Saliva is Comparable to Nasopharyngeal Swabs for Molecular Detection of SARS-CoV-2

Abstract

The continued need for molecular testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the potential for self-collected saliva as an alternative to nasopharyngeal (NP) swabs for sample acquisition led us to compare saliva to NP swabs in an outpatient setting without restrictions to avoid food, drink, smoking, or tooth-brushing. A total of 385 pairs of NP and saliva specimens were obtained, the majority from individuals presenting for initial evaluation, and were tested on two high-sensitivity reverse transcriptase PCR (RT-PCR) platforms, the Abbott m2000 and Abbott Alinity m (both with limits of detection [LoD] of 100 copies of viral RNA/ml). Concordance between saliva and NP swabs was excellent overall (Cohen's κ = 0.93) for both initial and follow-up testing, for both platforms, and for specimens treated with guanidinium transport medium as preservative as well as for untreated saliva (κ = 0.88 to 0.95). Viral loads were on average 16× higher in NP specimens than saliva specimens, suggesting that only the relatively small fraction of outpatients (∼8% in this study) who present with very low viral loads (<1,600 copies/ml from NP swabs) would be missed by testing saliva instead of NP swabs when using sensitive testing platforms. Special attention was necessary to ensure leak-resistant specimen collection and transport. The advantages of self-collection of saliva, without behavioral restrictions, will likely outweigh a minor potential decrease in clinical sensitivity in individuals less likely to pose an infectious risk to others for many real-world scenarios, especially for initial testing. IMPORTANCE In general, the most accurate COVID-19 testing is hands-on and uncomfortable, requiring trained staff and a "brain-tickling" nasopharyngeal swab. Saliva would be much easier on both fronts, since patients could collect it themselves, and it is after all just spit. However, despite much interest, it remains unclear how well saliva performs in real-world settings when just using it in place of an NP swab without elaborate or cumbersome restrictions about not eating/drinking before testing, etc. Also, almost all studies of COVID-19 testing, whether of NP swabs, saliva, or otherwise, have been restricted to reporting results in the abstruse units of "C_T values," which only mean something in the context of a specific assay and testing platform. Here, we compared saliva versus NP swabs in a real-world setting without restriction and report all results in natural units-the amount of virus being shed-showing that saliva is essentially just as good as NP swabs.

Keywords: COVID-19; NP swab; SARS-CoV-2; limit of detection; saliva.

FIG 1

Numbers of participants in each study arm.

FIG 2

LoD for treated and untreated saliva on Abbott m2000 and Alinity m platforms. Lowest two datapoints with 24 replicates each; others in triplicate.

FIG 3

Stability of replication-incompetent SARS-CoV-2 surrogate virus in untreated saliva samples over time. Gray, triplicate measurements; black, geometric means; red, exponential decay fit.

FIG 4

Viral load in saliva versus NP swab samples, Cohen’s kappa (κ) concordance values, and contingency tables for overall study (a), subjects presenting for initial presentation (within 5 days of first COVID-19 RT-PCR test) (b), subjects presenting for follow-up testing (c), samples treated with GITC transport buffer as a preservative after receipt at the central laboratory (d), untreated samples (e), samples run on the Alinity m platform (f), and samples run on the m2000 (g). Diagonal lines in scatterplots, 1:1. Gray shaded areas in the scatterplots are below the LoD (100 copies/ml). Gray shaded cells in the contingency tables highlight discordant results.

FIG 5

Sample processing times ranked by increasing order of total time. Sample-to-login time is the time between sample acquisition and login at the central laboratory. Login-to-processing time is the time between login and arrival of the specimen in the molecular laboratory when GITC treatment and RT-PCR testing are performed.