SARS-CoV-2 nucleic acid testing (NAT) has been routinely used for COVID-19 diagnosis during this pandemic; however, there have been concerns about its high false negative rate. We dissected its detection efficiency with a large COVID-19 cohort study.

We analyzed SARS-CoV-2 NAT positive rates of 4,275 specimens from 532 COVID-19 patients in Sichuan Province with different disease severities, statuses, and stages, as well as different types and numbers of specimens.

The total positive rate of the 4,275 specimens was 37.5%. Among seven specimen types, BALF generated a 77.8% positive rate, followed by URT specimens (38.5%), sputum (39.8%), and feces/rectal swabs (34.1%). Specimens from critical cases generated a 43.4% positive rate, which was significantly higher than that of other severities. With specimens from patients at stable status, the SARS-CoV-2 positive rate was 40.6%, which was significantly higher than that of improved status (17.1%), but lower than that of aggravated status (61.5%). Notably, the positive rate of specimens from COVID-19 patients varied significantly from 85 to 95% during 3 days before and after symptom onset, to 20% at around 18 days after symptom onset. In addition, the detection rate increased from 72.1% after testing one throat swab, to 93.2% after testing three consecutive respiratory specimens from each patient.

SARS-CoV-2 NAT detection rates vary with patient disease severity and status, specimen type, number of specimens, and especially disease progression. Sampling as close to symptom onset as possible, and consecutively collecting more than one respiratory specimen could effectively improve SARS-CoV-2 NAT detection efficiency.

在这种大流行期间，SARS-CoV-2核酸检测（NAT）通常用于COVID-19诊断。但是，人们一直担心它的假阴性率很高。我们通过一项大型的COVID-19队列研究剖析了其检测效率。

我们分析了四川省532例COVID-19患者的4275份标本的SARS-CoV-2 NAT阳性率，这些标本具有不同的疾病严重程度，状态和阶段，以及标本的类型和数量也不同。

4,275个样本的总阳性率为37.5％。在7种标本中，BALF的阳性率为77.8％，其次是URT标本（38.5％），痰（39.8％）和粪便/直肠拭子（34.1％）。危重病例标本的阳性率为43.4％，明显高于其他严重程度。在患者状态稳定的标本中，SARS-CoV-2阳性率为40.6％，显着高于改善状态（17.1％），但低于严重状态（61.5％）。值得注意的是，来自COVID-19患者的标本的阳性率在症状发作前后的三天内从85％到95％显着变化，而在症状发作之后的18天左右则为20％。此外，检出一只咽拭子后的检出率从72.1％提高到93。

SARS-CoV-2 NAT检测率随患者疾病的严重程度和状态，标本类型，标本数量，尤其是疾病进展而变化。尽可能接近症状发作的采样，并连续收集多个呼吸道标本，可以有效提高SARS-CoV-2 NAT检测效率。