Performance of Saliva Samples for COVID-19 Diagnosis by Using the AllplexTM 2019-nCoV Assay Kit

Abstract

Background: Although the nasopharyngeal swab (NPS) is the reference sampling method for the detection of SARS-Cov-2, it is not always possible to collect NPS in some patients. Saliva represents an interesting sampling method because it is less invasive and more convenient in patients with nasal or pharyngeal lesions. Objective: To compare the RT-qPCR test performances of saliva samples with nasal mid-turbinate swab (NMTS) and NPS samples in a cohort of ambulatory patients suspected of having COVID-19. Study Design: For each of the 112 enrolled patients, NPS, NMTS, and saliva samples were collected and tested for SARS-Cov-2 detection using three different target genes (RdRP, N and E genes) by RT-qPCR. Results: Among the positive samples (56/112), saliva samples showed a lower percentage of SARS-Cov-2 detection compared to NPS samples, (85.7 vs. 96.4%), while still a lower percentage was observed for NMTS samples (78.6%). In average, saliva samples showed higher Ct values for all tested target genes, compared to those from NPS and NMTS samples. Conclusions: By using the Allplex^TM 2019-nCoV Assay Kit, saliva samples showed lower sensitivity for SARS CoV-2 compared to NPS samples; however, the not detected cases had lower viral burden in NPS samples (CT values >33) representing an interesting alternative sampling method in patients in which it is not possible to take a NPS sample.

Keywords: COVID-19; RT-qPCR; SAR-CoV-2; nasopharangeal swabs; saliva.

Figure 1

Comparison of the RT-qPCR performance between the distinct sampling methods. Boxplots of SARS-CoV-2 Cycle threshold (Ct) values (mean and interquartile range) obtained for (A) E target gene, (B) RdRP target gene, and (C) N target gene in nasopharyngeal swab (NPS), nasal mid-turbinate (NTMS) swab, and saliva (SALIVA) samples. Statistical differences were tested using the paired t-test. * p ≤ 0.05. ** p ≤ 0.01.

Figure 2

Comparison of the RT-qPCR efficiency between the distinct sampling methods. Correlation of SARS-CoV-2 Cycle threshold (Ct) values obtained for (A,B) E target gene, (C,D) RdRP target gene, (E,F) and N target gene between nasopharyngeal swab (NPS), nasal mid-turbinate swab (NTMS), and saliva (SALIVA) samples. NPS was considered as the sampling method reference.

Figure 3

Comparison of Ct values depending on the number of positive samples. Ct values of samples that are positive for the three sampling methods (three positive samples) and for at least two sampling methods (≤ 2 positive samples). NPS, nasopharyngeal swab; NTMS, nasal midturbinate swab; SALIVA, saliva.