Search Results

The Aptima® SARS-CoV-2 Assay is a nucleic acid amplification in vitro diagnostic test intended for the qualitative detection of RNA from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolated and purified from nasopharyngeal (NP) swab and anterior nasal (AN) swab specimens obtained from patients with signs and symptoms of COVID-19.

Positive results are indicative of the presence of SARS-CoV-2 RNA. The Aptima SARS-CoV-2 Assay is intended for use as an aid in the diagnosis of COVID-19 if used in conjunction with other clinical, epidemiological, and laboratory findings. Clinical correlation with patient history and other diagnostic information is necessary to determine patient infection status. Positive results do not rule out bacterial infection or co-infection with other viruses.

Negative results do not preclude SARS-CoV-2 infection and should not be used as the sole basis for patient management decisions. Negative results must be combined with clinical observations, patient history, and epidemiological information.

The Aptima SARS-CoV-2 Assay is a nucleic acid amplification in vitro diagnostic test developed for use on the fully automated Panther/Panther Fusion system to detect RNA from SARS-CoV-2 isolated and purified from nasopharyngeal and anterior nasal swab specimens collected into UTM/VTM or with the RespDirect Collection Kit.

The Aptima SARS-CoV-2 Assay combines the technologies of target capture, Transcription Mediated Amplification (TMA), and Dual Kinetic Assay (DKA).

Specimens are collected and transferred into their respective specimen transport tubes. The transport solutions in these tubes release the RNA target and protect them from degradation during storage. When the Aptima SARS-CoV-2 Assay is performed in the laboratory, the target RNA molecules are isolated from specimens by use of capture oligomers via target capture that utilizes magnetic microparticles. The capture oligomers contain sequences complementary to specific regions of the target molecules as well as a string of deoxyadenosine residues. A separate capture oligomer is used for each target. During the hybridization step, the sequence specific regions of the capture oligomers bind to specific regions of the target molecules. The capture oligomer:target complex is then captured out of solution by decreasing the temperature of the reaction to room temperature. This temperature reduction allows hybridization to occur between the deoxyadenosine region on the capture oligomer and the poly-deoxythymidine molecules that are covalently attached to the magnetic particles. The microparticles, including the captured target molecules bound to them, are pulled to the side of the reaction vessel using magnets and the supernatant is aspirated. The particles are washed to remove residual specimen matrix that may contain amplification reaction inhibitors. After the target capture steps are completed, the specimens are ready for amplification.

Target amplification assays are based on the ability of complementary oligonucleotide primers to specifically anneal and allow enzymatic amplification of the target nucleic acid strands. The Aptima SARS-CoV-2 Assay replicates specific regions of the RNA from SARS-CoV-2 virus. Detection of the RNA amplification product sequences (amplicon) is achieved using nucleic acid hybridization. Single-stranded chemiluminescent nucleic acid probes, which are unique and complementary to a region of each target amplicon and Internal Control (IC) amplicon, are labeled with different acridinium ester (AE) molecules. The AE-labeled probes combine with the amplicon to form stable hybrids. The Selection Reagent differentiates hybridized from unhybridized probe, eliminating the generation of signal from the unhybridized probe. During the detection step, light emitted from the labeled hybrids is measured as photon signals in a luminometer and are reported as Relative Light Units (RLU). In DKA, differences in the kinetic profiles of the labeled probes allow for the differentiation of signal; kinetic profiles are derived from measurements of photon output during the detection read time.

The Aptima SARS-CoV-2 Assay amplifies and detects 2 conserved regions of the ORF1ab gene in the same reaction, using the "glower" kinetic type. The 2 regions are not differentiated and amplification of either or both regions lead to RLU signal. The assay results are determined by a cut-off based on the total RLU and the kinetic curve type.

Here's a breakdown of the acceptance criteria and the study that proves the device meets them, based on the provided text:

Acceptance Criteria and Reported Device Performance

The acceptance criteria are implicitly defined by the performance metrics presented as evidence of substantial equivalence to the predicate device. The key metrics are Positive Percent Agreement (PPA) and Negative Percent Agreement (NPA). While explicit numerical acceptance thresholds are not provided in the document, the reported performance demonstrates "comparable" results to the predicate device.

Study Details:

1. Sample Sizes Used for the Test Set and Data Provenance:

   • Clinical Study 1 (NP Swab Specimens):
     • Total Enrolled: 1646 specimens
     • Evaluable (Final Data Set): 1495 NP swab specimens (1195 fresh, 300 frozen)
     • Provenance: Prospective multicenter study from four participating US pediatric/adolescent, private and/or university hospitals. Specimens collected between June-July 2020 and January-April 2023. Remnant specimens.
   • Clinical Study 2 (Anterior Nasal Swab Specimens):
     • Total Enrolled Subjects: 2301
     • Evaluable Subjects: 2177 individuals (1159 with evaluable anterior nasal swab specimens in UTM/VTM, and 1018 with evaluable nasal swab specimens in eSTM).
     • Provenance: Prospective, multicenter clinical study at nine geographically and ethnically diverse US sites during the 2022-2023 respiratory season.

2. Number of Experts Used to Establish the Ground Truth for the Test Set and Qualifications:

   • The document does not specify the number or qualifications of experts directly establishing the clinical ground truth. Instead, it relies on a Composite Comparator Algorithm (CCA). The CCA consists of "two highly sensitive US FDA EUA SARS-CoV-2 molecular tests" and a "validated PCR followed by bi-directional sequencing (PCR/BDS) assay." This implies that the 'expertise' comes from the validation and regulatory clearance of these comparator assays, rather than individual human experts adjudicating each case.

3. Adjudication Method for the Test Set:

   • Composite Comparator Algorithm (CCA): "A final CCA result was assigned when two of the three comparator assay results were in concordance." This serves as the adjudication method for determining the true positive/negative status of the clinical samples.

4. If a Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study Was Done:

   • No. This type of study (MRMC) is typically performed for diagnostic imaging devices where human readers interpret images with and without AI assistance. The Aptima SARS-CoV-2 Assay is an in vitro diagnostic (IVD), a laboratory test that detects nucleic acids, not an imaging device requiring human interpretation of visual data. Therefore, an MRMC study is not applicable here.

5. If a Standalone (i.e., algorithm only without human-in-the-loop performance) Was Done:

   • Yes, this is effectively a standalone performance study. The Aptima SARS-CoV-2 Assay is an automated nucleic acid amplification test run on the Panther/Panther Fusion system. Its performance is directly compared to the CCA, without human intervention in the interpretation of the device's results.

6. The Type of Ground Truth Used:

   • Clinical Studies: Composite Comparator Algorithm (CCA) based on the concordance of results from two highly sensitive FDA EUA SARS-CoV-2 molecular tests and a validated PCR/BDS assay. This is a form of reference standard derived from established and highly sensitive laboratory methods.
   • Analytical Studies (e.g., LoD, Reactivity, Specificity): The ground truth was established by known concentrations of SARS-CoV-2 virus strains or other microorganisms/interfering substances, prepared in controlled laboratory settings (e.g., "spiked with inactivated cultured SARS-CoV-2 virus").

7. The Sample Size for the Training Set:

   • The document describes performance evaluation studies (analytical and clinical) for market clearance. It does not provide information on the specific training set size used for the development or training of the assay's internal algorithms (e.g., for the kinetic curve analysis or cut-off determination). This information would typically be part of the assay development and validation, not necessarily detailed in a 510(k) summary unless it significantly changed or impacted performance during the clearance process for the specific assay rather than the underlying platform. The focus here is on the performance of the final, already "trained" device.

8. How the Ground Truth for the Training Set Was Established:

   • As noted above, details regarding the training set's ground truth establishment are not provided in this 510(k) summary. For IVD devices, ground truth for training internal algorithms typically involves using characterized positive and negative clinical samples, spiked samples with known viral loads, and potentially synthetic data, all carefully confirmed by highly sensitive reference methods or gold standard assays during the R&D phase of the product.

Ask a specific question about this device

cobas® SARS-CoV-2 Qualitative for use on the cobas®5800/6800/8800 Systems is a real-time RT-PCR test intended for the qualitative detection of nucleic acids from SARS-CoV-2 in nasopharyngeal swab specimens collected from individuals with signs and symptoms of COVID-19 and in anterior nasal swab specimens collected from any individuals with or without signs and symptoms of COVID-19.

Positive results are indicative of the presence of SARS-CoV-2 RNA. Positive results do not rule out bacterial infection or co-infection with other pathogens.

Negative results do not preclude SARS-CoV-2 infection and should not be used as the sole basis for patient management decisions. Results are meant to be used in conjunction with clinical observations, patient history, recent exposures, epidemiological information, and laboratory data, in accordance with the guided by the relevant public health authorities.

cobas® SARS-CoV-2 Qualitative is based on fully automated sample preparation (nucleic acid extraction and purification) followed by PCR amplification and detection. The cobas® 5800 System is designed as one integrated instrument. The cobas® 6800/8800 Systems consist of the sample supply module, the transfer module, the processing module, and the analytic module. Automated data management is performed by the cobas® 5800 or cobas® 6800/8800 Systems software(s), which assigns test results for all tests. Results can be reviewed directly on the system screen, and printed as a report.

