Detection of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) in outpatients: A multicenter comparison of self-collected saline gargle, oral swab, and combined oral–anterior nasal swab to a provider collected nasopharyngeal swab

Abstract

Background: Widespread testing for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) is necessary to curb the spread of coronavirus disease 2019 (COVID-19), but testing is undermined when the only option is a nasopharyngeal swab. Self-collected swab techniques can overcome many of the disadvantages of a nasopharyngeal swab, but they require evaluation. Methods: Three self-collected non-nasopharyngeal swab techniques (saline gargle, oral swab and combined oral-anterior nasal swab) were compared to a nasopharyngeal swab for SARS-CoV-2 detection at multiple COVID-19 assessment centers in Toronto, Canada. The performance characteristics of each test were assessed. Results: The adjusted sensitivity of the saline gargle was 0.90 (95% CI 0.86-0.94), the oral swab was 0.82 (95% CI, 0.72–0.89) and the combined oral–anterior nasal swab was 0.87 (95% CI, 0.77–0.93) compared to a nasopharyngeal swab, which demonstrated a sensitivity of ˜90% when all positive tests were the reference standard. The median cycle threshold values for the SARS-CoV-2 E-gene for concordant and discordant saline gargle specimens were 17 and 31 (P < .001), for the oral swabs these values were 17 and 28 (P < .001), and for oral–anterior nasal swabs these values were 18 and 31 (P = .007). Conclusions: Self-collected saline gargle and an oral–anterior nasal swab have a similar sensitivity to a nasopharyngeal swab for the detection of SARS-CoV-2. These alternative collection techniques are cheap and can eliminate barriers to testing, particularly in underserved populations.

One swab, two tests: Validation of dual SARS-CoV-2 testing on the Abbott ID NOW™

“…This study met the criteria of a quality improvement project in accordance with institutional guidelines. One swab was stored in McMaster Molecular Medium (MMM) (Bay Area Health Trustee Corp, Canada), a guanidine thiocyanate-based viral inactivation medium for rRT-PCR testing [12] , and the second was kept dry in a sterile 50 mL conical tube (Corning Inc., USA) for ID NOW™ testing. Individuals collecting specimens were advised to store the dry swabs for 1 hour at room temperature or 2-8 °C for up to 24 hours if delays in transport were anticipated.…”

“…All SARS-CoV-2 testing was performed at the Shared Hospital Laboratory (Toronto, Canada). Real-time RT-PCR testing to detect the E gene and UTR of SARS-CoV-2 was performed as previously described [ 11 , 12 ] . Testing with the ID NOW™ COVID-19 assay was performed as per manufacturer's recommendations (Abbott Diagnostics Inc, USA), with dry swabs being inoculated into the elution buffer within the Sample Receiver cartridge.…”

“…As this assay is designed for use at the point-of-care, testing may be performed by healthcare providers that are not experienced working with live virus. Prior to rRT-PCR assays, SARS-CoV-2 is typically inactivated using heat (65˚C for 30 minutes) or lysis solutions to avoid the biosafety risks associated with aerosol generation [11] , [12] , [13] . This combination of variables presents logistical challenges for specimens requiring transport between sites and could lead to COVID-19 cases evading laboratory detection, requiring a second swab that adds to patient discomfort and laboratory testing volumes.…”

Detection of SARS-CoV-2 infection in gargle, spit and sputum specimens

“…Previously, gargle specimens have also been estimated sensitive for SARS-CoV-2 infection diagnosis compared to NPS including 50 inpatients (26) and outpatients (10,27) with confirmed COVID-19. Ct values of gargle specimens were higher than in NPS in these three studies including one with 19 620 outpatients which is in line with findings in our study (10,26,27).…”

“…Previously, gargle specimens have also been estimated sensitive for SARS-CoV-2 infection diagnosis compared to NPS including 50 inpatients (26) and outpatients (10,27) with confirmed COVID-19. Ct values of gargle specimens were higher than in NPS in these three studies including one with 19 620 outpatients which is in line with findings in our study (10,26,27). Interestingly Goldfard et al, when analyzing 40 COVID-19 outpatients concluded that gargle specimens had higher sensitivity compared to saliva specimens (97.5 % CI 86.8-99.9 % compared to 78.8 CI 95 % 61.0-91.0 %) which is inconsistent with our results, although saliva collection methods were similar (10).…”