Sensitivity of Rapid Antigen Testing and RT-PCR Performed on Nasopharyngeal Swabs versus Saliva Samples in COVID-19 Hospitalized Patients: Results of a Prospective Comparative Trial (RESTART)

Abstract

Saliva sampling could serve as an alternative non-invasive sample for SARS-CoV-2 diagnosis while rapid antigen tests (RATs) might help to mitigate the shortage of reagents sporadically encountered with RT-PCR. Thus, in the RESTART study we compared antigen and RT-PCR testing methods on nasopharyngeal (NP) swabs and salivary samples. We conducted a prospective observational study among COVID-19 hospitalized patients between 10 December 2020 and 1 February 2021. Paired saliva and NP samples were investigated by RT-PCR (Cobas 6800, Roche-Switzerland, Basel, Switzerland) and by two rapid antigen tests: One Step Immunoassay Exdia^® COVID-19 Ag (Precision Biosensor, Daejeon, Korea) and Standard Q^® COVID-19 Rapid Antigen Test (Roche-Switzerland). A total of 58 paired NP-saliva specimens were collected. A total of 32 of 58 (55%) patients were hospitalized in the intensive care unit, and the median duration of symptoms was 11 days (IQR 5-19). NP and salivary RT-PCR exhibited sensitivity of 98% and 69% respectively, whereas the specificity of these RT-PCRs assays was 100%. The NP RATs exhibited much lower diagnostic performance, with sensitivities of 35% and 41% for the Standard Q^® and Exdia^® assays, respectively, when a wet-swab approach was used (i.e., when the swab was diluted in the viral transport medium (VTM) before testing). The sensitivity of the dry-swab approach was slightly better (47%). These antigen tests exhibited very low sensitivity (4% and 8%) when applied to salivary swabs. Nasopharyngeal RT-PCR is the most accurate test for COVID-19 diagnosis in hospitalized patients. RT-PCR on salivary samples may be used when nasopharyngeal swabs are contraindicated. RATs are not appropriate for hospitalized patients.

Keywords: RT-PCR; SARS-CoV-2 diagnosis; rapid antigen testing; saliva; viral transport medium.

Figure 1

Flowchart of screening process.

Figure 2

Viral load dynamics of NP RT-PCR versus saliva RT-PCR. (A) Kinetics of nasopharyngeal and salivary viral load according to symptom duration upon sampling. The lines connect the mean values of each period, and the shaded areas indicate the mean standard errors (SEM). The inferior grey shaded area represents the detection limit (1000 copies/mL). Specimens with undetectable viral load are shown within the grey dashed area. (B) Box and whisker plots comparing viral load between nasopharyngeal and salivary PCR on different periods since symptom onset. Boxes extend from 25th to 75th percentiles and whiskers show 5th and 95th percentiles. The lines in the middle of the boxes are plotted at median values. (Results were compared using Wilcoxon matched-pairs nonparametric test, *** = p < 0.001, ** = p < 0.01, ns = non-significant).

Figure 3

Viral load trend in person-matched NP and saliva samples (n = 49). (A) Patients hospitalized in the internal medicine ward and (B) patients hospitalized in the ICU. The dotted line and shaded grey area delimit our assay’s detection limit. For graphical representation purposes, samples within the undetectable area are represented with values determined to be at 500 copies/mL. The red and blue horizontal lines represent median values (**** = p < 0.0001 and *** = p < 0.001 with Wilcoxon signed-rank test).

Figure 4

Rapid antigen test results according to time since onset of symptoms and viral load. Full shaded symbols show positive results while no shaded symbols show negative RAT results.