Nucleic acid from patient samples and added internal control RNA (RNA IC) molecules are simultaneously extracted. Nucleic acid is released by addition of proteinase and lysis reagent to the sample. The released nucleic acid binds to the silica surface of the added magnetic glass particles. Unbound substances and impurities, such as denatured protein, cellular debris and potential PCR inhibitors, are removed with subsequent wash steps and purified nucleic acid is eluted from the magnetic glass particles with elution buffer at elevated temperature. External controls (positive and negative) are processed in the same way.

Selective amplification of target nucleic acid from the sample is achieved by the use of targetspecific forward and reverse primers for ORF1 a/b non-structural region that is unique to SARS-CoV-2. Additionally, a conserved region in the structural protein envelope E-gene were chosen for pan-Sarbecovirus detection. The pan-Sarbecovirus detection sets will also detect SARS-CoV-2 virus.

Selective amplification of RNA Internal Control is achieved by the use of non-competitive sequence specific forward and reverse primers which have no homology with the coronavirus genome. A thermostable DNA polymerase enzyme is used for amplification.

The cobas® SARS-CoV-2 Qualitative master mix contains detection probes which are specific for the coronavirus type SARS-CoV-2, members of the Sarbecovirus subgenus, and the RNA Internal Control nucleic acid. The coronavirus and RNA Internal Control detection probes are each labeled with unique fluorescent dyes that act as a reporter. Each probe also has a second dye which acts as a quencher. When not bound to the target sequence, the fluorescent signals of the intact probes are suppressed by the quencher dye. During the PCR amplification step, hybridization of the probes to the specific single-stranded DNA template results in cleavage of the probe by the 5' to 3' exonuclease activity of the DNA polymerase resulting in separation of the reporter and quencher dyes and the generation of a fluorescent signal. With each PCR cycle, increasing amounts of cleaved probes are generated and the cumulative signal of the reporter dye increases concomitantly. Each reporter dye is measured at defined wavelengths, which enables simultaneous detection and discrimination of the amplified coronavirus target and the RNA Internal Control. The master mix includes deoxyuridine triphosphate (dUTP), instead of deoxythimidine triphosphate (dTTP), which is incorporated into the newly synthesized DNA (amplicon). Any contaminating amplicons from previous PCR runs are destroyed by the AmpErase enzyme [uracil-N-glycosylase], which is included in the PCR mix, when heated in the first thermal cycling step. However, newly formed amplicons are not destroyed since the AmpErase enzyme is inactivated once exposed to temperatures above 55°C.

cobas® SARS-CoV-2 Qualitative is a qualitative nucleic acid test for use on the cobas® 5800/6800/8800 System for the detection of the 2019 novel coronavirus (SARS-CoV-2) RNA in individual nasal and nasopharyngeal swab samples collected in Copan Universal Transport Medium System (UTM-RT), BD™ Universal Viral Transport System (UVT), cobas® PCR Media, or 0.9% physiological saline. The RNA Internal Control, used to monitor the entire sample preparation and PCR amplification process, is introduced into each specimen.

Here's an analysis of the acceptance criteria and the study that proves the device meets them, based on the provided text:

Acceptance Criteria and Device Performance

The acceptance criteria are implicitly defined by the reported performance metrics of the device, which are Positive Percent Agreement (PPA) and Negative Percent Agreement (NPA) against a comparator algorithm. The device needs to demonstrate high agreement for both positive and negative results in asymptomatic individuals.

Table of Acceptance Criteria and Reported Device Performance:

Note: The document does not explicitly state numerical acceptance criteria in a dedicated section. The "acceptance criteria" are inferred from the robust performance demonstrated and the claim of "equivalent performance" to the predicate device.

Study Details for Demonstrating Acceptance Criteria:

The device's performance was evaluated through two clinical studies focusing on asymptomatic populations: the 2020 National Football League (NFL) COVID-19 Surveillance Program and the 2021 Test Us at Home (TUAH) study.

1. NFL COVID-19 Surveillance Program (Real-world evidence)

• Sample Size Used for the Test Set: A total of 1776 samples were selected for analysis.
• Data Provenance: The data was collected from the United States (NFL COVID-19 Surveillance Program participants). It was retrospective as it used data collected between August 2020-January 2021. Samples were prospectively collected for the surveillance program itself.
• Number of Experts Used to Establish Ground Truth & Qualifications: The document does not specify the number or qualifications of experts used for clinical adjudication within the NFL testing program. It mentions a "comparator algorithm that was based on molecular comparator test results and/or clinical adjudication."
• Adjudication Method: Not explicitly stated beyond "clinical adjudication" as part of the comparator algorithm.
• Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study: No, this type of study was not done. This device is a diagnostic test, not an AI-assisted human reading system.
• Standalone Performance: Yes, this study evaluates the standalone performance of the cobas® SARS-CoV-2 Qualitative device against a composite comparator algorithm.
• Type of Ground Truth Used: "molecular comparator test results and/or clinical adjudication performed within the NFL testing program." This indicates a composite ground truth method.
• Sample Size for the Training Set: Not applicable for a clinical performance evaluation study; this is a validation study. The training set for the development of the device itself is not provided in this document.
• How the Ground Truth for the Training Set was Established: Not applicable.

2. Test Us at Home (TUAH) Study (Clinical Study)

• Sample Size Used for the Test Set: 38,192 samples from the TUAH study were included.
• Data Provenance: The data was collected from the United States (TUAH study participants). It was prospective as samples were collected between October 2021 and April 2022 specifically for the longitudinal study.
• Number of Experts Used to Establish Ground Truth & Qualifications: The document does not specify the number or qualifications of experts. The comparator algorithm for this study relies on "two consecutive test results (molecular comparator)."
• Adjudication Method: The comparator algorithm used "two consecutive test results (molecular comparator) over 48 hours" to determine the ground truth. This is a form of algorithmic adjudication based on molecular tests, not human expert adjudication in the traditional sense.
• Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study: No, this type of study was not done.
• Standalone Performance: Yes, this study evaluates the standalone performance of the cobas® SARS-CoV-2 Qualitative device against a composite comparator algorithm based on molecular results.
• Type of Ground Truth Used: Comparator algorithm based on "two consecutive test results (molecular comparator)." This indicates a molecular test-based composite ground truth.
• Sample Size for the Training Set: Not applicable for a clinical performance evaluation study.
• How the Ground Truth for the Training Set was Established: Not applicable.

Summary of In Silico Analysis (Non-Clinical Performance):

• An in-silico analysis was conducted in January 2025 using SARS-CoV-2 sequences from the GISAID database (as of January 15, 2025).
• Sample Size for Test Set: 16,156,883 sequences from the GISAID database.
• Data Provenance: Global (various countries submitting to GISAID). Retrospective, as it used existing sequence data.
• Ground Truth: Bioinformatic analysis of shared viral sequences.
• Results: >99.9% of sequences for SARS-CoV-2 had no changes in primer/probe binding sites at both target regions simultaneously. All sequences were predicted to be detected by at least one of the two targets. This addresses potential variations in the virus that might affect detection.

This document clearly outlines the analytical and clinical performance of the device, particularly focusing on its effectiveness in detecting SARS-CoV-2 in asymptomatic individuals against established comparator methods.

Ask a specific question about this device

The Xpert Xpress CoV-2 plus test, performed on the GeneXpert Xpress System, is a rapid real-time RT-PCR test intended for the qualitative detection of SARS-CoV-2 RNA in nasopharyngeal and anterior nasal swab specimens collected from individuals with signs and symptoms of respiratory tract infection.

The Xpert Xpress CoV-2 plus test is intended for use as an aid in the diagnosis of COVID-19 if used in conjunction with other clinical, epidemiologic, and laboratory findings. Positive results are indicative of the presence of SARS-CoV-2 RNA. Positive results do not rule out bacterial infection or co-infection with other pathogens.

Negative results do not preclude SARS-CoV-2 infection. The results of this test should not be used as for diagnosis and patient management decisions.

The Xpert Xpress CoV-2 plus test is a rapid, automated in vitro diagnostic test for the qualitative detection of viral RNA from SARS-CoV-2 in nasopharyngeal swab (NPS) and anterior nasal swab (NS) specimens collected from individuals with signs and symptoms of respiratory tract infection.

The Xpert Xpress CoV-2 plus test is performed on GeneXpert Xpress System, which consist of a GeneXpert IV instrument that executes sample preparation, nucleic acid amplification and real-time fluorescent signal detection for the tests, and a GeneXpert Hub with preloaded GeneXpert Xpress software for running the tests and viewing the test results. The GeneXpert Hub accessory integrates the computer, touchscreen monitor and barcode scanner. Each of the GeneXpert modules in the GeneXpert IV instrument can perform independent sample preparation and testing. The GeneXpert Xpress System requires the use of single-use disposable cartridges that hold the RT-PCR reagents and host sample purification, nucleic acid amplification, and detection of the target sequences. Because the cartridges are selfcontained, cross-contamination between samples is minimized.

