What sample to test for COVID-19: nasopharyngeal or buccal?
Text updated on 2020-06-03
Oral swabs are preferable because they allow for autonomous sampling, are easier, and are less dangerous in terms of contamination. The United States, Japan, Switzerland, Australia, Italy, and the United Kingdom use them.
Although the nasopharyngeal swab has been the reference test since the beginning of the epidemic, many countries are taking advantage of oral swabs, which carry less risk to the sampler and do not require personal protective equipment.
Numerous studies, carried out in Italy, Australia, Hong Kong, Bangkok, Japan, and the United States (Connecticut and California) show that the SARS-CoV-2 coronavirus is detectable in oral swabs for several weeks after the onset of symptoms and in the saliva of asymptomatic cases. After fluidification and extraction of the viral RNA, the detection sensitivity is as good as with nasopharyngeal swabs since the viral load is high and the same PCR technique is used. It is recommended that the patient be kept rested for 2 hours prior to collection. Under these conditions, the coronavirus typically remains in saliva for 4-5 weeks, longer than what is typically found in the nasal swab.
In practice, oral swabs are taken in several ways:
- with a pipette that collects saliva without spitting,
- saliva is held in the mouth for several minutes before spitting,
- a mouthwash with a solution,
- a throat scraping before spitting in order to get a salivary spit.
Sputum appears to be the most reliable means of detecting SARS-CoV-2, but systematic comparative studies have yet to be done. Since SARS-CoV-2 resides in the airways, salivary sputum would allow the collection of oral and bronchial fluids in the same sample, thus increasing the chances of coronavirus detection.
Oral swabs have practical advantages over nasopharyngeal swabs:
(1) It is very easy to collect saliva or sputum. This sample can be given by those being tested, including children, without exposing others to the coronavirus. In contrast, nasopharyngeal swabbing is delicate and invasive and can cause pain or discomfort. It often leads to sneezing or coughing, which exposes the person taking the sample to a significant risk of contamination and forces him/her to protect themself. It is difficult to offer the nasopharyngeal swab repeatedly.
(2) no specific equipment is required for saliva collection. Nasopharyngeal sampling equipment (swabs) and sample protection equipment (gown, FFP2 mask, gloves, cap) is a limiting factor for large-scale testing.
Several recent good studies show that viral load is as high in saliva as nasopharyngeal swabbing between asymptomatic and symptomatic cases, and detection in asymptomatic cases is as good in saliva as the nasal swab. For an easy, contamination-free, and less invasive screening test: choose saliva!
A large number of viral particles are found in the saliva collected by the patients themselves in Hong Kong. This number decreases during the course of the disease and then disappears 8-10 days after the first symptoms. Out of 23 patients, 3 tested negative for the virus in their saliva. In this particular study, the PCR test was a home-made test and the saliva was collected in the morning after clearing the throat and coughing.To, K. K. W., Tsang, O. T. Y., Yip, C. C. Y., Chan, K. H., Wu, T. C., Chan, J. M. C., ... & Lung, D. C. (2020). Consistent detection of 2019 novel coronavirus in saliva. Clinical Infectious Diseases.
In Melbourne, out of 622 patients, 39 tested positive on nasopharyngeal swabs (NPS) and 33 of the 39 were also positive on saliva. Of the 50 negative PNPs, one was positive in saliva. In this study, patients held their saliva for 1 to 2 min and then spat out 1 to 2 mL. 85% of the PNP-positive patients had SARS-Cov-2 virus detected in their saliva by the PNP test. The amount of RNA detected was less in saliva than in the nasal swab. However, the results of PCR tests cannot be directly compared as they are not done in exactly the same way. In particular, the saliva must first be diluted in a fluidizing buffer prior to extracting the viral RNA. And in most studies like this one, the authors do not standardize their results with a sample control (a human gene quantified by PCR that allows one to know the number of human cells harvested in the sample).Williams, E., Bond, K., Zhang, B., Putland, M., & Williamson, D. A. (2020). Saliva as a non-invasive specimen for detection of SARS-CoV-2. Journal of Clinical Microbiology
The saliva of 25 seriously ill patients in the COVID-19 Intensive Care Unit in Varese (Italy) contained a large number of copies of the SARS-Cov-2 virus. In this study, the saliva was recovered using a pipette placed in the patient's mouth. For two of the patients the saliva was positive, but not PNP which, therefore, appears to be a less sensitive test. A recent study of this Italian group confirms two other patients who were saliva positive but PNP negative.Azzi, L., Carcano, G., Gianfagna, F., Grossi, P., Dalla Gasperina, D., Genoni, A., ... & Maurino, V. (2020). Saliva is a reliable tool to detect SARS-CoV-2. Journal of Infection.
