Salivary Detection of COVID-19
Authors: Lisa Caulley, Martin Corsten, Libni Eapen, Jonathan Whelan, Jonathan B. Angel, Kym Antonation, Nathalie Bastien, Guillaume Poliquin, Stephanie Johnson-Obaseki
Journal: Annals of Internal Medicine (2020)

Letters28 August 2020Salivary Detection of COVID-19FREELisa Caulley, MD, MPH, Martin Corsten, MD, Libni Eapen, MD, Jonathan Whelan, BSc, Jonathan B. Angel, MD, Kym Antonation, MPH, Nathalie Bastien, PhD, Guillaume Poliquin, MD, PhD*, and Stephanie Johnson-Obaseki, MD, MPH*Lisa Caulley, MD, MPHUniversity of Ottawa and Ottawa Hospital Research Institute, Ottawa, Ontario, Canada (L.C., J.B.A.)Search for more papers by this author, Martin Corsten, MDDalhousie University, Halifax, Nova Scotia, Canada (M.C.)Search for more papers by this author, Libni Eapen, MDUniversity of Ottawa, Ottawa, Ontario, Canada (L.E., J.W., S.J.)Search for more papers by this author, Jonathan Whelan, BScUniversity of Ottawa, Ottawa, Ontario, Canada (L.E., J.W., S.J.)Search for more papers by this author, Jonathan B. Angel, MDUniversity of Ottawa and Ottawa Hospital Research Institute, Ottawa, Ontario, Canada (L.C., J.B.A.)Search for more papers by this author, Kym Antonation, MPHNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada (K.A., N.B.)Search for more papers by this author, Nathalie Bastien, PhDNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada (K.A., N.B.)Search for more papers by this author, Guillaume Poliquin, MD, PhD*National Microbiology Laboratory, Public Health Agency of Canada, and University of Manitoba, Winnipeg, Manitoba, Canada (G.P.)Search for more papers by this author, and Stephanie Johnson-Obaseki, MD, MPH*University of Ottawa, Ottawa, Ontario, Canada (L.E., J.W., S.J.)Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/M20-4738 SectionsSupplemental MaterialAboutVisual AbstractPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail Background: Standard testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires a nasopharyngeal or oropharyngeal swab but is limited by modest sensitivity, the need for health care human resources and personal protective equipment, and the potential for transmission in transit to or at the testing center. An urgent need exists for innovative testing strategies to expedite identification of cases and facilitate mass testing.Objective: To determine the detection rate of SARS-CoV-2 using a novel, self-administered kit for saliva collection compared with standard swab testing.Methods: We prospectively enrolled consecutive, asymptomatic, high-risk persons and those with mild symptoms suggestive of coronavirus disease 2019 (COVID-19) at a centralized testing center in Ottawa, Canada. Eligible adults provided 1 saliva specimen using a self-collection kit (OMNIgene•ORAL, OM-505 [DNA Genotek]) concurrent with their standard swab test. These kits are designed for self-collection without expert assistance and can preserve viral material at room temperature for transport and analysis (1). Total nucleic acid extraction and polymerase chain reaction analysis for SARS-CoV-2 were done at the Eastern Ontario Regional Laboratory in Ottawa for swabs and at the National Microbiology Laboratory in Winnipeg for saliva. Outcomes were reported for detection of the SARS-CoV-2 envelope (E) gene with a cycle threshold value less than 37. The Supplement provides additional methodological details.Findings: Of the 1939 paired swab and saliva samples analyzed (Figure), SARS-CoV-2 E gene was detected in 70 samples (Table), 80.0% with swabs and 68.6% with saliva. Thirty-four participants (48.6%) tested positive for SARS-CoV-2 on both swab and saliva samples. Discordant test results were seen in 22 participants (31.4%) who tested positive with swab alone and in 14 (20%) who tested positive with saliva alone. Swabs were obtained from the nasopharynx in 35.7% of participants who tested positive with saliva alone, compared with 9.1% of participants who tested positive with swab alone.Figure. Study flow diagram.Standard swab and saliva sample collection during the study period. COVID-19 = coronavirus disease 2019.* Inclusion criteria were age ≥18 y, provision of informed consent, and being high-risk asymptomatic or having mild symptoms of COVID-19. Patients were screened before entry by a physician. Those with severe symptoms were redirected to an emergency department for formal clinical evaluation.† Eight participants were tested twice at the testing center (for both standard swab and saliva sample). Two tested positive on their initial oropharyngeal swab and negative on a saliva sample. These participants' results remained positive on an oropharyngeal swab and negative on a saliva sample on repeated testing (5 d and 8 d later). One participant tested positive on the initial oropharyngeal swab and negative on the saliva sample. This participant tested negative on both specimens 7 d later. The remaining 6 participants tested negative on initial and repeated testing for both specimens. Download figure Download PowerPoint Table. Characteristics of Population That Tested Positive for SARS-CoV-2Discussion: Our study found that standard diagnostic methods of nasopharyngeal and oropharyngeal swabs detected more COVID-19 cases than saliva testing among patients who were asymptomatic but at high risk or who were mildly symptomatic. Salivary detection of SARS-CoV-2 has been proposed as an alternative to standard swab diagnostic methods. Saliva testing presents potential advantages: Collection does not require trained staff or personal protective equipment, can be done outside testing centers, and may be better tolerated in challenging or pediatric populations.Because of RNA instability, use of raw saliva necessitates rapid transportation to a laboratory for extraction of viral material and polymerase chain reaction analysis. This study is unique in that it used a novel collection kit containing a preservative and viricidal fluid, allowing for