The Xpert Xpress CoV-2 plus test includes reagents for the detection of viral RNA from SARS-CoV-2 in NPS and NS specimens. The primers and probes in the Xpert Xpress CoV-2 plus test are designed to amplify and detect unique sequences in the genes that encode the following SARS-CoV-2 proteins: nucleocapsid (N2), envelope (E), and RNA-dependent RNA polymerase (RdRP). A Sample Processing Control (SPC) and a Probe Check Control (PCC) are also included in the cartridge serving as internal controls. The SPC is present to control for adequate processing of the sample and to monitor for the presence of potential inhibitor(s) in the RT-PCR reaction. The SPC also ensures that the RT-PCR reaction conditions (temperature and time) are appropriate for the amplification reaction and that the RT-PCR reagents are functional. The PCC verifies reagent rehydration, PCR tube filling, and confirms that all reaction components are present in the cartridge including monitoring for probe integrity and dye stability.

The Xpert Xpress CoV-2 plus test is designed for use with NPS or NS specimen collected with nylon flocked swabs and placed into viral transport medium (VTM), Universal Transport Medium (UTM) or eNAT®.

Acceptance Criteria and Study for Xpert Xpress CoV-2 plus

The Xpert Xpress CoV-2 plus test is a rapid real-time RT-PCR test for the qualitative detection of SARS-CoV-2 RNA in nasopharyngeal and anterior nasal swab specimens. The study aims to demonstrate substantial equivalence to a predicate device (K230440) by evaluating its analytical and clinical performance.

1. Table of Acceptance Criteria and Reported Device Performance

2. Sample Sizes and Data Provenance

• Test Set (Clinical Performance):

  • Total specimens: 1783
    • NPS (Nasopharyngeal Swab): 883
    • NS (Anterior Nasal Swab): 900
  • Data Provenance: Prospective clinical specimens collected from individuals showing signs and symptoms of respiratory infection in the United States (22 geographically diverse CLIA-waived sites). Data was collected in 2022.

• Analytical Performance Test Sets:

  • Limit of Detection (LoD):
    • NPS-UTM/VTM: At least 40 replicates (2 reagent lots x 20 replicates)
    • NPS-eNAT: At least 40 replicates (2 reagent lots x 20 replicates)
    • NS-UTM/VTM: At least 40 replicates (2 reagent lots x 20 replicates)
    • WHO First International Standard (NS-UTM/VTM): 20 replicates
  • Analytical Reactivity (Wet-testing): 61 SARS-CoV-2 strains, 3 replicates per strain (total 183 tests).
  • Analytical Specificity (Wet-testing): 62 microorganisms, 3 replicates per organism (total 186 tests).
  • Microbial Interference: 18 commensal microorganisms, 8 replicates per strain (total 144 tests) with SARS-CoV-2.
  • Potentially Interfering Substances: 23 substances, 8 replicates for negative samples and 8 replicates for positive samples (total up to 368 tests, plus re-tests).
  • Carryover Contamination: 40 positive samples, 42 negative samples.
  • Reproducibility: 3 panel members (Negative, Low Pos, Mod Pos), 90 observations per panel member (3 Sites x 3 Operators x 1 Lot x 5 Days x 1 Run x 2 Replicates = 90). Total 270 observations.

3. Number of Experts and Qualifications for Ground Truth (Test Set)

The document does not explicitly state the number of experts used to establish the ground truth for the clinical test set or their specific qualifications (e.g., radiologist with 10 years of experience). However, the ground truth was established by a "U.S. FDA-cleared molecular respiratory panel that included SARS-CoV-2," indicating an established and validated laboratory method. Discrepant results were investigated using a "U.S FDA EUA SARS-CoV-2 molecular test," further relying on FDA-authorized assays as the reference standard.

4. Adjudication Method (Test Set)

The adjudication method used for the clinical test set was a discrepant analysis. "Discrepant results between Xpert Xpress CoV-2 plus and the comparator were investigated using a U.S FDA EUA SARS-CoV-2 molecular test." This implies that for any cases where the Xpert Xpress CoV-2 plus result differed from the initial FDA-cleared comparator panel, a third, independent FDA EUA molecular test was used to determine the true positive or negative status.

5. Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study

There is no MRMC comparative effectiveness study mentioned in the provided text. The study focuses on the standalone performance of the device against a comparator device, not on human reader performance with or without AI assistance.

6. Standalone Performance Study

Yes, a standalone performance study was done. The entire "Performance Studies" section (1.4) details the analytical and clinical performance of the device itself (algorithm only, without human-in-the-loop performance). The clinical performance evaluation directly compares the Xpert Xpress CoV-2 plus test results to those of an FDA-cleared molecular respiratory panel.

7. Type of Ground Truth Used

For the clinical performance study, the ground truth was established by an FDA-cleared molecular respiratory panel and, in cases of discrepancy, by a U.S. FDA EUA SARS-CoV-2 molecular test. This falls under the category of reference standard laboratory testing rather than expert consensus, pathology, or outcomes data.

For analytical performance studies, the ground truth was established by spiking known concentrations/quantities of inactivated SARS-CoV-2 virus, genomic RNA, or other microorganisms into negative matrices, or by using established international standards (e.g., WHO First International Standard).

8. Sample Size for the Training Set

The document does not mention the sample size for the training set. This is a premarket notification (510(k)) and focuses on the performance testing of the final device, not on the developmental or training phases of its underlying algorithm. As a PCR-based diagnostic, it's unlikely to have a "training set" in the same sense as an AI/ML-based device; its analytical performance is determined by the specific primers and probes and their chemical/biological interactions.

9. How the Ground Truth for the Training Set was Established

Since no "training set" is explicit for this PCR diagnostic, there is no information provided on how its ground truth might have been established. The development of PCR assays typically involves careful design and validation of primers and probes against known genomic sequences and wet-lab testing with characterized samples, rather than machine learning training on a dedicated dataset.

Ask a specific question about this device

Alinity m SARS-CoV-2 is a real-time in vitro reverse transcription polymerase chain reaction (RT-PCR) assay for use with the automated Alinity m System for the qualitative detection of nucleic acid from SARS-CoV-2 from patients with signs and symptoms of COVID-19 in nasopharyngeal (NP) swab and anterior nasal swab (ANS) specimens.

Results are for the detection and identification of SARS-CoV-2 RNA. Alinity m SARS-CoV-2 assay is intended for use as an aid in the diagnosis of COVID-19 if used in comunction with other clinical, endemiologic, and laboratory findings. Positive results are indicative of the presence of SARS-CoV-2 RNA; clinical correlation with patient history and other diagnostic information is necessary to determine patient infection status. Positive results do not rule out bacterial infection or co-infection with other viruses.

Negative results do not preclude SARS-CoV-2 infection and should not be used as the sole basis for patient management decisions. Negative results must be combined with clinical observations, patient history, and epidemiological information.

Alinity m SARS-CoV-2 is a real-time in vitro reverse transcription polymerase chain reaction (RT-PCR) assay for use with the automated Alinity m System for the qualitative detection of nucleic acid from SARS-CoV-2 in specimens collected from patients with signs and symptoms of COVID-19.

The steps of the Alinity m SARS-CoV-2 assay consist of sample preparation, RT-PCR assembly, amplification/detection, and result reporting. All stages of the Alinity m SARS-CoV-2 assay procedure are executed automatically by the Alinity m System. No intermediate processing or transfer steps are performed by the user. The Alinity m System is designed to be a random-access analyzer that can perform the Alinity m SARS-CoV-2 assay in parallel with other Alinity m assays on the same instrument.

The Alinity m SARS-CoV-2 assay requires two separate assay specific kits as follows:

• . Alinity m SARS-CoV-2 AMP Kit; 09N78-096 is comprised of 2 types of multi-well trays: Alinity m SARS-CoV-2 AMP TRAY 1 and Alinity m SARS-CoV-2 ACT TRAY 2. The intended storage condition for the Alinity m SARS-CoV-2 AMP Kit is -15°C to -25°C.
• Alinity m SARS-CoV-2 CTRL Kit: 09N78-086 consists of negative controls and . positive controls, each supplied as liguid in single-use tubes. The Alinity m SARS-CoV-2 controls are used for validity determination of the Alinity m SARS-CoV-2 assay on the automated Alinity m System. These controls are intended to be used with the Alinity m SARS-CoV-2 assay. The intended storage condition for the Alinity m SARS-CoV-2 Control Kit is -15°C to -25°C.

