Evaluating diagnostic accuracy of saliva sampling methods for SARS-CoV-2 reveals differential sensitivity and association with viral load

ABSTRACT

Nasopharyngeal swabs are considered the preferential collection method for SARS-CoV-2 diagnostics. Alternative sampling procedures that are less invasive and do not require a healthcare professional, such as saliva collection, would be more preferable. We compared saliva specimens and nasopharyngeal (NP) swabs with respect to sensitivity in detecting SARS-CoV-2. We obtained a nasopharyngeal and two saliva specimens (collected by spitting or oral swabbing) from more than 2500 individuals. All samples were tested by RT-qPCR detecting RNA of SARS-CoV-2. We compared the test sensitivity on the two saliva collections with the nasopharyngeal specimen for all subjects and stratified by symptom status and viral load. Of the 2850 patients for which all three samples were available, 105 were positive on NP, whereas 32 and 23 were also positive on saliva spitting and saliva swabbing samples, respectively. The sensitivity of the RT-qPCR to detect SARS-CoV-2 among NP-positive patients was 30.5% (95% CI=1.9%-40.2%) for saliva spitting, and 21.9% (95% CI=14.4%-31.0%) for saliva swabbing. However, when focusing on subjects with medium to high viral load, sensitivity on saliva increased substantially: 93.9% (95% CI=79.8%-99.3%) and 76.9% (95% CI=56.4-91.0) for spitting and swabbing, respectively, regardless of symptomatic status. Our results suggest that saliva cannot readily replace nasopharyngeal sampling for SARS-CoV-2 diagnostics but may enable identification of the most contagious cases with medium to high viral loads.