Concordance between PCR-based extraction-free saliva and nasopharyngeal swabs for SARS-CoV-2 testing

Introduction: Saliva represents a less invasive alternative to
nasopharyngeal swab (NPS) for severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2) detection. SalivaDirect is a nucleic acid
extraction-free method for detecting SARS-CoV2 in saliva specimens.
Studies evaluating the concordance of gold standard NPS and newly
developed SalivaDirect protocols are limited. The aim of our study was to
assess SalivaDirect as an alternative method for COVID-19 testing.
Methods: Matching NPS and saliva samples were analysed from a cohort of
symptomatic (n=127) and asymptomatic (n=181) participants recruited from
hospital and university settings respectively. RNA was extracted from NPS
while saliva samples were subjected to the SalivaDirect protocol before
RT-qPCR analysis. The presence of SARS-Cov-2 was assessed using RdRP and
N1 gene targets in NPS and saliva respectively. Results: Overall we
observed 94.3% sensitivity (95% CI 87.2-97.5%), and 95.9% specificity (95%
CI 92.4-97.8%) in saliva when compared to matching NPS samples. Analysis
of concordance demonstrated 95.5% accuracy overall for the saliva test
relative to NPS, and a very high level of agreement (κ coefficient =
0.889, 95% CI 0.833–0.946) between the two sets of specimens. Fourteen of
308 samples were discordant, all from symptomatic patients. Ct values were
>30 in 13/14 and >35 in 6/14 samples. No significant
difference was found in the Ct values of matching NPS and saliva sample
(p=0.860). A highly significant correlation (r = 0.475, p<0.0001)
was also found between the Ct values of the concordant positive saliva and
NPS specimens. Conclusions: Use of saliva processed according to the
SalivaDirect protocol represents a valid method to detect SARS-CoV-2. Less
invasive and accurate saliva screening is an attractive alternative to
current testing methods based on NPS and would afford greater capacity to
test asymptomatic populations especially in the context of frequent
testing.