The Alinity m SARS-CoV-2 assay may utilize the following for collection and transport of anterior nasal swab specimens:

• Abbott Universal Collection Kit; 09N92-030 consists of one Transport Tube with a solid cap containing 1.65 mL Specimen Transport Buffer and one sterile Specimen Collection Swab. The Abbott Universal Collection Kit is intended for the collection and transport of anterior nasal swabs for testing with the Alinity m SARS-CoV-2 assay. The collected specimens are intended to be tested on the automated Alinity m System. The intended storage condition for the Abbott Universal Collection Kit is 15°C to 30°C.
• Abbott Universal Collection Kit II: 09N92-040 consists of one Transport Tube with . a pierceable cap containing 1.65 mL Specimen Transport Buffer, one sterile Specimen Collection Swab, and one absorbent pad. The Abbott Universal Collection Kit II is intended for the collection and transport of anterior nasal swabs for testing with the Alinity m SARS-CoV-2 assay. The collected specimens are intended to be tested on the automated Alinity m System; The intended storage condition for the Abbott Universal Collection Kit is 15℃ to 30℃.
  SARS-CoV-2 RNA from specimens is extracted automatically on-board the Alinity m System using the Alinity m Sample Prep Kit 2, Alinity m Lysis Solution, and Alinity m Diluent Solution. The Alinity m System employs magnetic microparticle technology to facilitate nucleic acid capture, wash and elution. The resulting purified nucleic acids are then combined with the liquid unit-dose activation reagent, liquid unit-dose amplification reagents, and Alinity m Vapor Barrier Solution, and transferred by the instrument to an amplification/detection module for reverse transcription, PCR amplification, and realtime fluorescence detection.

Assay controls are tested to help ensure that instrument and reagent performance remain satisfactory. During each control event, a negative control and a positive control are processed through sample preparation and RT- PCR procedures that are identical to those used for specimens. Assay controls are used to demonstrate proper sample processing and assay validity. Each Alinity m SARS-CoV-2 CTRL kit contains 12 vials (1.3 mL fill volume) of Negative Control and 12 vials (1.3 mL fill volume) of Positive Control.

The Alinity m SARS-CoV-2 amplification reagents include primers and probes that amplify and detect an exogenous internal control (containing an armored RNA sequence). Amplification and detection of the internal control demonstrates proper sample processing. The internal control is used to demonstrate assay validity.

Patient results are automatically reported on the Alinity m instrument. The Alinity m SARS-CoV-2 application parameters will be contained in an assay application specification file.

The Alinity m SARS-CoV-2 assay also utilizes the following:

• . Alinity m SARS-CoV-2 Assay Application Specification File, List No. 09N78-05A
  The Alinity m SARS-CoV-2 application specification file is intended for use with the Alinity m SARS-CoV-2 assay on the automated Alinity m System to allow for processing of assay controls and patient samples.

• Alinity m System and System Software, List No. 08N53-002 •

• Alinity m Sample Prep Kit 2, List No. 09N12-001

• Alinity m Tubes and Caps, List No. 09N49:

  • Alinity m Transport Tubes Pierceable Capped, List No. 09N49-010
  • . Alinity m Transport Tube, List No. 09N49-011
  • . Alinity m Pierceable Cap, List No. 09N49-012
  • . Alinity m Aliquot Tube, List No. 09N49-013

• Alinity m System Solutions, List No. 09N20 •

• . Alinity m Lysis Solution, List No. 09N20-001

• Alinity m Diluent Solution, List No. 09N20-003

• Alinity m Vapor Barrier Solution, List No. 09N20-004

The Alinity m SARS-CoV-2 assay is a real-time in vitro reverse transcription polymerase chain reaction (RT-PCR) assay designed for the qualitative detection of SARS-CoV-2 nucleic acid. The study evaluated its performance for in vitro diagnostic use.

1. Table of Acceptance Criteria and Reported Device Performance

The acceptance criteria for qualitative assays like this are typically based on positive percent agreement (PPA) and negative percent agreement (NPA) with a composite comparator. While explicit acceptance criteria values (e.g., minimum PPA/NPA) are not directly stated in the provided text, the reported device performance is presented. The study results aim to demonstrate performance comparable to a predicate device, supporting substantial equivalence.

2. Sample Sizes Used for the Test Set and Data Provenance

• Study 1 (Nasopharyngeal Swab):

  • Sample Size: 535 specimens included in the analysis (from an initial 627 UVT NPS specimens tested).
  • Data Provenance: Prospective clinical study, collected at 8 geographically distributed locations in the US from January to February 2021.

• Study 2 (Anterior Nasal Swab):

  • Sample Size (ANS UCK): 766 specimens included in the analysis (from an initial 792 ANS UCK specimens available).
  • Sample Size (ANS UVT): 759 specimens included in the analysis (from an initial 787 ANS UVT specimens available).
  • Data Provenance: Prospective clinical study, collected at 8 geographically distributed locations in the US from September 2021 to January 2022.

The data is explicitly stated as prospective and collected from the US.

3. Number of Experts Used to Establish the Ground Truth for the Test Set and Qualifications of Those Experts

The ground truth for the clinical studies was established using a composite comparator (CC) derived from a minimum of two and up to three highly sensitive EUA SARS-CoV-2 molecular assays. The document does not specify the number or qualifications of experts involved in interpreting the results of these comparator assays or in establishing the final composite result. The ground truth relies on the performance of these other molecular assays.

4. Adjudication Method for the Test Set

The adjudication method for the composite comparator ground truth was:

• CC Positive: If a minimum of 2 comparator positive results were reported.
• CC Negative: If a minimum of 2 comparator negative results were reported.
• CC Indeterminate: If a CC could not be determined due to missing results from the comparator assays.

This method resembles a "2-out-of-X" or "majority vote" approach among the comparator assays.

5. If a Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study Was Done, If So, What Was the Effect Size of How Much Human Readers Improve with AI vs Without AI Assistance

This document describes a diagnostic assay (Alinity m SARS-CoV-2) for the detection of nucleic acid, not an AI-assisted diagnostic imaging device or a system involving human "readers." Therefore, a multi-reader multi-case (MRMC) comparative effectiveness study focusing on the improvement of human readers with AI assistance is not applicable and was not performed or reported in this context. The Alinity m System is an automated platform, and the assay's output is a "positive," "negative," or "not detected" result based on the instrument's analysis of the PCR reaction.

6. If a Standalone (i.e., algorithm only without human-in-the-loop performance) Was Done

Yes, the studies presented evaluate the standalone performance of the Alinity m SARS-CoV-2 assay on the automated Alinity m System. The device is designed to perform all assay steps automatically (sample preparation, RT-PCR assembly, amplification/detection, and result reporting) without intermediate user intervention. The clinical performance data presented in Table 13 directly reflects this standalone, algorithm-only performance against the composite comparator.

7. The Type of Ground Truth Used

The ground truth used for the clinical studies was a composite comparator established using a minimum of two and up to three highly sensitive EUA SARS-CoV-2 molecular assays. This falls under the category of using established, high-performing diagnostic tests as a reference standard.

8. The Sample Size for the Training Set

The document describes performance data for the Alinity m SARS-CoV-2 assay but does not provide details about a specific training set size for the development of the assay's underlying algorithms or parameters. Molecular assays like RT-PCR involve established biochemical principles and reagents rather than general-purpose machine learning algorithms that typically require large, explicit training datasets for model development in the same way an imaging AI algorithm would. The development of such assays often involves extensive analytical verification and validation, including optimization of primer/probe designs and reaction conditions, rather than a "training set" in the common AI sense.

9. How the Ground Truth for the Training Set Was Established

As noted in point 8, the concept of a "training set" and its "ground truth" in the context of this specific molecular diagnostic assay is not directly applicable or detailed in the provided summary as it would be for an AI/ML-based device. The assay's analytical characteristics (e.g., Limit of Detection, Inclusivity, Cross-reactivity) are established through controlled laboratory experiments using quantified viral material and known biological samples, which serve to define the assay's performance characteristics rather than "train" an algorithm with a labeled dataset.

Ask a specific question about this device

The TaqPath™ COVID-19 Diagnostic PCR Kit is a real-time reverse transcription polymerase chain reaction (RT-PCR) test intended for the qualitative detection of nucleic acid from SARS-CoV-2 in nasopharyngeal and anterior nasal specimens from individuals with signs and symptoms of respiratory tract infection.

The TaqPath™ COVID-19 Diagnostic PCR Kit is intended for use as an aid in the diagnosis of COVID-19 if used in conjunction with other clinical observations, epidemiological information and laboratory findings. The SARS-CoV-2 RNA is generally detectable in upper respiratory (anterior nasal and nasopharyngeal swabs) specimens during the acute phase of infection. Positive results are indicative of the presence of SARS-CoV-2 RNA. Positive results do not rule out bacterial infection or co-infection with other pathogens. The agent detected may not be the definite cause of disease.

Negative results do not preclude SARS-CoV-2 infection and should not be used as the sole basis for patient management decisions.

