Comparison of SARS-CoV-2 detection with the cobas® 6800/8800 system on gargle samples using two sample processing methods with combined oropharyngeal/nasopharyngeal swab

BACKGROUND: Gargle samples have been proposed as a non-invasive method for detection of SARS-CoV-2 RNA. The clinical performance of gargle specimens diluted in cobas® PCR Media and in cobas® Omni Lysis Reagent was compared to oropharyngeal/nasopharyngeal swab (ONPS) for the detection of SARS-CoV-2 RNA. STUDY DESIGN: Participants were recruited prospectively in two COVID-19 screening clinics. In addition to the ONPS, participants gargled with 5 mL of natural spring water split in the laboratory as follows: 1 mL was added to 4.3 mL of PCR Media and 400 μL was added to 200 μL of lysis buffer. Testing was performed with the cobas® SARS-CoV-2 test on the cobas® 6800 or 8800 platforms. RESULTS: Overall, 134/647 (20.7%) participants were considered infected because the ONPS or at least one gargle tests was positive. ONPS had respectively a sensitivity of 96.3% (95%CI 91.3-98.5); both gargle processing methods were slightly less but equally sensitive [90.3% (95%CI 83.9-94.3)]. When ONPS and gargle specimens were both positive, the mean cycle threshold (Ct) was significantly higher for gargles, suggesting lower viral loads. CONCLUSION: Gargle specimens directly added in PCR Media provides a similar clinical sensitivity to chemical lysis, both having a slightly, not significantly, lower sensitivity to ONPS. This article is protected by copyright. All rights reserved.