Comparison of Two Commercial Platforms and a Laboratory-Developed Test for Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) RNA

Abstract

Mitigation of the ongoing coronavirus disease 2019 (COVID-19) pandemic requires reliable and accessible laboratory diagnostic services. In this study, the performance of one laboratory-developed test (LDT) and two commercial tests, cobas SARS-CoV-2 (Roche) and Amplidiag COVID-19 (Mobidiag), were evaluated for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in respiratory specimens. A total of 183 specimens collected from suspected COVID-19 patients were studied with all three methods to compare their performance. In relation to the reference standard, which was established as the result obtained by two of the three studied methods, the positive percent agreement was highest for the cobas test (100%), followed by the Amplidiag test and the LDT (98.9%). The negative percent agreement was lowest for the cobas test (89.4%), followed by the Amplidiag test (98.8%), and the highest value was obtained for the LDT (100%). The dilution series of positive specimens, however, suggests significantly higher sensitivity for the cobas assay in comparison with the other two assays, and the low negative percent agreement value may be due to the same reason. In general, all tested assays performed adequately. Clinical laboratories need to be prepared for uninterrupted high-throughput testing during the coming months to mitigate the pandemic. To ensure no interruption, it is critical that clinical laboratories maintain several simultaneous platforms in their SARS-CoV-2 nucleic acid testing.

Figure 1

Flowchart of the samples analyzed in this study. Altogether, 237 samples were collected. Fifty-four samples that were positive for other respiratory viruses were used to evaluate the analytical specificity of the three methods. A total of 183 samples sent for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) analyses were collected, 37 in the early phase of the epidemic in Finland and a further 146 in the late phase of the epidemic. These 183 samples were tested with each of the three methods evaluated.

Figure 2

Comparison of the performance of the three studied methods using a dilution series in Copan UTM or 0.9% saline tubes. A known positive sample was diluted in either a pooled Copan-collected negative specimen or saline-collected negative specimen. A: Cobas SARS-CoV-2 test results. The test was positive for both targets at dilution 1:20,000 for both Copan and saline samples. Target 2 was detected with both tubes still in dilution 1:100,000. B: Amplidiag COVID-19 results. The Amplidiag test was positive for both targets in Copan and saline tubes at 1:200 dilutions, but at 1:1000 and 1:2000, only in Copan tubes (positive for both targets at 1:1000 and only N gene positive at 1:2000). No target was detected at dilutions 1:10,000 to 1:100,000. C: Laboratory-developed test (LDT) assay. No target was detected at dilutions 1:2000 to 1:100,000. The y axis is modified to show only C_T values 24 to 40 to allow for a better visualization of the differences.