The TaqPath™ COVID-19 Diagnostic PCR Kit is intended for use by qualified clinical laboratory personnel specifically instructed and trained in the techniques of real-time PCR and in vitro diagnostic procedures.

The Applied BioSystems™ TaqPath™ COVID-19 Diagnostic PCR Kit (TaqPath™ COVID-19 Diagnostic PCR Kit) includes the assays and controls for a multiplex real-time RT-PCR test for the qualitative detection of RNA from SARS-CoV-2 in nasopharyngeal and anterior nasal specimens from individuals with signs and symptoms of respiratory tract infection.

Each kit includes the following components:

• Multiplexed assays that contain three primer/probe sets specific to different SARS-CoV-2 genomic regions and primers/probes for bacteriophage MS2
• MS2 Phage Control as an internal process control for nucleic acid extraction
• TaqPath™ COVID-19 Diagnostic PCR Control as a positive RNA control that contains targets specific to the SARS-CoV-2 genomic regions targeted by the assays.

The workflow begins with nucleic acid extraction from upper respiratory specimens (nasopharyngeal and anterior nasal swabs) that arrive in the testing site in transport media. Nucleic acids are isolated and purified from the specimens using the MagMAX™ Viral/Pathogen II Nucleic Acid Isolation Kit. Nucleic acid isolation is performed via an automated process using the KingFisher™ Flex Purification System. The nucleic acid is reverse transcribed into cDNA and amplified using the TaqPath™ COVID-19 Diagnostic PCR Kit and one of the following real-time PCR instruments:

• Applied Biosystems™ 7500 Fast Dx Real-Time PCR Instrument
• Applied Biosystems™ QuantStudio™ 5 Dx Real-Time PCR Instrument

In the process, the probes anneal to three (3) specific SARS-CoV-2 target sequences located between three (3) unique forward and reverse primers for the following genes:

• ORF1ab
• N gene
• S gene

During the extension phase of the PCR cycle, the 5' nuclease activity of Taq polymerase degrades the probe, causing the reporter dye to separate from the quencher dye, generating a fluorescent signal. With each PCR cycle, additional reporter dye molecules are cleaved from their respective probes, increasing the fluorescent intensity, which is measured at each cycle by the real-time PCR instrument.

Following RT-PCR, the data from the instrument's data collection software are imported into COVID-19 Interpretive Software IVD Edition for analysis and interpretation. After data import, the software analyzes the run data, performs quality check (QC) analysis, and calculates the interpretive results for each sample and control. The imported data and interpretive results for each run are saved as a batch in the software. Results can be exported as CSV files and reports can be generated in PDF format.

Validation of the results is performed automatically by the COVID-19 Interpretive Software based on performance of the positive and negative controls. The following results are automatically generated using the calling rules, plate validity and the CT cutoff values for assay targets:

1. Repeat the test by re-extracting the
   original sample and repeating the
   RT-PCR.
   IMPORTANT! Samples with a
   result of SARS-CoV-2 Inconclusive
   shall be retested one time.
2. After retesting one time, report the
   results to the healthcare provider.
3. If the repeat result remains
   inconclusive, the healthcare
   provider should conduct additional
   confirmation testing with a new
   specimen, if clinically indicated. |
   | | Two or more SARS-CoV-2 targets
   = POS | | POS or
   NEG | VALID | Positive SARS-
   CoV-2 | REPORT
   Report the results to the healthcare
   provider. |

A minimum of one negative control and one positive control must be present for each run. Additional negative control wells shall be run for each extraction that is represented on a realtime RT-PCR plate. All control wells must pass for the real-time RT-PCR plate to be considered valid. Recommended actions of retest or report are also provided depending on the results generated.

The provided FDA 510(k) summary for the "Applied BioSystems™ TaqPath™ COVID-19 Diagnostic PCR Kit" details various studies to establish its performance. Here's a breakdown of the acceptance criteria and study proving device performance, as per your request:

Acceptance Criteria and Reported Device Performance

The acceptance criteria for each study are implicitly demonstrated by the reported performance meeting the standards required for the 510(k) clearance, primarily aiming for high Positive Percent Agreement (PPA) and Negative Percent Agreement (NPA) compared to a composite comparator method, along with demonstrating robustness in analytical performance.

Here's a table summarizing key performance characteristics and the reported results:

Study Details to Prove Device Meets Acceptance Criteria

The studies primarily focus on analytical and clinical performance of the PCR kit itself, rather than an AI-driven device with human-in-the-loop interaction. Therefore, aspects related to MRMC studies or expert ground truth for image interpretation are not applicable here.

1. Sample sizes used for the test set and the data provenance:

   • Limit of Detection (LoD):
     • Preliminary LoD: Serial dilutions (number of replicates not specified beyond "three (3) replicates per concentration level" in the WHO Standard test).
     • Confirmatory LoD: 20 replicates at three concentration levels (3x, 1x, 0.33x LoD) for both SARS-CoV-2 USA-WA1/2020 and WHO Standard.
     • Provenance: Contrived samples using inactivated SARS-CoV-2 virus spiked into pooled negative NP specimen matrix. No geographical provenance for these samples is specified, but likely from US. Retrospective in nature as samples are manipulated.
   • Reproducibility and Within-Laboratory Precision: 270 replicates per sample at each test level (0x LoD, 1.5x LoD, 5x LoD) on each PCR instrument model.
     • Provenance: Contrived samples (inactivated SARS-CoV-2 virus in pooled negative NP specimen matrix). Testing performed at three sites (two external, one internal), indicating multi-center analytical study. No geographical provenance for specimens specified. Retrospective.
   • Interfering Substances: 3 replicates per substance level (positive and negative). Some substances tested with 6 replicates at certain concentrations (e.g., Oxymetazoline, Triamcinolone).
     • Provenance: Contrived samples (inactivated SARS-CoV-2 virus at 3x LoD or negative matrix) spiked with interferents. Negative pooled NP samples were used as matrix.
   • Cross-Reactivity and Microbial Interference: 3 replicates of each of 46 microorganisms.
     • Provenance: Microorganisms spiked into pooled negative NP specimen matrix (for cross-reactivity) or contrived positive NP specimen matrix (for microbial interference).
   • Analytical Reactivity (Inclusivity): 3 replicates for each of 15 SARS-CoV-2 variants.
     • Provenance: Contrived samples (inactivated SARS-CoV-2 virus spiked into negative pooled NP specimen).
   • Carry-Over Cross-Contamination: 470 negative samples tested (47 replicates across 10 extraction runs x 2 instruments).
     • Provenance: Contrived samples with high viral titers and negative NP samples.
   • Specimen Storage Stability: Not explicitly stated, but implies multiple replicates at various time points for both positive and negative contrived samples.
     • Provenance: Contrived positive and negative NP samples in VTM.
   • Fresh vs Frozen Equivalency Study: 10 replicates for 0x and 5x LoD; 40 replicates for 1.5x LoD.
     • Provenance: Contrived NP samples in VTM.
   • Clinical Validation (Primary Test Set):
     • Total Subjects: 1076 subjects enrolled across 11 geographically diverse sites in the U.S. (April 2023 - August 2023).
     • Evaluable Samples: 1055 nasopharyngeal swabs (NP) and 1052 anterior nasal swabs (AN). Exclusions resulted in 1053 evaluable NP specimens and 1049 (7500 Fast Dx) / 1052 (QS5 Dx) evaluable AN specimens.
     • Provenance: Prospectively collected from individuals with signs and symptoms of respiratory tract infection in the U.S. "All-comers fashion". Both fresh (tested within 72 hours) and frozen (stored ≤-70°C, tested within 30 days) Category I and Category II specimens. This is prospective data from the US.

2. Number of experts used to establish the ground truth for the test set and the qualifications of those experts:

   • For this PCR diagnostic kit, the "ground truth" for clinical validation is established by a composite comparator method using multiple highly sensitive SARS-CoV-2 molecular assays (other FDA-cleared or authorized PCR tests). Qualified clinical laboratory personnel presumably performed these comparator tests. There is no mention of human expert consensus/adjudication typically seen in AI imaging studies.

3. Adjudication method for the test set:

   • Clinical Validation: A composite comparator approach was used. Samples were tested by two comparator assays (Test A and Test B). If there was discordance between the first two assays, a third comparator assay (Test C) was used to resolve the discrepancy. The "two-out-of-three" rule determined the composite comparator result, which served as the ground truth.

4. If a multi reader multi case (MRMC) comparative effectiveness study was done, If so, what was the effect size of how much human readers improve with AI vs without AI assistance:

   • No. This is a diagnostic PCR kit, not an AI-based imaging or interpretive device that requires human readers. Therefore, an MRMC study is not applicable. The device provides a direct biological result (presence/absence of viral RNA).

5. If a standalone (i.e. algorithm only without human-in-the-loop performance) was done:

   • Yes, in essence. The analytical performance studies (LoD, reproducibility, cross-reactivity, inclusivity, etc.) evaluate the kit's performance independently of human interpretation nuances beyond standard laboratory procedures and instrument operation. The clinical validation also assesses its performance against a composite ground truth, effectively as a "standalone" diagnostic test. The "COVID-19 Interpretive Software IVD Edition" analyzes data and generates results automatically, which is an algorithmic standalone component.

