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

Abstract

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.

Keywords: COVID-19; Nasopharyngeal swab; Real-time RT-PCR; SARS CoV-2; Saliva.

Fig. 1

Cycle threshold (Ct) values for N2 and RNAse P (RP) for NPS and saliva specimens. A) N2 Ct values by testing concordance. The N2 Ct value was set to 41 for samples in which only the N1 target was detected. The horizontal dashed line is at Ct = 40, the assay cut-off. Horizontal lines indicate the median and interquartile range (IQR). The median and IQR for each group are: 28.56 (18.3 to 33.5), 30.18 (20.32 to 36.66), 33.68 (32.5 to 37.99), and 37.62 (36.98 to 38.26) for Both (NPS), Both (Saliva), NPS Only, and Saliva Only, respectively. B) N2 Ct values for paired NPS and saliva samples. Pairs are connected by a line. The N2 Ct was set to 41 for samples in which N2 was not detected including those negative for SARS-CoV-2 RNA. The horizontal dashed line is at Ct = 40, the assay cut-off. Ct values were significantly lower for NPS when compared by Wilcoxon matched-pairs signed rank test (p = 0.0331). C) RP Ct values for NPS and saliva specimens. Median and IQR are 24.27 (23.46 to 24.96) and 22.63 (21.88 to 23.85), respectively.