Performance of saliva specimens for the molecular detection of SARS-CoV-2 in the community setting: does sample collection method matter?

Background Data on the performance of saliva specimens for diagnosing COVID-19 in ambulatory patients are scarce and inconsistent. We assessed saliva-based specimens for detecting SARS-CoV-2 by RT-PCR in the community setting and compared three different collection methods. Method Prospective study conducted in three primary care centres. RT-PCR was performed in 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 centres: supervised collection (SVC), oropharyngeal washing (OPW) and self-collection (SC). Results NPS and saliva pairs of 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 and kappa coefficients (KƘ) for SVC, OPW and SC were 95% (Ƙ=0.85), 93.4% (Ƙ=0.76), and 93.3% (Ƙ=0.76), respectively. The sensitivity (95% CI) of the saliva specimens varied from 86% (72.6-93.7) for SVC to 66.7% (50.4-80) for SC samples. The sensitivity was higher in samples with lower cycle threshold (Ct) values. The best performance of RT-PCR was observed for SVC, with sensitivity (95% CI) for Ct values ≤32 of 97% (82.5-99.8) in symptomatic, and 88.9% (50.7-99.4) in asymptomatic individuals. Conclusions 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 with higher risk of transmission in real life conditions.