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.