The sensitivity and specificity of the saliva RT-PCR test were 84% and 99%, respectively, using the PNP test as a reference, in 200 patients at a Bangkok hospital. In this study, the buccal swab was recovered after forced coughing.Pasomsub, E., Watcharananan, S. P., Boonyawat, K., Janchompoo, P., Wongtabtim, G., Suksuwan, W., ... & Phuphuakrat, A. (2020). Saliva sample as a non-invasive specimen for the diagnosis of coronavirus disease-2019 (COVID-19): a cross-sectional study. Clinical Microbiology and Infection.
In a group of patients (88) and non-hospitalized convalescents (24) from California, the sensitivity of the saliva test was compared to that of the PNP test. Of the 88 patients, 98% were PNP positive and 69% were saliva positive. Of the 24 convalescents, 4 were saliva positive and PNP positive, 5 were PNP positive but saliva negative and 1 was saliva negative. Limitations of this study include the lack of clinical data on patients, the fact that the tests were performed at three sites and that saliva was collected from two different kits. Lu, J., Becker, D., Sandoval, E., Amin, A., De Hoff, P., Leonetti, N., ... & Grzymski, J. (2020). Saliva is less sensitive than nasopharyngeal swabs for COVID-19 detection in the community setting. medRxiv.Lu, J., Becker, D., Sandoval, E., Amin, A., De Hoff, P., Leonetti, N., ... & Grzymski, J. (2020). Saliva is less sensitive than nasopharyngeal swabs for COVID-19 detection in the community setting. medRxiv.
In 76 subjects (10 patients and 66 suspects), saliva was collected in a tube and the virus detected by PCR. 8 of the 10 patients were PNP positive and saliva positive, 1 PNP positive and saliva negative, and 1 PNP negative and saliva positive.Iwasaki, S., Fujisawa, S., Nakakubo, S., Kamada, K., Yamashita, Y., Fukumoto, T., ... & Hayasaka, K. (2020). Comparison of SARS-CoV-2 detection in nasopharyngeal swab and saliva. medRxiv.
A meta-analysis of about ten articles on the detection of SARS-Cov-2 in saliva, highlighting the difficulty of comparison given the variations in extraction methods, PCR with the use of various kits and the quality of samples: saliva, sputum or oropharyngeal samples.Santosh, T. S., Parmar, R., Anand, H., Srikanth, K., & Saritha, M. (2020). A review of salivary diagnostics and its potential implication in detection of Covid-19. Cureus, 12(4).
The start-up, CURATIVE, in Los Angeles has received approval from the Food and Drug Administration (FDA) for 24-hour testing of oral fluids, targeting one million tests per week. The test is also expected to be used in the UK. The Food and Drug Administration (FDA) had already approved the first SARS-CoV-2 test on saliva samples developed by Rutgers University in New Jersey. A dedicated kit is sent to the patient, who spits several times and returns it within 48 hours to Rutgers Clinical Genomics Laboratory, which then performs the PCRs.Start-up Curative.
In France, the SKILLCELL consortium, the CNRS SYS2DIAG laboratory, and VOGO announce the industrialization of EasyCov, a saliva screening test to be marketed in France and Europe in June. In less than an hour! The test is performed on saliva mixed with reagents and incubated at 65°C for 30 min.L'Helgouach, N, Champigneux, P, Santos Schneider, F, Molina, L, Espeut, J, Alali, M, Baptiste, J, Cardeur, L, Dubuc, B, Foulongne, V, Galtier, F, Makinson, A, Marin, G, Picot, MC, Prieux-Lejeune, A, Quenot, M, Robles, FC, Salvetat, N, Vetter, D, Reynes, J, Molina, F. EasyCOV: LAMP based rapid detection of SARS-CoV-2 in saliva.