6. The type of ground truth used (expert consensus, pathology, outcomes data, etc):

   • A composite comparator method using other molecular diagnostic (RT-PCR) assays. This is considered the clinical reference standard for nucleic acid detection of SARS-CoV-2.

7. The sample size for the training set:

   • For a molecular diagnostic kit like this, a traditional "training set" in the machine learning sense isn't explicitly defined as it would be for an AI algorithm. The development and optimization of the primers, probes, and reaction conditions (which is analogous to "training" in developing molecular assays) are based on extensive genomic data of SARS-CoV-2 and related viruses. The document describes validation studies, not a separate training phase. The "control" elements (positive/negative controls, MS2 Phage internal control) are part of the kit's design to ensure proper function and validate each run.

8. How the ground truth for the training set was established:

   • Not applicable as there is no explicitly defined "training set" in the context of an AI algorithm or a separately identified ground truth for such a set. The "training" for such a device is likely the iterative design and optimization of the molecular components to achieve specificity and sensitivity based on known viral sequences and biological principles.

Ask a specific question about this device

The Xpert Xpress CoV-2 plus test, performed on the GeneXpert Infinity Systems, is a rapid real-time RT-PCR test intended for the qualitative detection of SARS-CoV-2 RNA in nasopharyngeal and anterior nasal swab specimens collected from individuals with signs and symptoms of respiratory tract infection.

The Xpert Xpress CoV-2 plus test is intended for use as an aid in the diagnosis of COVID-19 if used in conjunction with other clinical, epidemiologic, and laboratory findings. Positive results are indicative of the presence of SARS-CoV-2 RNA. Positive results do not rule out bacterial infection or co-infection with other pathogens.

Negative results do not preclude SARS-CoV-2 infection. The results of this test should not be used as for diagnosis and patient management decisions.

The Xpert Xpress CoV-2 plus test is a rapid, automated in vitro diagnostic test for the qualitative detection of viral RNA from SARS-CoV-2 in nasopharyngeal swab (NPS) and anterior nasal swab (NS) specimens obtained from individuals with signs and symptoms of respiratory tract infection.

The Xpert Xpress CoV-2 plus test is performed on the Cepheid GeneXpert® Instrument Systems (GeneXpert Dx, GeneXpert Infinity-48s and GeneXpert Infinity-80 systems), which consist of an instrument, computer and preloaded software for running tests and viewing the results. The GeneXpert Instrument Systems automate and integrate sample preparation, nucleic acid extraction and amplification, and detection of the target sequences in simple or complex samples using real-time reverse transcription (RT)-polymerase chain reaction (PCR) and PCR assays. Depending on the instrument, the GeneXpert Instrument Systems can have from 1 and up to 80 randomly accessible modules, each capable of performing separate sample preparation and real-time RT-PCR and PCR tests. Each module contains a syringe drive for dispensing fluids (i.e., the syringe drive activates the plunger that works in concert with the rotary valve in the cartridge to move fluids between chambers), an ultrasonic horn for lysing cells or spores, and a proprietary I-CORE® thermocycler for performing real-time RT-PCR and PCR as well as detection. The systems require the use of single-use disposable cartridges that hold the RT-PCR reagents and host sample purification, nucleic acid amplification, and detection of the target sequences. Because the cartridges are selfcontained, cross-contamination between cartridges during the testing process is minimized.

The Xpert Xpress CoV-2 plus test includes reagents for the detection of viral RNA from SARS-CoV-2 in NPS and NS specimens. The primers and probes in the Xpert Xpress CoV-2 plus test are designed to amplify and detect sequences in the genes that encode the following SARS-CoV-2 proteins: nucleocapsid (N2), envelope (E), and RNA-dependent RNA polymerase (RdRP). A Sample Processing Control (SPC) and a Probe Check Control (PCC) are also included in the cartridge utilized by the GeneXpert instrument. The SPC is present to control for adequate processing of the sample and to monitor for the presence of potential inhibitor(s) in the RT-PCR reaction. The SPC also ensures that the RT-PCR reaction conditions (temperature and time) are appropriate for the amplification reaction and that the RT-PCR reagents are functional. The PCC verifies reagent rehydration. PCR tube filling, and confirms that all reaction components are present in the cartridge including monitoring for probe integrity and dve stability.

The Xpert Xpress CoV-2 plus test is designed for use with NPS or NS specimen collected with nylon flocked swabs and placed into a viral transport medium (VTM), Universal Transport Medium (UTM) or eNAT®.

Here's a breakdown of the acceptance criteria and the study details for the Cepheid Xpert Xpress CoV-2 plus, based on the provided document:

Acceptance Criteria and Device Performance

Note: The document explicitly states the "claimed LoD" which can be interpreted as an acceptance criterion for analytical sensitivity. For clinical performance, the reported PPA and NPA values serve as the acceptance criteria.

Study Details

2. Sample size used for the test set and the data provenance (e.g. country of origin of the data, retrospective or prospective)

• Clinical Performance Test Set:

  • Initial Specimens: 4047 specimens (2029 Nasopharyngeal Swab (NPS) and 2018 Anterior Nasal Swab (NS)).
  • Valid Specimens (after exclusions): 3750 specimens (1879 NPS and 1871 NS).
  • Data Provenance: United States (32 geographically diverse sites), prospectively collected, fresh (98.6%) and frozen (1.4%) clinical specimens collected in 2022.

• Analytical Performance Test Sets:

  • LoD (NPS & NS): Replicates of 20 per reagent lot (2 lots).
  • LoD (WHO Standard): 20 replicates.
  • Analytical Inclusivity (Wet Testing): 61 SARS-CoV-2 strains, 3 replicates each.
  • Analytical Exclusivity (Wet Testing): 62 microorganisms, 3 replicates each.
  • Microbial Interference: 18 commensal microorganisms, 8 replicates each with SARS-CoV-2.
  • Potentially Interfering Substances: 23 substances, 8 replicates each for negative and positive samples.
  • Carryover Contamination: 40 positive samples and 42 negative samples.
  • Reproducibility: 144 observations per panel member (3 sites x 2 operators x 3 lots x 2 days/lot x 2 runs x 2 replicates).
  • Single-Site Precision: 80 observations per panel member (1 site x 1 operator x 1 lot x 20 days x 2 runs x 2 replicates).
  • Data Provenance: Not explicitly stated for analytical studies, but typically performed in-house or by contracted labs. The substances and strains used are clearly defined.

3. Number of experts used to establish the ground truth for the test set and the qualifications of those experts (e.g. radiologist with 10 years of experience)

• The clinical performance study used a U.S. FDA-cleared molecular respiratory panel that includes SARS-CoV-2 as the comparator (reference method). This type of comparator assay is itself considered a "ground truth" established by its own regulatory clearance process, relying on its validated accuracy rather than individual expert adjudication for each case in this study.
• Qualifications of experts: Not applicable as ground truth was established by a cleared molecular diagnostic test.

4. Adjudication method (e.g. 2+1, 3+1, none) for the test set

• Clinical Performance: The comparator was a U.S. FDA-cleared molecular respiratory panel. For discrepant results with this comparator, additional testing was performed using a U.S. FDA EUA SARS-CoV-2 molecular test. The text indicates that these discrepant test results were used to resolve the discrepancies (e.g., 7/9 SARS-CoV-2 negative; 8/28 SARS-CoV-2 positive from the specific footnotes), implying a third party or a consensus reference method was used for discordant samples. This suggests a form of discrepant analysis, where a third, highly accurate method or a re-test with a known method, is used to resolve differences between the investigational device and the primary comparator.

5. If a multi reader multi case (MRMC) comparative effectiveness study was done, If so, what was the effect size of how much human readers improve with AI vs without AI assistance

• Not applicable. This submission describes a molecular diagnostic test (in vitro diagnostic device), not an imaging-based AI diagnostic device requiring human reader interpretation in an MRMC study. The device provides a direct qualitative result (POSITIVE/NEGATIVE).

6. If a standalone (i.e. algorithm only without human-in-the-loop performance) was done

• Yes, this is a standalone device. The Xpert Xpress CoV-2 plus test is an automated, real-time RT-PCR test performed on GeneXpert Instrument Systems. Its output is a qualitative result (SARS-CoV-2 POSITIVE or NEGATIVE) based on the algorithm within the instrument, without human interpretation of raw data for diagnosis. Although human operators load samples and review results, the diagnostic determination itself is made by the system.

7. The type of ground truth used (expert consensus, pathology, outcomes data, etc)

• Clinical Performance: The ground truth for clinical performance was established by concordance with a U.S. FDA-cleared molecular respiratory panel and, for discrepant cases, a U.S. FDA EUA SARS-CoV-2 molecular test. This represents a highly accurate molecular diagnostic reference method.
• Analytical Performance: Ground truth for analytical studies was established using known concentrations of inactivated SARS-CoV-2 virus, WHO International Standard for SARS-CoV-2 RNA, genomic RNA/DNA of various microorganisms, and in silico analyses against sequence databases.

