Comparison of three sample-to-answer RT-PCR testing platforms for the detection of SARS-CoV-2 RNA in positive nasopharyngeal and nasal swabs

Luethy, Paul M; Johnson, J Kristie

INTRODUCTION: The COVID-19 pandemic has strained clinical microbiology laboratories due to testing supply allocations. As a result, laboratories have had to invest in multiple COVID-19 assays performed on different testing instruments. Comparing the results achieved by testing positive samples between in-use assays can provide insights into which platforms may be interchangeable for testing in times of supply chain emergencies. METHODS: Nasopharyngeal and nasal swab specimens collected in viral transport media that tested positive on the Xpert® Xpress SARS-CoV-2 assay were tested on the ePlex® SARS-CoV-2 and BD SARS-CoV-2 Reagents for BD Max™ assays. Positive percent agreement was calculated using the Xpert® Xpress SARS-CoV-2 assay as the reference method. RESULTS: We tested 78 positive swabs, resulting in a positive percent agreement (PPA) of 92% [CI 84-97%] for the BD SARS-CoV-2 assay and 58% [CI 47-70%] for the ePlex® assay. Following development of a new workflow for the ePlex®, we detected SARS-CoV-2 in 7 additional samples, resulting in a new PPA of 68% [CI 56-78]. CONCLUSIONS: During times of supply allocation and shortage of the Xpert® Xpress SARS-CoV-2 assay, the BD SARS-CoV-2 assay is well suited for test substitutions due to its high positive percent agreement.