#BIOFIRE DIAGNOSTICS SOFTWARE#

Performance comparison between the SARS-CoV-2 component of the BioFire RP2.1 assay and reference SARS-CoV-2 assays Linear regression was performed in GraphPad Prism 8 (version 8.4.1).ģ.1. A standard curve was generated to estimate the quantity of viral RNA in NP swab specimens based on LDT Ct values.

#BIOFIRE DIAGNOSTICS SOFTWARE#

The QuantStudio Dx and QuantStudio Test Development Software version 1.0.3 (Applied Biosystems, Foster City, CA) were used for thermal cycling and data acquisition. The EDX SARS-CoV-2 RNA standard (Exact Diagnostics), which contains quantitated synthetic RNA transcripts comprised of five SARS-CoV-2 gene targets (E, N, ORF1ab, RdRp, and S) was diluted in Ambion RNA storage solution (ThermoFisher Scientific) to 5000, 2000, 1000, 500, 250, and 125 RNA copies/mL and extracted in triplicate. For all samples in which amplification of the E gene target was not detected, successful RNA extraction was confirmed by an identical PCR reaction using primers and probe specific for the cellular RNaseP gene that have been described by the Centers for Disease Control and Prevention. RNA was extracted from 400 μL of sample using a KingFisher Flex automated extractor and the MagMAX Viral/Pathogen Nucleic Acid Isolation Kit (Applied Biosystems) and eluted in 50 μL. Additional NPS specimens collected before December 2019 and therefore presumed to be negative for SARS-CoV-2 were provided by BioFire Diagnostics.Ĭonventional RT-PCR testing was performed by a Nebraska Medicine LDT for SARS-CoV-2 E gene detection adapted from Corman 600 nM and 800 nM concentrations of the forward and reverse primers, respectively, were used.

Specimens were frozen upon study enrollment to allow for storage and shipping.

Original specimen testing for SARS-CoV-2 was conducted according to manufacturer’s instructions at ARUP laboratories using the Hologic Panther Fusion SARS-CoV-2 assay (FDA EUA), at the University of Nebraska Medical Center using the Roche cobas SARS-CoV-2 assay (FDA EUA), or at the University of Washington using a laboratory developed test based on the CDC N1 and N2 SARS-CoV-2 assays (Washington EUA) conducted as described in Perchetti et al. Residual natural nasopharyngeal swab in transport media (NPS) specimens leftover from SARS-CoV-2 testing performed as part of patient care were collected during March and April of 2020 at the University of Washington (Seattle, WA), University of Nebraska Medical Center (Omaha, NE), and ARUP laboratories (Salt Lake City, UT). In this study, we clinically evaluated the BioFire RP2.1 SARS-CoV-2 assay in comparison to three other SARS-CoV-2 EUA assays.Ģ.1. It therefore detects 22 viral and bacterial respiratory pathogens including SARS-CoV-2. The BioFire RP2.1 was created by adding primers for the membrane (M) and spike (S) genes of SARS-CoV-2 to the existing FDA-cleared and CE-marked BioFire® Respiratory Panel 2 (RP2) test. BioFire recently received FDA Emergency Use Authorization (EUA) to distribute the syndromic BioFire® Respiratory Panel 2.1 (RP2.1) for use on BioFire® FilmArray® 2.0 and BioFire® Torch Systems. This multiplex, sample-to-answer, nucleic acid amplification platform utilizes syndromic panels for infectious disease diagnosis. The BioFire® FilmArray® System (BioFire Diagnostics, LLC, Salt Lake City, UT, “BioFire”) is another testing platform that is widely used in multiple laboratory environments. To date, the BioFire COVID-19, Cepheid Xpert Xpress SARS-CoV-2, DiaSorin Simplexa and the GenMark ePlex SARS-CoV-2 tests have emerged as rapid COVID19 testing platforms that fill this niche.

As SARS-CoV-2 prevalence increases, decentralized testing capability is needed to facilitate rapid identification of SARS-CoV-2 cases. This has led to the centralization of SARS-CoV-2 testing, meaning that turnaround time may be prolonged by the need to transport specimens over long distances. High-throughput platforms are mostly utilized in larger reference laboratories, state public health laboratories, and academic medical centers, but these assays are not well-suited to use in other settings that lack large testing volumes or the capacity to perform high complexity tests. Sample-to-answer nucleic acid amplification assays for the detection of SARS-CoV-2 RNA are available for a limited number of high-throughput diagnostic platforms including the Roche cobas 6800/8800, the Hologic Panther and Panther Fusion, ,, ], and the Abbott m2000. The gold standard for SARS-CoV-2 diagnosis is detection of viral RNA in nasopharyngeal (NP) swab specimens.

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