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

Abstract

The urgent need to implement and rapidly expand testing for Severe Acute Respiratory Syndrome Coronavirus‐2 (SARS‐CoV‐2) infection has led to 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 Real‐Time RT‐PCR test (LDT) based on a modified Centers for Disease Control and Prevention (CDC) protocol, for the detection of SARS‐CoV‐2 in samples submitted to the Clinical Laboratories of the Mount Sinai Health System. 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‐CoV2 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‐CoV2 test reported 706 positives and 300 negatives. The LDT reported 640 positives, 323 negatives, 34 inconclusive, and 9 invalids. When excluding inconclusive and invalid results, the overall percent agreement between the two platforms was 95.8%. Cohen's kappa coefficient (κ) was 0.904 (95 % CI 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.