8. The sample size for the training set

• Not explicitly stated in terms of a "training set". For molecular diagnostic tests, "training" typically refers to the development and optimization of the primer and probe design, and algorithmic thresholds. This development process often involves internal studies and iterations rather than a distinct "training set" in the machine learning sense. The extensive analytical performance studies (LoD, inclusivity, exclusivity) serve to validate the developed algorithm's performance against diverse known samples. In silico analyses involved millions of SARS-CoV-2 sequences.

9. How the ground truth for the training set was established

• As noted above, a distinct "training set" in the machine learning context is not explicitly described. However, the ground truth for optimizing the assay's primers, probes, and detection thresholds would have been established through:
  • Known concentrations of synthetic SARS-CoV-2 genetic material or inactivated virus.
  • In silico analysis against extensive public sequence databases (e.g., GISAID, NCBI) to identify target regions and ensure inclusivity of variants while maintaining exclusivity against other pathogens.
  • Laboratory-prepared samples with known microbial content and concentrations used to optimize and validate analytical performance characteristics like sensitivity and specificity.

Ask a specific question about this device

cobas® SARS-CoV-2 Qualitative for use on the cobas® 5800/6800/8800 Systems is a real-time RT-PCR test intended for the qualitative detection of nucleic acids from SARS-CoV-2 in nasal and nasopharyngeal specimens collected from symptomatic individuals suspected of COVID-19 by their healthcare provider.

Results are for the detection of SARS-CoV-2 RNA. Positive results are indicative of the presence of SARS-CoV-2 RNA; clinical correlation with patient history and other diagnostic information is necessary to determine patient infection status. Positive results do not rule out bacterial infection or co-infection with other pathogens.

Negative results do not preclude SARS-CoV-2 infection and should not be used as the sole basis for patient management decisions. Results are meant to be used in conjunction with clinical observations, patient history, recent exposures and epidemiological information, and laboratory data, in accordance with the guidelines provided by the relevant public health authorities. cobas® SARS-CoV-2 Qualitative is intended for use by qualified clinical laboratory personnel specifically instructed and trained in the techniques of real-time PCR and on the use of the cobas® 5800/6800/8800 Systems.

cobas® SARS-CoV-2 Qualitative is based on fully automated sample preparation (nucleic acid extraction and purification) followed by PCR amplification and detection. The cobas® 5800 System is designed as one integrated instrument. The cobas® 6800/8800 Systems consist of the sample supply module, the transfer module, the processing module, and the analytic module. Automated data management is performed by the cobas® 5800 or cobas® 6800/8800 Systems software(s), which assigns test results for all tests. Results can be reviewed directly on the system screen, and printed as a report.

Nucleic acid from patient samples and added internal control RNA (RNA IC) molecules are simultaneously extracted. Nucleic acid is released by addition of proteinase and lysis reagent to the sample. The released nucleic acid binds to the silica surface of the added magnetic glass particles. Unbound substances and impurities, such as denatured protein, cellular debris and potential PCR inhibitors, are removed with subsequent wash steps and purified nucleic acid is eluted from the magnetic glass particles with elution buffer at elevated temperature. External controls (positive and negative) are processed in the same way.

Selective amplification of target nucleic acid from the sample is achieved by the use of targetspecific forward and reverse primers for ORF1 a/b non-structural region that is unique to SARS-CoV-2. Additionally, a conserved region in the structural protein envelope E-gene were chosen for pan-Sarbecovirus detection. The pan-Sarbecovirus detection sets will also detect SARS-CoV-2 virus.

Selective amplification of RNA Internal Control is achieved by the use of non-competitive sequence specific forward and reverse primers which have no homology with the coronavirus genome. A thermostable DNA polymerase enzyme is used for amplification.

The cobas® SARS-CoV-2 Qualitative master mix contains detection probes which are specific for the coronavirus type SARS-CoV-2, members of the Sarbecovirus subgenus, and the RNA Internal Control nucleic acid. The coronavirus and RNA Internal Control detection probes are each labeled with unique fluorescent dyes that act as a reporter. Each probe also has a second dye which acts as a quencher. When not bound to the target sequence, the fluorescent signals of the intact probes are suppressed by the quencher dye. During the PCR amplification step, hybridization of the probes to the specific single-stranded DNA template results in cleavage of the probe by the 5' to 3' exonuclease activity of the DNA polymerase resulting in separation of the reporter and quencher dyes and the generation of a fluorescent signal. With each PCR cycle, increasing amounts of cleaved probes are generated and the cumulative signal of the reporter dye increases concomitantly. Each reporter dye is measured at defined wavelengths, which enables simultaneous detection and discrimination of the amplified coronavirus target and the RNA Internal Control. The master mix includes deoxyuridine triphosphate (dUTP), instead of deoxythimidine triphosphate (dTTP), which is incorporated into the newly synthesized DNA (amplicon). Any contaminating amplicons from previous PCR runs are destroyed by the AmpErase enzyme [uracil-N-glycosylase], which is included in the PCR mix, when heated in the first thermal cycling step. However, newly formed amplicons are not destroyed since the AmpErase enzyme is inactivated once exposed to temperatures above 55°C.

The provided text is a 510(k) Summary for the cobas SARS-CoV-2 Qualitative test. It primarily focuses on demonstrating substantial equivalence to a predicate device after software updates (ASAPs) and does not contain detailed acceptance criteria and performance data in the format typically required for a full clinical study report. The document states that the overall assay performance claims were not impacted by the changes implemented in the software updates.

Therefore, I cannot provide a detailed answer to all parts of your request based on the information given. However, I can extract the following:

1. A table of acceptance criteria and the reported device performance:

The document explicitly states that the "overall cobas® SARS-CoV-2 Qualitative assay performance claims were not impacted by changes implemented in SW cobas® SCoV2-QL ASAP 12.4.1 and SW cobas® 5800 SCoV2-QL ASAP 1.3.1, when compared to the current commercially available version of the ASAPs SW cobas® SCoV2-QL ASAP 12.1.0 and SW cobas® 5800 SCoV2-QL ASAP 1.1.1." This implies that the performance of the updated device is considered equivalent to the predicate device, which had already met its own set of acceptance criteria. However, the specific numerical acceptance criteria or the reported performance data for parameters like sensitivity, specificity, or LOD are not provided in this summary. The summary only asserts that the performance has not changed.

2. Sample size used for the test set and the data provenance (e.g. country of origin of the data, retrospective or prospective):

This information is not provided in the given 510(k) summary. The document focuses on changes to the Assay Specific Analysis Packages (ASAPs) and states that performance claims were not impacted. It does not describe a new clinical or analytical study with specific sample sizes or data provenance for the test set.

3. Number of experts used to establish the ground truth for the test set and the qualifications of those experts (e.g. radiologist with 10 years of experience):

This information is not provided in the given 510(k) summary. As an in-vitro diagnostic (IVD) PCR test, ground truth for such devices is typically established through a composite reference method, often including another highly sensitive and specific RT-PCR assay, rather than expert consensus on images.

4. Adjudication method (e.g. 2+1, 3+1, none) for the test set:

This information is not provided in the given 510(k) summary.

5. If a multi reader multi case (MRMC) comparative effectiveness study was done, If so, what was the effect size of how much human readers improve with AI vs without AI assistance:

This is not applicable to this device. The cobas SARS-CoV-2 Qualitative test is an in-vitro diagnostic (IVD) RT-PCR assay for qualitative detection of viral nucleic acids, not an imaging device that requires human reader interpretation, nor does it incorporate AI for decision support.

6. If a standalone (i.e. algorithm only without human-in-the-loop performance) was done:

The device described is an automated RT-PCR test system. Its performance, by nature, is "standalone" in terms of the algorithm generating a result based on the sample processing. The results are then interpreted by qualified laboratory personnel. The summary indicates "Automated data management is performed by the cobas® 5800 or cobas® 6800/8800 Systems software(s), which assigns test results for all tests." This suggests algorithm-only processing for the primary result.

7. The type of ground truth used (expert consensus, pathology, outcomes data, etc.):

While not explicitly stated in this summary, for a SARS-CoV-2 qualitative RT-PCR test, the ground truth in performance studies (especially for the original clearance of K213804) would typically be established using a reference molecular method (e.g., another FDA-authorized RT-PCR test or a validated in-house RT-PCR assay), often combined with clinical data in some cases. The document does not describe the specific ground truth method used for the studies that established the initial performance claims of the predicate device (K213804), which are referenced as unchanged.

8. The sample size for the training set:

This information is not provided in the given 510(k) summary. This document describes software updates to an already cleared device, focusing on ensuring that the updates did not negatively impact its previously established performance. It's unlikely that new "training sets" in the machine learning sense were used for these specific software updates, which appear to refine interpretation logic rather than train a new model.