safe and stable storage and transport of the samples. Our findings add to those of previous studies, which have focused on salivary tests of symptomatic or hospitalized patients (2); these studies have suggested that saliva tests may be more sensitive. By design, we included asymptomatic and mildly symptomatic persons to simulate mass screening for COVID-19.Our study has important limitations. First, evaluating the performance of a novel diagnostic test in the absence of a true gold standard reference is challenging. The reported false-negative rate of reverse transcriptase polymerase chain reaction–based testing for SARS-CoV-2 using swabs is approximately 38% at symptom onset and as high as 100% shortly after exposure (3). In our study, 20% of COVID-19 cases were detected by saliva alone, further supporting the notion that standard swab testing may be an unreliable reference standard. Second, nasopharyngeal or oropharyngeal swabbing was done according to swab availability at the testing center even though nasopharyngeal swabs are preferred in symptomatic persons and those later in the illness course (4), which may have affected our results. Analyses of the influence of swab site on study results were not done because of limited sample size. Third, analysis of swab and saliva samples was split between 2 laboratories to accommodate the demand for testing resources in a pandemic. The potential effect of assay differences was mitigated by a targeted evaluation of the E gene, a widely accepted and sensitive target gene for SARS-CoV-2 (5). Finally, more than half of eligible patients declined participation.Nonetheless, our study shows the feasibility of a simple, safe collection tool for salivary detection of SARS-CoV-2 in the setting of a COVID-19 testing center. Despite a lower estimated rate of detection relative to swab testing, saliva testing may be of particular benefit for remote, vulnerable, or challenging populations.References1. Wasserman JK, Rourke R, Purgina B, et al. HPV DNA in saliva from patients with SCC of the head and neck is specific for p16-positive oropharyngeal tumours. J Otolaryngol Head Neck Surg. 2017;46:3. [PMID: 28061890] doi:10.1186/s40463-016-0179-6 CrossrefMedlineGoogle Scholar2. Czumbel LM, Kiss S, Farkas N, et al. Saliva as a candidate for COVID-19 diagnostic testing: a meta-analysis. Front Med (Lausanne). 2020;7:465. doi:10.3389/fmed.2020.00465 CrossrefMedlineGoogle Scholar3. Kucirka LM, Lauer SA, Laeyendecker O, et al. Variation in false-negative rate of reverse transcriptase polymerase chain reaction–based SARS-CoV-2 tests by time since exposure. Ann Intern Med. 2020;173:262-267. doi:10.7326/M20-1495 LinkGoogle Scholar4. Patel MR, Carroll D, Ussery E, et al. Performance of oropharyngeal swab testing compared to nasopharyngeal swab testing for diagnosis of COVID-19—United States, January-February 2020. Clin Infect Dis. 2020. [PMID: 32548635] doi:10.1093/cid/ciaa759 CrossrefGoogle Scholar5. Corman VM, Landt O, Kaiser M, et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. 2020;25. [PMID: 31992387] doi:10.2807/1560-7917.ES.2020.25.3.2000045 CrossrefMedlineGoogle Scholar Comments 0 Comments Sign In to Submit A Comment Burton AbramsNo institutional affiliation28 August 2020 Discrimination of swab analysis Can processing of either the nasal swabs or saliva swabs discriminate between RNA from active viruses vs. inactive viruses? Emmah StevensonNo institutional affiliation20 March 2021 Selection of Participants How were subjects selected for this study? Author, Article, and Disclosure InformationAuthors: Lisa Caulley, MD, MPH; Martin Corsten, MD; Libni Eapen, MD; Jonathan Whelan, BSc; Jonathan B. Angel, MD; Kym Antonation, MPH; Nathalie Bastien, PhD; Guillaume Poliquin, MD, PhD; Stephanie Johnson-Obaseki, MD, MPHAffiliations: University of Ottawa and Ottawa Hospital Research Institute, Ottawa, Ontario, Canada (L.C., J.B.A.)Dalhousie University, Halifax, Nova Scotia, Canada (M.C.)University of Ottawa, Ottawa, Ontario, Canada (L.E., J.W., S.J.)National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada (K.A., N.B.)National Microbiology Laboratory, Public Health Agency of Canada, and University of Manitoba, Winnipeg, Manitoba, Canada (G.P.)Acknowledgment: The authors thank Jill Allan, RN, BN, of the Ottawa Hospital Research Institute for her clinical and methodological assistance to the investigators as a clinical research assistant; John Trickett, RN, for facilitating the research study as Clinical Director of The Ottawa Hospital and the COVID-19 Assessment Center; H. Chaim Birnboim, MD, MSc, former Chief Scientific Officer at DNA Genotek, for his expertise in the functionality of the saliva collection kits; Karamchand Ramotar, PhD, Associate Professor of Pathology and Laboratory Medicine at the University of Ottawa, for his guidance and collaboration in comparing saliva samples with the swab reference standard from the Eastern Ontario Regional Laboratory Association; Rafal Iwasiow, PhD, of DNA Genotek for his vital contribution of saliva collection kits and expertise in their functionality; and Stephanie Burke Schinkel, MSc, of the Ottawa Hospital Research Institute for her valuable assistance to the investigators.Disclosures: Authors have disclosed no conflicts of interest. Forms can be viewed at www.acponline.org/authors/icmje/ConflictOfInterestForms.do?msNum=M20-4738.Reproducible Research Statement: Study protocol: Not available. Statistical code and data set: Available from Dr. Johnson-Obaseki (e-mail, stjohnson@toh.ca).Corresponding Author: Stephanie Johnson-Obaseki, MD, MPH, Ottawa Hospital Research Institute, Department of Otolaryngology - Head and Neck Surgery, University of Ottawa, S3, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada; e-mail, stjohnson@toh.ca.This article was published at Annals.org on 28 August 2020.* Drs. Poliquin and Johnson-Obaseki contributed equally to this work. 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