Saliva is a reliable and accessible source for the detection of SARS-CoV-2

Abstract

Objectives: The aim of this study was to investigate the feasibility of saliva sampling as a non-invasive and safer tool to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and to compare its reproducibility and sensitivity with nasopharyngeal swab samples (NPS). The use of sample pools was also investigated.

Methods: A total of 2107 paired samples were collected from asymptomatic healthcare and office workers in Mexico City. Sixty of these samples were also analyzed in two other independent laboratories for concordance analysis. Sample processing and analysis of virus genetic material were performed according to standard protocols described elsewhere. A pooling analysis was performed by analyzing the saliva pool and the individual pool components.

Results: The concordance between NPS and saliva results was 95.2% (kappa 0.727, p = 0.0001) and 97.9% without considering inconclusive results (kappa 0.852, p = 0.0001). Saliva had a lower number of inconclusive results than NPS (0.9% vs 1.9%). Furthermore, saliva showed a significantly higher concentration of both total RNA and viral copies than NPS. Comparison of our results with those of the other two laboratories showed 100% and 97% concordance. Saliva samples are stable without the use of any preservative, and a positive SARS-CoV-2 sample can be detected 5, 10, and 15 days after collection when the sample is stored at 4 °C.

Conclusions: The study results indicate that saliva is as effective as NPS for the identification of SARS-CoV-2-infected asymptomatic patients. Sample pooling facilitates the analysis of a larger number of samples, with the benefit of cost reduction.

Keywords: COVID-19; Diagnostic test; Pooling strategy; SARS-CoV-2; Saliva testing.

Graphical abstract

Figure 1

Frequencies and percentages of positive, negative, and inconclusive samples in 2107 paired nasopharyngeal swab and saliva samples: (A) nasopharyngeal swabs; (B) saliva samples.

Figure 2

Cycle threshold values (Ct) in nasopharyngeal swab versus saliva. (A) RNAse P gene in all samples; (B) N1 in SARS-CoV-2-positive samples; (C) N2 in SARS-CoV-2-positive samples. RNAse P had a significantly higher concentration of total RNA in saliva compared to nasopharyngeal swab; p < 0.00001 (t-test).

Figure 3

Total viral copies in nasopharyngeal swab versus saliva. (A) RNAse P gene in all samples; (B) N1 in SARS-CoV-2-positive samples; (C) N2 in SARS-CoV-2-positive samples. RNAse P had significantly higher copies in saliva than nasopharyngeal swab; p < 0.00001 (Mann–Whitney U-test).

Figure 4

Analysis of pooled (1:5 and 1:10) saliva and swab paired samples. Saliva and nasopharyngeal swab pools were generated by mixing one positive sample with four/nine known negative samples. Positive samples with early and late Ct of the N gene were selected to evaluate the impact of dilution on its detection. (A) and (B) show saliva pooled 1:10; (C) and (D) show nasopharyngeal swab pooled 1:10; (E) shows saliva pooled 1:5.