Comparison of Nasal Swabs, Nasopharyngeal Swabs, and Saliva Samples for the Detection of SARS-CoV-2 and other Respiratory Virus Infections

Abstract

Background: Nasal swabs and saliva samples are being considered alternatives to nasopharyngeal swabs (NPSs) for detecting severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2); however, few studies have compared the usefulness of nasal swabs, NPSs, and saliva samples for detecting SARS-CoV-2 and other respiratory virus infections. We compared the positivity rates and concentrations of viruses detected in nasal swabs, NPSs, and saliva samples using cycle threshold (Ct) values from real-time PCR tests for respiratory viruses.

Methods: In total, 236 samples (48 five-rub and 10 10-rub nasal swabs, 96 NPSs collected using two different products, 48 saliva swabs, and 34 undiluted saliva samples) from 48 patients (34 patients with SARS-CoV-2 and 14 with other respiratory virus infections) and 40 samples from eight healthy controls were obtained. The PCR positivity and Ct values were compared using Allplex Respiratory Panels 1/2/3 and Allplex SARS-CoV-2 real-time PCR.

Results: NPSs showed the lowest Ct values (indicating the highest virus concentrations); however, nasal and saliva samples yielded positive results for SARS-CoV-2 and other respiratory viruses. The median Ct value for SARS-CoV-2 E gene PCR using nasal swab samples collected with 10 rubs was significantly different from that obtained using nasal swabs collected with five rubs (Ct=24.3 vs. 28.9; P=0.002), but not from that obtained using NPSs.

Conclusions: Our results confirm that the NPS is the best sample type for detecting respiratory viruses, but nasal swabs and saliva samples can be alternatives to NPSs. Vigorously and sufficiently rubbed nasal swabs can provide SARS-CoV-2 concentrations similar to those obtained with NPSs.

Keywords: Nasal; Nasopharynx; PCR; Respiratory virus; SARS-CoV-2; Saliva; Swab.

Fig. 1

Photograph of the five types of sample collection devices and the transport medium. (A) NPS (NFS-1; Noble Bio), (B) NPS (Copan), (C) nasal swab (SS-1, Noble Bio), (D) saliva swab (SLS-1; Noble Bio), (E) saliva collection tube (Noble Bio), and (F) clinical transport medium (Noble Bio). Abbreviation: NPS, nasopharyngeal swab.

Fig. 2

Comparison of Ct values of real-time PCR targeting SARS-CoV-2 genes and RNase P among the six collection methods (N=10). (A) SARS-CoV-2 E gene, (B) SARS-CoV-2 RdRP gene, (C) SARS-CoV-2 N gene, and (D) Human RNase P gene. The positivity rate of each method is expressed as a percentage. *indicates P<0.05. Abbreviations: Ct, cycle threshold; SARS-CoV-2, severe acute respiratory syndrome-coronavirus 2; NPS, nasopharyngeal swab; Nasal (5), nasal swab with five rotations in one nostril; Nasal (10), nasal swab with 10 rotations in one nostril.