A Community Study of SARS-CoV-2 Detection by RT-PCR in Saliva: A Reliable and Effective Method

Abstract

Efficient, wide-scale testing for SARS-CoV-2 is crucial for monitoring the incidence of the infection in the community. The gold standard for COVID-19 diagnosis is the molecular analysis of epithelial secretions from the upper respiratory system captured by nasopharyngeal (NP) or oropharyngeal swabs. Given the ease of collection, saliva has been proposed as a possible substitute to support testing at the population level. Here, we used a novel saliva collection device designed to favour the safe and correct acquisition of the sample, as well as the processivity of the downstream molecular analysis. We tested 1003 nasopharyngeal swabs and paired saliva samples self-collected by individuals recruited at a public drive-through testing facility. An overall moderate concordance (68%) between the two tests was found, with evidence that neither system can diagnose the infection in 100% of the cases. While the two methods performed equally well in symptomatic individuals, their discordance was mainly restricted to samples from convalescent subjects. The saliva test was at least as effective as NP swabs in asymptomatic individuals recruited for contact tracing. Our study describes a testing strategy of self-collected saliva samples, which is reliable for wide-scale COVID-19 screening in the community and is particularly effective for contact tracing.

Keywords: COVID-19; SARS-CoV-2 detection; molecular diagnosis; saliva testing.

Figure 1

Description of the organisation of the analytical process. (a) The saliva collection device used in this study consists of a standard 13 mm tube provided with an insert to aid the deposition of saliva, which remains inside the tube without interfering with the introduction of pipette tips. (b) The analytical process begins with the tubes being prepared on racks (I). They are accepted by a robotised, multichannel pipettor with adjustable tip spacing (II), which produces 96-well formatted plates for batched RNA extraction (III). PCR plates are then assembled with a dedicated, robotised pipettor (IV) before amplification in a thermocycler (V). Transition between steps is performed by an operator.

Figure 2

Global concordance between SARS-CoV-2 detection in saliva and NP swabs. (a) Heat map showing the individuals that tested positive (green) or negative (grey) for SARS-CoV-2 in the saliva or NP swabs. The percentage of agreements between results from saliva samples and NP swabs and the kappa index with 95% confidence interval (CI) is indicated. (b) Ct values of all positive NP swabs and saliva samples. Mean and standard deviation in indicated for each group. (c) Correlation between RT-PCR cycle threshold (Ct) values of paired nasopharyngeal swabs and self-administered saliva samples (n = 1003). Shown is the fitted curve of the linear regression, the Pearson correlation coefficient (r), the goodness of fit (R2) and the 95% confidence interval (CI). LOD: limit of detection. (d) Ct values of saliva samples and NP swabs from individuals testing positive with only one of the two methods, categorized by group of subjects as indicated by the colours specified in the legend. Indicated are the mean values and the standard deviations of the populations plotted.

Figure 3

Concordance between SARS-CoV-2 detection in saliva samples and NP swabs in different groups of individuals tested. (a–d) In each panel, the heat maps show of individuals that tested positive and negative, and dot plots the RT-PCR cycle threshold (Ct) values of the paired nasopharyngeal swabs and self-administered saliva samples. The percentage of agreements between results from saliva samples and NP swabs and the kappa index with 95% confidence interval (CI) is indicated below the histograms, as well as the fitted curve of the linear regression in the dot plots, with the Pearson correlation coefficient (r), the goodness of fit (R²) and the 95% confidence interval (CI). LOD: limit of detection. (e) Ct values observed in NP swabs and saliva samples form total convalescent and contact tracing individuals (N+ and S+) as well as in discordant samples (NP+ S- and NP- S+). Indicated are mean values and standard deviations.