Nasopharyngeal swab vs. saliva for COVID-19 diagnosis

One thing has become apparent in the ongoing pandemic of COVID-19. Early diagnosis and treatment, when necessary, is crucial to prevent the progression of the disease to critical and life-threatening stages where the mortality rate is much higher than otherwise. Rapid diagnosis is also key to containing outbreaks by allowing for efficient contact tracing in hospitals as well as in communities.

Study: Comparison of SARS-CoV-2 detection in nasopharyngeal swab and saliva. Image Credit: Cryptographer / Shutterstock
Study: Comparison of SARS-CoV-2 detection in nasopharyngeal swab and saliva. Image Credit: Cryptographer / Shutterstock

A new study on the preprint server medRxiv* in May 2020 compares the reliability of testing results obtained from saliva vs nasopharyngeal swabs (NPS), suggesting the feasibility of relying on the former as a quicker and easier way of obtaining test specimens with a lower risk of exposure and less need for training and protective equipment.

The rationale for using NPS specimens for the diagnosis of COVID-19 by RT-PCR is the abundance of angiotensin-converting enzyme 2 (ACE2) receptors in the upper respiratory tract.

However, ACE2 is also found at high levels on the tongue, which explains why the mouth is a prime site for infection with the virus, how the saliva can pass on the infection even before symptoms appear, and the occurrence of ageusia. This indicates the high possibility of using saliva for the diagnosis of COVID-19, with even better sensitivity than NPS.

The current study is aimed at exploring the diagnostic value of the two sample types in a prospectively designed manner.

Comparing paired NPS and saliva specimens

The researchers collected pairs of specimens, one NPS and one saliva, from all suspected COVID-19 cases as well as from patients referred with the diagnosis of COVID-19, and tested by RT-PCR.

There were 33 patients, 9 with confirmed disease, and 24 suspected cases. Most of the former subgroup had mild or moderate symptoms. The median age was 70 years.

The median day of sample collection for confirmed patients was 10 days from symptom onset. All NPS samples in this group of 9 were positive for the virus, and in 90% of cases, in saliva as well. The one negative saliva sample came 19 days after symptoms appeared.

The mean viral load was 6.1 and 4.2 in NPS and saliva, respectively. This was due to the later time of collection in many patients. At earlier time points, the viral load was equivalent in both groups.

All patients were put on favipiravir, and PCR was done after symptomatic relief to assess the possible date of discharge. All samples (11/27) within two weeks of symptom onset were positive in both types of specimens, but not in all cases after this point. It would appear that saliva loses viral positivity earlier than NPS specimens.

What did the study find?

Of 27 NPS and saliva samples taken from 24 suspected patients, both types of specimen were found to be negative for the virus in all cases.

The researchers quote similarly impressive rates of viral positivity in saliva samples, in studies from different parts of the world, including Hong Kong, Italy, New Haven, and Australia. They comment, “Taken together, these results consistently support the use of saliva as an effective alternative to nasopharyngeal swabs for diagnosis and screening of COVID-19.”

It is known that the viral load in saliva is highest at the onset of symptoms, especially over the first week. It then goes down with time. The current study confirms these findings, with the virus being detectable in all saliva specimens taken within two weeks of the first symptom.

Assessing virus clearance using saliva testing

Using PCR, live, and dead virus cannot be distinguished. Studies from South Korea suggest that the persistence of dead viral particles in the nasopharynx could result in false positives.

On the other hand, the current study suggests that PCR results become negative in saliva earlier than in NPS, which could mean that the saliva clears dead viral particles from the mouth more efficiently. This could make saliva testing a better way to examine the clearance of the virus from the body in COVID-19 cases.

Two other studies making the same comparison found conflicting results. Whereas one declared a higher viral load in saliva compared to NPS, the other determined that the sensitivity of detection was lower for saliva, using CT as a reference.

Sensitivity of saliva vs. NPS

The current study points out that the timing of specimen collection is a factor in determining test positivity. At earlier time points, both saliva and NPS show equivalent rates of positive results, but this changes as time elapses from symptom onset.

Some reasons could include the difference in timing of sampling since no samples were taken in the first week from symptom onset when the salivary viral load is the highest. Variations in the sampling method could also be a factor in the observed differences in sample sensitivity.

For instance, the current study used 1 mL of saliva compared to a third of a cup in another study. NPS collection methodology, however, remained highly repeatable and reliable in the current study, unlike in some others. The use of favipiravir may also have played a role in rapid viral clearance from the oral cavity.

The investigators summarize: “Given the large benefits of saliva collection that does not require health worker specialists and protective equipment, our results together with recent studies support the use of saliva as a noninvasive alternative to nasopharyngeal swabs to greatly facilitate widespread PCR testing.”

*Important Notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:
Dr. Liji Thomas

Written by

Dr. Liji Thomas

Dr. Liji Thomas is an OB-GYN, who graduated from the Government Medical College, University of Calicut, Kerala, in 2001. Liji practiced as a full-time consultant in obstetrics/gynecology in a private hospital for a few years following her graduation. She has counseled hundreds of patients facing issues from pregnancy-related problems and infertility, and has been in charge of over 2,000 deliveries, striving always to achieve a normal delivery rather than operative.


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