Clinical Validation of a Sensitive Test for Saliva

Rapid and accurate diagnostic tests are essential for controlling the ongoing Covid-19 pandemic. Although the current standard involves testing of nasopharyngeal swab specimens by quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR) to detect SARS-CoV-2, saliva specimens may be an alternative diagnostic sample.1-4 Rigorous evaluation is needed to determine how saliva specimens compare with nasopharyngeal swab specimens with respect to sensitivity in detection of SARS-CoV-2 during the course of infection.

A total of 70 inpatients with Covid-19 provided written informed consent to participate in our study (see the Methods section in Supplementary Appendix 1, available with the full text of this letter at). After Covid-19 was confirmed with a positive nasopharyngeal swab specimen at hospital admission, we obtained additional samples from the patients during hospitalization. We tested saliva specimens collected by the patients themselves and nasopharyngeal swabs collected from the patients at the same time point by health care workers.



Using primer sequences from the Centers for Disease Control and Prevention, we detected more SARS-CoV-2 RNA copies in the saliva specimens (mean log copies per milliliter, 5.58; 95% confidence interval [CI], 5.09 to 6.07) than in the nasopharyngeal swab specimens (mean log copies per milliliter, 4.93; 95% CI, 4.53 to 5.33) (Figure 1A, and Fig. S1 in Supplementary Appendix 1).

In addition, a higher percentage of saliva samples than nasopharyngeal swab samples were positive up to 10 days after the Covid-19 diagnosis (Figure 1B). At 1 to 5 days after diagnosis, 81% (95% CI, 71 to 96) of the saliva samples were positive, as compared with 71% (95% CI, 67 to 94) of the nasopharyngeal swab specimens. These findings suggest that saliva specimens and nasopharyngeal swab specimens have at least similar sensitivity in the detection of SARS-CoV-2 during the course of hospitalization.

Because the results of testing of nasopharyngeal swab specimens to detect SARS-CoV-2 may vary with repeated sampling in individual patients,5 we evaluated viral detection in matched samples over time. The level of SARS-CoV-2 RNA decreased after symptom onset in both saliva specimens (estimated slope, −0.11; 95% credible interval, −0.15 to −0.06) (Figure 1C) and nasopharyngeal swab specimens (estimated slope, −0.09; 95% credible interval, −0.13 to −0.05) (Figure 1D).

In three instances, a negative nasopharyngeal swab specimen was followed by a positive swab at the next collection of a specimen (Figure 1D); this phenomenon occurred only once with the saliva specimens (Figure 1C). During the clinical course, we observed less variation in levels of SARS-CoV-2 RNA in the saliva specimens (standard deviation, 0.98 virus RNA copies per milliliter; 95% credible interval, 0.08 to 1.98) than in the nasopharyngeal swab specimens (standard deviation, 2.01 virus RNA copies per milliliter; 95% credible interval, 1.29 to 2.70) .

Recent studies have shown that SARS-CoV-2 can be detected in the saliva of asymptomatic persons and outpatients. We therefore screened 495 asymptomatic health care workers who provided written informed consent to participate in our prospective study, and we used RT-qPCR to test both saliva and nasopharyngeal samples obtained from these persons.

We detected SARS-CoV-2 RNA in saliva specimens obtained from 13 persons who did not report any symptoms at or before the time of sample collection. Of these 13 health care workers, 9 had collected matched nasopharyngeal swab specimens by themselves on the same day, and 7 of these specimens tested negative (Fig. S2). The diagnosis in the 13 health care workers with positive saliva specimens was later confirmed in diagnostic testing of additional nasopharyngeal samples by a CLIA (Clinical Laboratory Improvement Amendments of 1988)–certified laboratory.


Variation in nasopharyngeal sampling may be an explanation for false negative results, so monitoring an internal control for proper sample collection may provide an alternative evaluation technique. In specimens collected from inpatients by health care workers, we found greater variation in human RNase P cycle threshold (Ct) values in nasopharyngeal swab specimens (standard deviation, 2.89 Ct; 95% CI, 26.53 to 27.69) than in saliva specimens (standard deviation, 2.49 Ct; 95% CI, 23.35 to 24.35).

