Comparison of SARS-CoV-2 detection from combined nasopharyngeal/oropharyngeal swab samples by a laboratory-developed real-time RT-PCR test and the Roche SARS-CoV-2 assay on a cobas 8800 instrument

J Clin Virol. 2020 Nov;132:104615. doi: 10.1016/j.jcv.2020.104615. Epub 2020 Sep 4.

Abstract

Objective: Although several assays have been developed to detect SARS-CoV-2 RNA in clinical specimens, their relative performance is unknown.

Methods: The concordance between the cobas 8800 SARS-CoV-2 and a laboratory developed (LD) reverse transcriptase-polymerase chain reaction (RT-PCR) assay was assessed on 377 combined nasopharyngeal/oropharyngeal swabs in Hanks medium.

Results: The positive and negative agreement between these assays were 99.3 % (95 % CI, 97.3-99.9) and 77.1 % (95 % CI, 67.7-84.4), respectively, for an overall agreement of 93.6 % (95 % CI, 90.7-95.7) beyond random chance (kappa of 0.82, 95 % CI, 0.75-0.85). Of the 22 samples positive by cobas SARS-CoV-2 only, 9 were positive only for ORF-1 gene and had Cycle thresholds (Ct) > 35.1, 8 were positive only for the E gene with Ct > 35.5 and 5 were positive for both targets with Ct > 33.9. Samples positive only with the cobas assay were more often positive with only one gene target (77.3 %) than samples positive in both assays (16.9 %, p < 0.0001). Ct values in the cobas SARS-CoV-2 assay were significantly higher in the 279 samples testing positive in both assays (32.9 %, 95 % CI 32.3-33.6) compared to the 22 samples with discordant results (36.6 %, 95 % CI 36.2-37.1; p = 0.0009). An excellent correlation (r2 = 0.98) was obtained between Ct values of the ORF-1 and E targets in the cobas assays and a good correlation was obtained between LD RT-PCR test and cobas SARS CoV-2 ORF-1 target (r2 = 0.82).

Conclusion: Our study demonstrated an excellent concordance between a LD RT-PCR and the cobas SARS-CoV-2 tests on the 8800 platform.

Keywords: Cobas; Real time PCR; SARS-Cov-2.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • COVID-19 / diagnosis*
  • COVID-19 Testing / methods*
  • Humans
  • Limit of Detection
  • Molecular Diagnostic Techniques
  • Nasopharynx / virology
  • Oropharynx / virology
  • Reverse Transcriptase Polymerase Chain Reaction / methods*
  • SARS-CoV-2 / genetics*