Comparison of Throat Washings, Nasopharyngeal Swabs and Oropharyngeal Swabs for Detection of SARS-CoV-2

Abstract

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) RNA is detected by reverse-transcription quantitative real-time PCR (RT-qPCR) from respiratory specimens. This study compares throat washings (TW), nasopharyngeal swabs (NS) and oropharyngeal swabs (OS). A total of 102 samples from 34 adult patients with confirmed SARS-CoV-2 infection were analysed by RT-qPCR with absolute quantification. The median concentrations and diagnostic sensitivities were 5.8×104 copies/mL, 85% (NS), 1.4×104, 79% (OS) and 4.3×103, 85% (TW). Concentration differences were significant between NS and TW (P = 0.019). Saliva (SA) was available from 21 patients (median 3.4×103). OS and TW can be considered for SARS-CoV-2 diagnostics, although with slightly lower concentrations.

Keywords: COVID-19; PCR; RT-qPCR; SARS-CoV-2; diagnostic sensitivity; nasopharyngeal swab; nucleic acid test; oropharyngeal swab; saliva; throat washing.

Figure 1

SARS-CoV-2 RNA concentrations in samples of 34 study participants. Measurements are separated into sampling site groups (TW, throat washing; NS, nasopharyngeal swab; OS, oropharyngeal swab). Samples with the result not detected were set to 10⁰ cp/mL and are plotted below the dashed lines. (A) Levels of SARS-CoV-2 viral loads across sampling sites. The respective median concentrations are shown as horizontal lines. The statistically significant difference between the groups was assessed by post-hoc tests based on the linear mixed-effects model and is indicated by a horizontal line with the corresponding P value < 0.05 on top of the data panels. (B) Concentration patterns A–F as found by combinatorial analysis of the quantitative results. Data from six subjects with ≤1 positive result are not shown. (C) comparative SARS-CoV-2 RNA quantification plots, sorted by concentration pattern and decreasing median viral load. Subject identification numbers are indicated on the x-axis.

Figure 2

SARS-CoV-2 RNA concentrations in samples of 21 study participants. Measurements are separated into sampling site groups (TW, throat washing; NS, nasopharyngeal swab; OS, oropharyngeal swab; SA, saliva). Connected datapoints represent results from one patient. Samples with the result not detected were set to 10⁰ cp/mL and are plotted below the dashed lines. (A) Levels of SARS-CoV-2 viral loads across sampling sites. The respective median concentrations are shown as horizontal lines. No statistically significant differences between the four sampling groups were found by linear mixed-effects model analysis. (B) comparative SARS-CoV-2 RNA quantification plots, sorted by concentration pattern and decreasing median viral load. Subject identification numbers are indicated on the x-axis.