This study reports the comparison of salivary and nasopharyngeal swabs on 145 samples simultaneously collected on the day of diagnosis, and 2 and 7 days afterwards. Of the 145 specimens, 19 specimens were positive for saliva and 19 for nasopharyngeal. From these specimens, saliva acts like a mucus that is very easy to collect on its own and is at least as sensitive as the nasopharyngeal specimen for the detection of CoV-2-SARS.Byrne, RL, Kay, GA, Kontogianni, K, Brown, L, Collins, AM, Cuevas, LE, Ferreira, D, Fraser, AJ, Garrod, G, Hill, H, Menzies, S, Mitsi, E, Owen, SI, Williams, CT, Hyder-Wright, A, Adams, ER, Cubas-Atienzar, AI. Saliva offers a sensitive, specific and non-invasive alternative to upper respiratory swabs for SARS-CoV-2 diagnosis. MedRxiv, July 11 2020.
One of the first studies published by the Charity groups in Germany shows that the results on PNP and sputum are very similar (all 7 patients are followed up over time after the onset of symptoms). Note that the virus remains in the sputum after the end of symptoms and that the coronavirus was not found infectious in the stool. Detection of the virus in saliva and respiratory secretions may take longer than the symptoms:Wölfel, R, Corman, VM, Guggemos, W, Seilmaier, M, Zange, S, Müller, MA, Niemeyer, D, Jones, TC, Vollmar, P, Rothe, C, Hoelscher, M, Bleicker, T, Brünink, S, Schneider, J, Ehmann, R, Zwirglmaier, K, Drosten, C, & Wendtner, C. Virological assessment of hospitalized patients with COVID-2019. Nature volume 581, pages 465-469 (2020).
A meta-analysis of about ten articles on the detection of SARS-CoV-2 in saliva, highlighting the difficulty of comparison given the variations in extraction methods, PCR with the use of various kits and the quality of samples: saliva, sputum, or oropharyngeal samples.Santosh, T. S., Parmar, R., Anand, H., Srikanth, K., & Saritha, M. (2020). A review of salivary diagnostics and its potential implication in detection of Covid-19. Cureus, 12(4).
Start-up CURATIVE in Los Angeles has received approval from the Food and Drug Administration (FDA) for 24-hour testing of oral fluids, targeting one million tests per week. The test is also expected to be used in the UK. The Food and Drug Administration (FDA) had already approved the first test of SARS-CoV-2 on saliva samples developed by Rutgers University in New Jersey.A dedicated kit is sent to the patient who spits several times and then sends it back within 48 hours to Rutgers Clinical Genomics Laboratory which then performs the PCRs.
The EasyCOV detection kit using RT-LAMP after pre-treatment of saliva allows the detection of SARS-CoV-2 in 40 min with a sensitivity of 87.5% according to their first study carried out on 220 people.A total of 720 people should be integrated by the end of the study.
Researchers at Yale University show that saliva tests are more sensitive than those performed on nasopharyngeal samples (n = 70 patients COVID):Wyllie, A. L., Fournier, J., Casanovas-Massana, A., Campbell, M., Tokuyama, M., Vijayakumar, P., ... & Petrone, M. E. (2020). Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs. New England Journal of Exp. Medicine, Sept 24 2020, 383: 1283-1286.
The virus is stable in saliva for more than a week at room temperature, more than 2 weeks at 4°C and months in the freezer at -80°C. These observations suggest that a simple and inexpensive collection system is possible:Ott, IM, Strine, MS, Watkins, AE, Boot, M, Kalinich, CC, Harden, CA, Vogels, CBF, Casanovas-Massana, A, Moore, AJ, Muenker, MC, Nakahata, M, Tokuyama, M, Nelson, A, Fournier, J, Bermejo, S, Campbell, M, Datta, R, Dela Cruz, CS, Farhadian, SF, Ko, AI, Iwasaki, A, Grubaugh, ND, Wilen, CB, Wyllie, AL. Simply saliva: stability of SARS-CoV-2 detection negates the need for expensive collection devices.
