Nasopharyngeal Swabs Are More Sensitive Than Oropharyngeal Swabs for COVID-19 Diagnosis and Monitoring the SARS-CoV-2 Load

Abstract

Objective: Detection of SARS-CoV-2 by oropharyngeal swabs (OPS) and nasopharyngeal swabs (NPS) is an essential method for coronavirus disease 2019 (COVID-19) management. It is not clear how detection rate, sensitivity, and the risk of exposure for medical providers differ in two sampling methods. Methods: In this prospective study, 120 paired NPS and OPS specimens were collected from 120 inpatients with confirmed COVID-19. SARS-CoV-2 nucleic acid in swabs were detected by real-time RT-PCR. The SARS-CoV-2 detection rate, sensitivity, and viral load were analyzed with regards NPS and OPS. Sampling discomfort reported by patients was evaluated. Results: The SARS-CoV-2 detection rate was significantly higher for NPS [46.7% (56/120)] than OPS [10.0% (12/120)] (P < 0.001). The sensitivity of NPS was also significantly higher than that of OPS (P < 0.001). At the time of sampling, the time of detectable SARS-CoV-2 had a longer median duration (25.0 vs. 20.5 days, respectively) and a longer maximum duration (41 vs. 39 days, respectively) in NPS than OPS. The mean cycle threshold (Ct) value of NPS (37.8, 95% CI: 37.0-38.6) was significantly lower than that of OPS (39.4, 95% CI: 38.9-39.8) by 1.6 (95% CI 1.0-2.2, P < 0.001), indicating that the SARS-CoV-2 load was significantly higher in NPS specimens than OPS. Patient discomfort was low in both sampling methods. During NPS sampling, patients were significantly less likely to have nausea and vomit. Conclusions: NPS had significantly higher SARS-CoV-2 detection rate, sensitivity, and viral load than OPS. NPS could reduce droplets production during swabs. NPS should be recommended for diagnosing COVID-19 and monitoring SARS-CoV-2 load. Chinese Clinical Trial Registry, number: ChiCTR2000029883.

Keywords: COVID-19; SARS-CoV-2; nasopharyngeal swab; oropharyngeal swab; sensitivity; viral load.

Figure 1

SARS-CoV-2 detection by NPS and OPS. (A) The detection rate (with 95% CI) of NPS and OPS with the development of the time course. (B) Time course (with IQR) of the detectable SARS-CoV-2 by paired NPS and OPS from 120 patients. (C) Time course of the detectable SARS-CoV-2 by paired NPS and OPS form 61 patients who needed one more negative SARS-CoV-2 result to meet the discharge criteria.

Figure 2

PCR cycle threshold (Ct) value detected in NPS and OPS specimens. (A) Comparison of Ct values of 120 paired NPS and OPS specimens. Each data point represents the Ct values of NPS and OPS from one patient. (B) Ct values for NPS and OPS during treatment. Solid curves represent the trend derived by locally weighted scatterplot smoothing method. (C) Comparison of Ct values (with 95% CI) of paired NPS and OPS from 120 patients. (D) Comparison of Ct values (with 95% CI) of paired NPS and OPS from 57 patients with positive SARS-CoV-2. A lower Ct value corresponds to a higher viral load.

Figure 3

Patient discomfort levels during NPS and OPS sampling (N = 103). (A) Percentage of four varying discomfort levels reported by patients during swab sampling. (B) Mean scores (with standard deviation) of symptoms during sampling. (C) Frequency of each symptom during sampling. *P < 0.01, **P < 0.001.