Comparison of Three Sample-To-Answer RT-PCR Testing Platforms for the Detection of SARS-CoV-2 RNA in Positive Nasopharyngeal and Nasal Swabs

Abstract

Background: 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 XpertV® Xpress SARS-CoV-2 assay were tested on the ePlexV® SARS-CoV-2 and BD SARS-CoV-2 Reagents for BD MaxTM 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 percentage 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 to test substitutions due to its high PPA.