Natural spring water gargle samples as an alternative to nasopharyngeal swabs for SARS‐CoV‐2 detection using a laboratory‐developed test

Abstract

The objective of this study was to validate the use of spring water gargle (SWG) as an alternative to oral and nasopharyngeal swab (ONPS) for SARS-CoV-2 detection with a laboratory-developed test. Healthcare workers and adults from the general population, presenting to one of two COVID-19 screening clinics in Montréal and Québec City, were prospectively recruited to provide a gargle sample in addition to the standard ONPS. The paired specimens were analyzed using thermal lysis followed by a laboratory-developed nucleic acid amplification test (LD-NAAT) to detect SARS-CoV-2, and comparative performance analysis was performed. An individual was considered infected if a positive result was obtained on either sample. A total of 1297 adult participants were recruited. Invalid results (n = 18) were excluded from the analysis. SARS-CoV-2 was detected in 144/1279 (11.3%) participants: 126 from both samples, 15 only from ONPS, and 3 only from SWG. Overall, the sensitivity was 97.9% (95% CI: 93.7-99.3) for ONPS and 89.6% (95% CI: 83.4-93.6; p = 0.005) for SWG. The mean ONPS cycle threshold (C t ) value was significantly lower for the concordant paired samples as compared to discordant ones (22.9 vs. 32.1;

Evaluation of water gargle samples for SARS‐CoV‐2 detection using Abbott ID NOW COVID‐19 assay

“…Limitations of our study include a possible overestimation of the performance by using gargle as SOC for NAAT, which is associated with lesser sensitivity than using standard NPS 6 . On the other hand, we may have underestimated the performance of gargle samples on ID NOW by comparing to PCR assays, rather than comparing two different sampling methods directly on ID NOW (side by side study compared with nasal swab obtained at the same time of gargle sample).…”

“…There is also no risk of spillage adding this volume of sample in the blue sample receiver, since there is enough space to add more than 500 µl without interfering with the transfer cartridge process. Water gargle samples have been shown as an adequate alternative to NPS in previous studies 5,6,12,14 . Even if viral RNA concentrations is lower in gargle samples compared to NPS, 5,6 the improved patient acceptability and the ease of the sampling protocols are benefits that likely exceed the slight loss of clinical sensitivity of the method 13 .…”

“…Commercial assays are: Simplexa™ COVID‐19 Direct Kit (DiaSorin Molecular LLC), cobas® SARS‐CoV‐2 performed with the cobas®6800/8800 systems (Roche), and Allplex™ 2019‐nCoV assay with thermal lysis (Seegene). Laboratory developed tests (LDTs) targeting the structural protein envelope E gene were performed on LightCycler® 480 II Instrument (Roche) and CFX96 Touch Real‐Time PCR System (BioRad) after thermal lysis or RNA extraction using NucliSens easyMAG (bioMérieux) as previously described 4,6 . Samples were considered positive if they met the interpretation criteria of the manufacturer or if C t values were ≤40 for LDTs.…”

“…In the three institutions, water gargle samples are acceptable specimens for SARS‐CoV‐2 detection by NAAT for routine COVID‐19 testing. Gargle samples were collected as described before 5,6,14 . Briefly, patients were asked not to eat, drink, or smoke for 15 min before sampling.…”

“… 3 Nasal swab, saliva, or water mouth rinse/gargle have been the most studied alternative specimens for SARS‐CoV‐2 detection by RT‐PCR. 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 In the province of Québec, natural spring water gargle has been extensively used for SARS‐CoV‐2 detection following the G‐SPIT study that showed acceptable performance compared to oronasopharyngeal swab, particularly for symptomatic patients. 6 , 14 , 15…”