Challenges in use of saliva for detection of SARS CoV-2 RNA in symptomatic outpatients

Background: A major expansion in SARS CoV-2 testing is urgently needed. Saliva is an attractive option as an alternative for nasopharyngeal swabs (NPS), since saliva can be self-collected, is non-invasive, and sample quality is not dependent on the expertise of the collector. Objective: To compare SARS CoV-2 positivity on paired NPS and saliva samples. Study design: NPS and paired saliva samples were prospectively collected from symptomatic outpatients suspected of having COVID-19 and were tested by real-time RT-PCR. Results: In total, 35/124 (26.6 %) samples were RT-PCR positive, with 33/35 positive by NPS (sensitivity = 94.3 % (95 % CI 81.4%-99.0%)) and 30/35 by pure saliva (sensitivity = 85.7 % (95 % CI 70.6%-93.7%)), for an overall agreement of 117/124 (94.4 %). The median cycle threshold value was significantly lower for NPS than for saliva (p = 0.0331). A third or more of pure saliva samples from symptomatic patients were thick, stringy, and difficult to pipet. Conclusions: Real-time RT-PCR of pure saliva had an overall sensitivity for SARS CoV-2 RNA detection of 85.7 % when compared to simultaneously collected NPS. Our study highlighted the need to optimize collection and processing before saliva can be used for high volume testing.