When health care workers collected their own specimens, we also found greater variation in RNase P Ct values in nasopharyngeal swab specimens (standard deviation, 2.26 Ct; 95% CI, 28.39 to 28.56) than in saliva specimens (standard deviation , 1.65 Ct; 95% CI, 24.14 to 24.26) (Fig. S3).

Collection of saliva samples by patients themselves negates the need for direct interaction between health care workers and patients. This interaction is a source of major testing bottlenecks and presents a risk of nosocomial infection. Collection of saliva samples by patients themselves also alleviates demands for supplies of swabs and personal protective equipment. Given the growing need for testing, our findings provide support for the potential of saliva specimens in the diagnosis of SARS-CoV-2 infection.

The clinical performance of saliva compared with nasopharyngeal swabs (NPSs) has shown conflicting results in healthcare and community settings. In the present study, a total of 429 matched NPS and saliva sample pairs, collected in either healthcare or community setting, were evaluated. Phase-1 (protocol U) tested 240 matched NPS and saliva sample pairs; phase 2 (SalivaAll protocol) tested 189 matched NPS and saliva sample pairs, with an additional sample homogenization step before RNA extraction.


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A total of 85 saliva samples were evaluated with both protocols. In phase-1, 28.3% (68/240) samples tested positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from saliva, NPS, or both. The detection rate from saliva was lower compared with that from NPS samples (50.0% versus 89.7%).


In phase-2, 50.2% (95/189) samples tested positive for SARS-CoV-2 from saliva, NPS, or both. The detection rate from saliva was higher compared with that from NPS samples (97.8% versus 78.9%). Of the 85 saliva samples evaluated with both protocols, the detection rate was 100% for samples tested with SalivaAll, and 36.7% with protocol U.

The limit of detection with SalivaAll protocol was 20 to 60 copies/mL. The pooled testing approach demonstrated a 95% positive and 100% negative percentage agreement. This protocol for saliva samples results in higher sensitivity compared with NPS samples and breaks the barrier to using pooled saliva for SARS-CoV-2 testing.

Regional policies have been primarily dictated by the positivity rate in the respective region(s). Thus, rapid and accurate detection of SARS-CoV-2 is the foremost and likely most essential component in controlling this outbreak and has immediate clinical, epidemiologic, and policy implications. Various clinical specimens such as bronchoalveolar lavage, sputum, saliva, nasopharyngeal swabs (NPSs), oropharyngeal swabs (OPSs), feces, and blood have been evaluated for detection of SARS-CoV-2 virus.2 NPS and OPS samples are the current standard upper respiratory tract specimens recommended for COVID-19 diagnostic testing.

However, the collection of NPS samples poses challenges such as exposure risk to healthcare workers, supply chain constraints pertaining to swabs and personal protective equipment, and difficulties with self-collection. Inappropriate sampling may lead to false-negative results.

Amidst the several other sample types under investigation for COVID-19 testing, saliva samples are of significant interest owing to their ease of collection, and ability to alleviate some of the challenges associated with NPS sampling. True saliva is defined as the naturally collecting clear liquid that accumulates in the mouth.

However, saliva from patients can be confounded with the presence of mucus or blood, thereby rendering it difficult to process in the laboratory. Several reports evaluating the clinical performance of saliva compared with NPS/OPS samples have demonstrated conflicting results.

In a healthcare setting, studies have demonstrated comparable and even higher sensitivity of saliva/early morning saliva collection11 compared with NPS samples, as well as reported higher viral titer values in saliva. Conversely, deep-throat saliva12 and typical saliva samples have also been demonstrated to be less sensitive compared with NPS samples in both healthcare13 and community settings. Furthermore, saliva samples are difficult to pipet by the testing personnel, which leads to increased processing time.

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