.5%/37.5% for NPS/NS/SS samples (cobas). For samples up to 9 d after onset, the corresponding values were 100.0%/86.4%/63.6%. NS samples are more reliable than SS samples and can be an alternative to NPS samples. They can be a useful diagnostic method in the future.当前新型冠状病毒肺炎（coronavirus disease, COVID-19）诊断的金标准，是采用实时逆转录聚合酶链反应（real-time reverse transcription–polymerase chain reaction, RT-PCR）技术，对鼻咽拭子（nasopharyngeal swab, NPS）样本中的严重急性呼吸综合征冠状病毒2型（severe acute respiratory syndrome coronavirus 2, SARS-CoV-2）RNA进行检测。替代采样方式包括鼻拭子（nasal swab, NS）或唾液拭子（saliva swab, SS）标本，但现有检测准确性相关数据较为有限。 本研究旨在评估NPS/NS/SS样本的诊断准确性。 本研究纳入10名符合要求的患者：所有患者均经传染病研究所（National Institute of Infectious Disease）指南规定的NPS样本SARS-CoV-2 RT-PCR检测呈阳性。以该常规诊断方法为参照，采用cobas 6800系统RT-PCR设备对采集的NPS/NS/SS样本进行检测。为探究cobas检测方法的应用价值及不同采样类型间的性能差异，本研究计算了检测一致性与灵敏度指标。 每名患者在5至6天的总周期内共采集5至6份样本。最终共收集到57组NPS/NS/SS样本，其中40组经常规方法检测为COVID-19阳性。 整体而言，以常规方法为参照时，NPS/NS/SS样本经cobas检测的符合率分别为86.0%、70.2%、54.4%；而针对发病后9天及以内采集的样本（共22份阴性、1份阳性标本），对应符合率分别为95.7%、87.0%、65.2%。 三类样本经cobas检测的整体灵敏度估算值分别为100.0%、67.5%、37.5%；针对发病后9天及以内的样本，对应灵敏度估算值分别为100.0%、86.4%、63.6%。 综上，鼻拭子（NS）样本的检测可靠性优于唾液拭子（SS）样本，可作为鼻咽拭子（NPS）样本的替代采样方式，未来有望成为实用的新冠诊断手段。