Clinical Evaluation of Three Sample-to-Answer Platforms for Detection of SARS-CoV-2

Abstract

17Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has now spread across the 18 globe. As part of the worldwide response, many molecular diagnostic platforms have been granted 19Emergency Use Authorization (EUA) by the Food and Drug Administration (FDA) to identify SARS-CoV-2 20 positive patients. Our objective was to evaluate three sample-to-answer molecular diagnostic platforms 21 (Cepheid Xpert® Xpress SARS-CoV-2 [Xpert Xpress], Abbott ID NOW™ COVID-19 [ID NOW], GenMark 22 ePlex® SARS-CoV-2 Test [ePlex]) to determine analytical sensitivity, clinical performance, and workflow 23 for the detection of SARS-CoV-2 in nasopharyngeal swabs from 108 symptomatic patients. We found 24 that the Xpert Xpress had the lowest limit of detection (100% detection at 100 copies/mL), followed by 25 the ePlex (100% detection at 1,000 copies/mL), and the ID NOW (20,000 copies/mL). The Xpert Xpress 26 also had highest positive percent agreement (PPA) when compared to our reference standard (98.3%) 27 followed by the ePlex (91.4%) and ID now (87.7%). All three assays showed 100% negative percent 28 agreement (NPA). In the workflow analysis, the ID NOW produced the most rapid time to result per 29 specimen (~17 minutes) as compared to the Xpert Xpress (~46 minutes) and the ePlex (~1.5 hours), but 30 what the ID NOW gained in rapid results, it lost in analytical and clinical performance. The ePlex had the 31 longest time to results and showed a slight improvement in PPA over the ID NOW. Information about 32 the clinical and analytical performance of these assays, as well as workflow, will be critical in making 33 informed and timely decisions on testing platform. 34 35

Comparison of the Accula SARS-CoV-2 Test with a Laboratory-Developed Assay for Detection of SARS-CoV-2 RNA in Clinical Nasopharyngeal Specimens

“…Of the multiple EUA assays for diagnosis of SARS-CoV-2, only the Xpert Xpress, the ID NOW, and the Accula are CLIA-waived (6). Recent data support the test performance of the Cepheid Xpert SARS-CoV-2 assay, with agreement over 99% compared to high-complexity EUA assays (8, 16, 17). In contrast, some studies have raised concern regarding the diagnostic accuracy of the ID NOW, with positive percent agreement ranging from 75-94% compared to reference assays (8–10, 18).…”

“…Recent data support the test performance of the Cepheid Xpert SARS-CoV-2 assay, with agreement over 99% compared to high-complexity EUA assays (8, 16, 17). In contrast, some studies have raised concern regarding the diagnostic accuracy of the ID NOW, with positive percent agreement ranging from 75-94% compared to reference assays (8–10, 18). Given the poor diagnostic performance of the ID NOW, and uncertainty regarding availability of Xpert Xpress cartridges, the Accula system has been tauted as an interesting POCT alternative but data were previously lacking on its clinical performance.…”

“…The Accula SARS-CoV-2 test is a POCT that requires only 30 minutes from sample to answer and utilizes the existing palm-sized Accula dock system originally developed for rapid influenza and RSV testing. Despite the multiple potential benefits of POC assays, concern has been raised regarding their lower sensitivity for COVID-19 diagnosis compared to standard high complexity molecular based tests (8–10). It remains unclear whether this decreased sensitivity is due to test validation studies being limited to in silico predictions and contrived samples using reference materials, as is the case currently for the Accula SARS-CoV-2 test.…”

SARS-CoV2 Testing: The Limit of Detection Matters

“…This method can be used to estimate the clinical sensitivity of assays with other LoDs. For example, an assay with LoD of 1,000 copies/mL, such as that of the CDC assay (8) or Genmark ePlex EUA (9), is expected to detect 77%, or 3 in 4, of infected individuals, for a false-negative rate of 22%. With an LoD of 6,250 copies/mL, the LabCorp COVID-19 RT-PCR EUA test has an estimated clinical sensitivity of 67% and a false-negative rate of 33%, missing approximately 1 in 3 infected individuals.…”

Analytical and Clinical Comparison of Three Nucleic Acid Amplification Tests for SARS-CoV-2 Detection

“…The majority of the SARS-CoV-2 NAAT tests available today are based on real time reverse transcription polymerase chain reaction (RT-PCR) methods, including the BioFire Diagnostics COVID-19 test (BioFire) and the Hologic Panther Fusion SARS-CoV-2 assay (Fusion) evaluated in the present study. Clinical comparative data have been obtained for the Fusion assay ( 6, 7, 8, 9 ), but to our knowledge there have been no comparative studies of the BioFire assay. Recently, Hologic has developed a second NAAT, the Aptima SARS-CoV-2 assay (Aptima), which has been submitted to the Food and Drug Administration (FDA) for Emergency Use Authorization (EUA); this NAAT is based on target capture and transcription-mediated amplification (TMA) technologies and is run on the Panther instrument.…”