Performance of Saliva Specimens for the Molecular Detection of SARS-CoV-2 in the Community Setting: Does Sample Collection Method Matter?

Abstract

Data on the performance of saliva specimens for diagnosing coronavirus disease 2019 (COVID-19) in ambulatory patients are scarce and inconsistent. We assessed saliva-based specimens for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by reverse transcriptase PCR (RT-PCR) in the community setting and compared three different collection methods. This prospective study was conducted in three primary care centers. RT-PCR was performed on paired nasopharyngeal swabs (NPS) and saliva samples collected from outpatients with a broad clinical spectrum of illness. To assess differences in collection methods, saliva specimens were obtained in a different way in each of the participating centers: supervised collection (SVC), oropharyngeal washing (OPW), and self-collection (SC). Pairs of NPS and saliva samples from 577 patients (median age, 39 years; 44% men; 42% asymptomatic) were collected and tested, and 120 (20.8%) gave positive results. The overall agreement with NPS results and kappa coefficients (κ) for saliva samples obtained by SVC, OPW, and SC were 95% (κ = 0.85), 93.4% (κ = 0.76), and 93.3% (κ = 0.76), respectively. The sensitivities (95% confidence intervals [95% CI]) of the saliva specimens ranged from 86% (72.6% to 93.7%) for SVC to 66.7% (50.4% to 80%) for SC samples. Sensitivity was higher for samples with lower cycle threshold (C_T ) values. The best RT-PCR performance was observed for SVC, with sensitivities (95% CI) of 100% (85.9% to 100%) in symptomatic individuals and 88.9% (50.7% to 99.4%) in asymptomatic individuals at C_T values of ≤30. We conclude that saliva is an acceptable specimen for the detection of SARS-CoV-2 in the community setting. Specimens collected under supervision perform comparably to NPS and can effectively identify individuals at higher risk of transmission under real-life conditions.

Keywords: COVID-19; PCR; SARS-CoV-2; diagnostics; saliva.

FIG 1

Positivity for SARS-CoV-2 RNA in nasopharyngeal swabs (NPS) and in the different saliva specimens, including cycle threshold values of discordant specimens. The asterisk indicates one positive saliva specimen for which a negative NPS was confirmed 6 days later.

FIG 2

Cycle threshold values for pairs of nasopharyngeal swabs (NPS) and saliva specimens from all positive individuals. Each dot represents the C_T value (in RT-PCR) for a positive specimen: NPS (n = 113), saliva obtained under supervised collection (SVC) (n = 43), saliva obtained after oropharyngeal washing (OPW) (n = 21), or saliva obtained by self-collection (SC) (n = 28).

FIG 3

Sensitivities of the different specimens for SARS-CoV-2 detection according to the C_T value with nasopharyngeal swabs. In cases with a negative nasopharyngeal swab and positive saliva, the C_T value of the saliva specimen was taken.