Comparison of SARS‐CoV‐2 detection from nasopharyngeal swab samples by the Roche cobas 6800 SARS‐CoV‐2 test and a laboratory‐developed real‐time RT‐PCR test

• Published in: Journal of Medical Virology 2020-09, Vol.92 (9), p.1695-1698
• Main Authors: Pujadas, Elisabet, Ibeh, Nnaemeka, Hernandez, Matthew M., Waluszko, Aneta, Sidorenko, Tatyana, Flores, Vanessa, Shiffrin, Biana, Chiu, Numthip, Young‐Francois, Alicia, Nowak, Michael D., Paniz‐Mondolfi, Alberto E., Sordillo, Emilia M., Cordon‐Cardo, Carlos, Houldsworth, Jane, Gitman, Melissa R.
• Format: Article
• Language: English
• Subjects: Assaying; Confidence intervals; coronavirus; Coronaviruses; COVID-19; COVID-19 - diagnosis; COVID-19 - virology; Discordance; Disease control; Humans; Infections; Laboratories; Nasopharynx - virology; Platforms; Polymerase chain reaction; Prevention; Reagent Kits, Diagnostic; Reproducibility of Results; Respiratory diseases; Reverse Transcriptase Polymerase Chain Reaction - instrumentation; Reverse Transcriptase Polymerase Chain Reaction - methods; Reverse transcription; RNA extraction; RNA, Viral; SARS; SARS-CoV-2 - classification; SARS-CoV-2 - genetics; SARS-CoV-2 - isolation & purification; Sensitivity and Specificity; Severe acute respiratory syndrome coronavirus 2; Short Communication; Short Communications; Statistical analysis; Statistical methods; Viral diseases; Virology
• ISSN: 0146-6615; 1096-9071
• DOI: 10.1002/jmv.25988

The urgent need to implement and rapidly expand testing for severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) infection has led to the development of multiple assays. How these tests perform relative to one another is poorly understood. We evaluated the concordance between the Roche Diagnostics cobas 6800 SARS‐CoV‐2 test and a laboratory‐developed test (LDT) real‐time reverse transcription‐polymerase chain reaction based on a modified Centers for Disease Control and Prevention protocol, for the detection of SARS‐CoV‐2 in samples submitted to the Clinical Laboratories of the Mount Sinai Health System. A total of 1006 nasopharyngeal swabs in universal transport medium from persons under investigation were tested for SARS‐CoV‐2 as part of routine clinical care using the cobas SARS‐CoV‐2 test with subsequent evaluation by the LDT. Cycle threshold values were analyzed and interpreted as either positive (“detected” or “presumptive positive”), negative (not detected), inconclusive, or invalid. Statistical analysis was performed using GraphPad Prism 8. The cobas SARS‐CoV‐2 test reported 706 positive and 300 negative results. The LDT reported 640 positive, 323 negative, 34 inconclusive, and 9 invalid results. When excluding inconclusive and invalid results, the overall percent agreement between the two platforms was 95.8%. Cohen's κ coefficient was 0.904 (95% confidence interval, 0.875‐0.933), suggesting almost perfect agreement between both platforms. An overall discordance rate of 4.2% between the two systems may reflect differences in primer sequences, assay limit of detection, or other factors, highlighting the importance of comparing the performance of different testing platforms. Highlights In this study, we compared the detection of SARS‐CoV‐2 in clinical samples from patients being evaluated for CoVID‐19 infection by two different RT‐PCR assays, the cobas® 6800 SARS‐CoV‐2 test from Roche Molecular Systems and a laboratory‐developed test (LDT) using the Centers for Disease Control and Prevention 2019‐nCoV primers and probes. Overall there was excellent agreement between the two tests methods, although our results suggest that the cobas® SARSCoV‐2 test may have a lower limit of detection than the LDT.