From April 16 through May 19, 2020, sample collection was conducted at one Assessment Center in Ontario, Canada. Standardized testing, in the form of a nasopharyngeal or oropharyngeal swab, was performed in individuals that qualified for testing based on public health recommendations. We enrolled consecutive adults (over 18 years of age) for saliva testing who were asymptomatic high-risk persons or who demonstrated mild symptoms suggestive of COVID-19, and were able to provide a saliva sample of at least 1 mL. Demographic data, including patient age and gender was collected for descriptive statistics. All participants provided informed consent.
Participants were provided with a printed description of the study. Study participation did not alter the standard of care. Only the results from the standard swab were made available to participants.
Standard swabs and saliva samples were collected from participants meeting the study eligibility criteria during a single visit to the testing center. Standardized tests were collected by a certified healthcare provider. Standard swabs were transported in universal transport medium to ensure RNA stability until testing was performed. Use of nasopharyngeal or oropharyngeal swabs was based on resource availability at the testing center. Swab collection and testing was completed as per the government of Ontario protocol and no member of the research team was involved.
Saliva samples of at least 1 mL were collected using OMNIgene•ORAL, OM-505 by DNA Genotek, Inc. according to standard technique. OMNIgene•ORAL, OM-505 kits are designed for saliva selfcollection without expert assistance and can be stored at room temperature with no degradation of viral material over 21 days (1, 2) . Participants were instructed how to collect saliva samples and were guided through each step to ensure samples were collected using clean techniques.
Specifically, participants were instructed how to open the cap on the test kit, expectorate saliva into the tube, and close the cap. A preservative/viricidal fluid mixture was automatically released into the sealed saliva sample and mixed vigorously with the sample such that RNA stability was maintained until testing was performed. Each saliva sample was coded with a patient-specific study number and stored at the Ottawa Hospital Research Institute (Ottawa, Canada). The individuals collecting the standard swabs and saliva samples were blinded to the test results.
Testing was split between two laboratories to accommodate the demand for testing resources within the pandemic context. Standard swabs were analyzed at the Eastern Ontario Regional (3). The E gene screening assay is a widely accepted and highly sensitive target gene for SARS-CoV-2 (4). Saliva samples with an E assay cycle threshold value less than 37, were repeated and followed by confirmation with an assay to detect RdRp gene according to the National Microbiology Laboratory of Canada testing guidelines.
Since the performance of multi-target and single-target PCR assays adds some complexity and testing methods differed across laboratories, a direct comparison was performed of the target E gene with a cycle threshold value less than 37 in the saliva and standard swab samples.
The study was reviewed and approved by the Ottawa Hospital Research Ethics Board (CRRF ID: 2102) as well as the Health Canada-Public Health Agency of Canada REB (2020-005P). The study was supported by The Ottawa Hospital Academic Medical Organization COVID-19 Innovation Project. The granting agency was not involved in the design, conduct, or analysis of this study, or in the decision to submit the manuscript for publication. OMNIgene•ORAL, OM-505, saliva collection kits were donated by DNA Genotek, Inc. DNA Genotek, Inc was not involved in the design, conduct, or analysis of this study, or in the decision to submit the manuscript for publication.
Continuous variables were displayed as median and interquartile range and categorical variables were reported as counts and percentages. The proportion of positive cases in the population was defined as any positive RT-PCR results from either standard swab or saliva sample. That is, a positive saliva test was assumed to be a true positive that was missed by swab testing. Data was analyzed using R Studio version 1.2.5042 (R Studio Team, Boston, USA).