Multiplatform Assessment of Saliva for SARS-CoV-2 Molecular Detection in Symptomatic Healthcare Personnel and Patients Presenting to the Emergency Department

Abstract

Background: Saliva has garnered great interest as an alternative specimen type for molecular detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Data are limited on the relative performance of different molecular methods using saliva specimens and the relative sensitivity of saliva to nasopharyngeal (NP) swabs.

Methods: To address the gap in knowledge, we enrolled symptomatic healthcare personnel (n = 250) from Barnes-Jewish Hospital/Washington University Medical Center and patients presenting to the Emergency Department with clinical symptoms compatible with coronavirus disease 2019 (COVID-19; n = 292). We collected paired saliva specimens and NP swabs. The Lyra SARS-CoV-2 assay (Quidel) was evaluated on paired saliva and NP samples. Subsequently we compared the Simplexa COVID-19 Direct Kit (Diasorin) and a modified SalivaDirect (Yale) assay on a subset of positive and negative saliva specimens.

Results: The positive percent agreement (PPA) between saliva and NP samples using the Lyra SARS-CoV-2 assay was 63.2%. Saliva samples had higher SARS-CoV-2 cycle threshold values compared to NP swabs (P < 0.0001). We found a 76.47% (26/34) PPA for Simplexa COVID-19 Direct Kit on saliva and a 67.6% (23/34) PPA for SalivaDirect compared to NP swab results.

Conclusion: These data demonstrate molecular assays have variability in performance for detection of SARS-CoV-2 in saliva.

Fig. 1

SARS-CoV-2 C_T values differ significantly between saliva and concurrently run paired NP swab. (A) XY plot depicting the correlation between C_T values for saliva and paired NP swab. (B) Dot plot depicting SARS-CoV-2 C_T values for saliva and paired NP swab specimens using the Lyra Saliva Assay. (C) Dot plot showing differences in C_T values between saliva and paired NP swab when broken up by study site. ****P < 0.0001; *P = 0.0132.

Fig. 2

Processing control PRC values differ significantly between saliva and concurrently run paired NP swab. (A) Dot plots demonstrating that overall there is a statistically significant decrease in the PRC C_T values for saliva compared to the paired NP swab but no difference (B) when just the specimens that are positive for SARS-CoV-2 target are examined. ****P < 0.0001. Red line represents the median value. The median value for saliva is 28.62 and 29.57 for (A) and (B), respectively. The median value for paired NP is 29.62 and 29.13 for (A) and (B), respectively.

Fig. 3

Cross platform correlation between C_T values on saliva. Correlation was highest between Lyra saliva and the (A) Simplexa orf1ab target (R² = 0.57) and comparable between Lyra saliva and (B) Simplexa S gene target (R² = 0.47) and (C) SalivaDirect N gene (R² = 0.48). Values depicted in gray represent specimens that were not identified by Lyra saliva but were identified by the other platform; the Lyra C_T value was designated 40, the manufacturer cutoff.