The French COVISAL study conducted in the Amazonian forest in French Guiana in the field under poorly explained conditions reveals variations between groups sampled under laboratory conditions (Yale University, Hokkaido University) and in the field. This study based on 25 asymptomatic cases contradicts several international studies. Nevertheless, at the end of September 2020, it led the French National Authority for Health to carry out saliva tests only on people with symptoms.Nacher, M, Mergeay-Fabre, M, Blanchet, D, Benois, O, Pozl, T, Mesphoule, P, Sainte-Rose, V, Vialette, V, Toulet, B, Moua, A, Simon, S, Guidarelli, M, Galindo, M, Biche, B, Faurous, W, Abad, F, Fahrasmane, A, Rochemont, D, Vignier, N, Vabret, A, Demar, M. COVISAL Guyane, Nacher, M, Demar, M. Prospective comparison of saliva and nasopharyngeal swab sampling for mass screening for COVID-19.
Pooling the samples within a household could optimize the detection of infected outbreaks in the population:Hogan, C. A., Sahoo, M. K., & Pinsky, B. A. (2020). Sample Pooling as a Strategy to Detect Community Transmission of SARS-CoV-2. JAMA.
A recent Japanese study with 55 asymptomatic COVID cases shows that saliva is a very effective method of collecting samples to detect SARS-CoV-2, even in asymptomatic patients:92% sensitivity for salivary sampling and 86% for nasopharyngeal sampling, with a 99.8% probability of agreement. The tests were carried out on more than 1,950 people in contact or on arrival at airports: Yokota, I, Shane, P, Okada, K, Unoki, Y, Yang Y, Tasuku, I, Sakamaki, K, Iwasaki, S, Hayasaka, K, Sugita, J, Nishida, M, Fujisawa, S, Teshima, T. (2020). Mass screening of asymptomatic persons for SARS-CoV-2 using saliva. 10.1101/2020.08.13.20174078.
A Japanese study of 103 positive cases comparing different RT-qPCR systems and one RT-LAMP system concludes that the sensitivity of RT-qPCR is better. Note that in this study there was no pre-treatment of saliva prior to RT-LAMP, which could affect the results obtained.Ikeda, M, Imai, K, & Tabata, S, Miyoshi, K, Mizuno, T, Murahara, N, Horiuchi, M, Kato, K, Imoto, Y, Iwata, M, Mimura, S, Ito, T & Tamura, K, Kato, Y. (2020). Clinical evaluation of self-collected saliva by RT-qPCR, direct RT-qPCR, RT-LAMP, and a rapid antigen test to diagnose COVID-19. 10.1101/2020.06.06.20124123.
Tests grouped from 5 to 20 in saliva samples by the Yale University team also behind the SalivaDirect test:Watkins, A. E., Fenichel, E. P., Weinberger, D. M., Vogels, C. B., Brackney, D. E., Casanovas-Massana, A., ... & Cruz, C. S. D. (2020). Pooling saliva to increase SARS-CoV-2 testing capacity. medRxiv.
The University of Illinois in Urbana-Champaign has been developing saliva pooling tests for all its staff since the summer of 2020 and has carried out more than 800,000 saliva tests with RT-qPCR as of November 14, 2020. If a pool is positive, the PCR test is done for each person in the pool.Ranoa, DR, Holland, RL, Alnaji, FG, Green, KJ, Wang, L, Brooke, CB, Burke, MD, Fan, TM, Hergenrother, PJ. Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Extraction. https://www.biorxiv.org/content/10.1101/2020.06.18.159434v1
A surveillance program on the Duke University campus in the United States discovered by testing students with their saliva several COVID-19 cases, 50% of whom were asymptomatic with sometimes high viral loads.Denny TN, Andrews L, Bonsignori M, et al. Implementation of a Pooled Surveillance Testing Program for Asymptomatic SARS-CoV-2 Infections on a College Campus - Duke University, Durham, North Carolina, August 2-October 11, 2020. MMWR Morb Mortal Wkly Rep. ePub: 17 November 2020. DOI: http://dx.doi.org/10.15585/mmwr.mm6946e1external icon