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

Gobeille Paré, Sarah; Bestman-Smith, Julie; Fafard, Judith; Doualla-Bell, Florence; Jacob-Wagner, Mariève; Lavallée, Christian; Charest, Hugues; Beauchemin, Stéphanie; Coutlée, François; Dumaresq, Jeannot; Busque, Lambert; St-Hilaire, Manon; Lépine, Guylaine; Boucher, Valérie; Desforges, Marc; Goupil-Sormany, Isabelle; Labbé, Annie-Claude

OBJECTIVE 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. METHODS 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 a comparative performance analysis was performed. An individual was considered infected if a positive result was obtained on either sample. RESULTS 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 97.7 to 99.3) for ONPS and 89.6% (95% CI 83.4 to 93.6; p=0.004) for SWG. Mean ONPS cycle threshold (Ct) value was significantly lower for the concordant paired samples as compared to discordant ones (22.9 vs 32.1; p<0.001). CONCLUSION Using an LD-NAAT with thermal lysis, SWG is a less sensitive sampling method than the ONPS. However, the higher acceptability of SWG might enable a higher rate of detection on a population-based perspective. Nonetheless, in patients with a high clinical suspicion of COVID-19, a repeated analysis with ONPS should be considered. The sensitivity of SWG using LD-NAAT preceded by chemical extraction should be evaluated. This article is protected by copyright. All rights reserved.