9. How the ground truth for the training set was established:

This information is not provided in the given 510(k) summary. See point 8.

Ask a specific question about this device

cobas SARS-CoV-2 Qualitative for use on the cobas 6800/8800 Systems is a real-time RT-PCR test intended for the qualitative detection of nucleic acids from SARS-CoV-2 in nasal and nasopharyngeal specimens collected from symptomatic individuals suspected of COVID-19 by their healthcare provider.

Results are for the detection of SARS-CoV-2 RNA. Positive results are indicative of the presence of SARS-CoV-2 RNA; clinical correlation with patient history and other diagnostic information is necessary to determine patient infection status. Positive results do not rule out bacterial infection or co-infection with other pathogens.

Negative results do not preclude SARS-CoV-2 infection and should not be used as the sole basis for patient management decisions. Results are meant to be used in conjunction with clinical observations, patient history, recent exposures and epidemiological information, and laboratory data, in accordance with the guidelines provided by the relevant public health authorities. cobas SARS-CoV-2 is intended for use by qualified clinical laboratory personnel specifically instructed and trained in the techniques of real-time PCR and on the use of the cobas 6800/8800 Systems.

cobas SARS-CoV-2 Qualitative is based on fully automated sample preparation (nucleic acid extraction and purification) followed by PCR amplification and detection. The cobas 6800/8800 Systems consist of the sample supply module, the transfer module, the processing module, and the analytic module. Automated data management is performed by the cobas 6800/8800 Systems software(s), which assigns test results for all tests. Results can be reviewed directly on the system screen and printed as a report.

Nucleic acid from patient samples and added internal control RNA (RNA IC) molecules are simultaneously extracted. Nucleic acid is released by addition of proteinase and lysis reagent to the sample. The released nucleic acid binds to the silica surface of the added magnetic glass particles. Unbound substances and impurities, such as denatured protein, cellular debris and potential PCR inhibitors, are removed with subsequent wash steps and purified nucleic acid is eluted from the magnetic glass particles with elution buffer at elevated temperature. External controls (positive and negative) are processed in the same way.

Selective amplification of target nucleic acid from the sample is achieved by the use of target-specific forward and reverse primers for ORF1 a/b non-structural region that is unique to SARS-CoV-2. Additionally, a conserved region in the structural protein envelope E-gene were chosen for pan-Sarbecovirus detection. The pan-Sarbecovirus detection sets will also detect SARS-CoV-2 virus.

Selective amplification of RNA Internal Control is achieved by the use of non-competitive sequence specific forward and reverse primers which have no homology with the coronavirus genome. A thermostable DNA polymerase enzyme is used for amplification.

The cobas SARS-CoV-2 Qualitative master mix contains detection probes which are specific for the coronavirus type SARS-CoV-2, members of the Sarbecovirus subgenus, and the RNA Internal Control nucleic acid. The coronavirus and RNA Internal Control detection probes are each labeled with unique fluorescent dyes that act as a reporter. Each probe also has a second dye which acts as a quencher. When not bound to the target sequence, the fluorescent signals of the intact probes are suppressed by the quencher dye. During the PCR amplification step, hybridization of the probes to the specific single-stranded DNA template results in cleavage of the probe by the 5' to 3' exonuclease activity of the DNA polymerase resulting in separation of the reporter and quencher dyes and the generation of a fluorescent signal. With each PCR cycle, increasing amounts of cleaved probes are generated and the cumulative signal of the reporter dye increases concomitantly. Each reporter dye is measured at defined wavelengths, which enables simultaneous detection and discrimination of the amplified coronavirus target and the RNA Internal Control. The master mix includes deoxyuridine triphosphate (dUTP), instead of deoxythimidine triphosphate (dTTP), which is incorporated into the newly synthesized DNA (amplicon). Any contaminating amplicons from previous PCR runs are destroyed by the AmpErase enzyme [uracil-N-glycosylase], which is included in the PCR mix, when heated in the first thermal cycling step. However, newly formed amplicons are not destroyed since the AmpErase enzyme is inactivated once exposed to temperatures above 55℃.

Here's a detailed breakdown of the acceptance criteria and the study proving the device meets them, based on the provided text:

Acceptance Criteria and Device Performance

1. Table of Acceptance Criteria and Reported Device Performance

Note: The document does not explicitly state "acceptance criteria" for clinical performance in a pass/fail format with numerical targets. Instead, it presents the achieved performance. Therefore, the "Acceptance Criteria" column below reflects typical expectations for such devices based on the reported performance.

2. Sample Size Used for the Test Set and Data Provenance

• Clinical Performance Test Set (Clinical Specimens):

  • Total Participants enrolled: 1,154
  • Participants included in evaluation: 968
  • Reasons for exclusion: 184 specimens due to shipment issues/testing completion issues, 2 subjects for being previously enrolled.
  • Evaluable NPS results: 938 (961 participants contributed NPS, 4 failed/invalid cobas results)
  • Evaluable NS results: 934 (8 invalid/missing cobas NS results)
  • Confirmed infected status (NPS comparator): 942 participants
  • Data Provenance: Multi-center study with three external testing sites, involving prospectively collected clinical specimens (NPS and NS) from individuals with signs and symptoms of respiratory infection. Participants from 12 geographically distributed enrollment centers. The specific countries are not mentioned, but "US Food & Drug Administration" implies a US-based study or one for US market approval.

• Analytical Performance Test Sets:

  • Analytical Sensitivity (LoD): 5 concentration levels, 24 replicates per concentration, 3 independent dilution series with 3 lots of reagents.
  • Inclusivity: 9 SARS-CoV-2 strains, 4 replicates each.
  • Precision: 3 concentration levels, 90 replicates per concentration (over 15 instrument days).
  • Reproducibility: 4-member panel (positive/negative), 216 tests per concentration (at 3 testing sites, 3 reagent lots, 6 days, 2 runs/day, 3 replicates/run).
  • Analytical Specificity/Cross-reactivity: 47 microorganisms (at specified concentrations) tested in absence and presence of SARS-CoV-2 target.
  • Interference (Exogenous/Endogenous): Multiple substances at specified concentrations, tested in absence and presence of SARS-CoV-2 target.
  • Matrix Equivalency: 3 matrices (simulated, NPS, NS), 3 concentration levels (approx. 3x LoD, 1x LoD, 0.3x LoD), 25 replicates per concentration.
  • Collection Media Equivalency: 3 media types (UTM-RT, CPM, NaCl), 2 concentration levels (approx. 2x LoD, 4x LoD), at least 20 replicates for low positive, 10 for moderate positive.
  • Data Provenance: All these analytical studies appear to be laboratory-based and controlled, usually performed by the manufacturer or authorized labs. No specific country of origin is stated for these analytical studies, but they are part of the submission to the US FDA.

3. Number of Experts Used to Establish the Ground Truth for the Test Set and Their Qualifications

The document refers to "healthcare provider" for collecting specimens and for associating patient history and diagnostic information, but does not specify the number or qualifications of experts (e.g., radiologists) used to establish the ground truth for the test set specifically for interpreting images or providing expert consensus.

Instead, for the clinical performance evaluation, the ground truth was established using a composite comparator method (described below), rather than expert consensus on a subjective measure. For laboratory-based analytical studies, ground truth is based on known concentrations of viral material.

4. Adjudication Method for the Test Set

The ground truth for the clinical test set was established using a composite comparator method:

• Method: Laboratory sites used up to three highly sensitive EUA SARS-CoV-2 molecular assays.
• Initial Comparison: The composite comparator result was defined as the concordant results from two initial comparator assays (Test A and Test B) on the NPS specimen from each subject.
• Discordance Resolution: In case of discordance between the initial two comparator assays, the sample was tested by a third assay (Test C), and the result of the third test determined the composite comparator result.
• Indeterminate Results: The composite comparator result was deemed indeterminate if valid results could not be obtained from two assays (e.g., insufficient volume for repeat testing or invalid/failed results).

5. If a Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study Was Done

No, a Multi-Reader Multi-Case (MRMC) comparative effectiveness study was not done. This document describes the performance of a diagnostic assay (RT-PCR test), not an AI-assisted diagnostic imaging device that involves human readers. Therefore, there is no mention of human readers or improvement with AI assistance.

6. If a Standalone (Algorithm Only Without Human-in-the-Loop Performance) Was Done

Yes, the performance study presented is a standalone (algorithm only) performance. The device is an automated RT-PCR test system (cobas SARS-CoV-2 Qualitative for use on the cobas 6800/8800 Systems). Its performance characteristics (analytical sensitivity, specificity, precision, clinical PPA/NPA) are measured directly against established standards or a composite comparator, without human interpretation of the assay results changing its output. The system software assigns test results.

7. The Type of Ground Truth Used

• Clinical Performance: Composite comparator method using up to three highly sensitive EUA SARS-CoV-2 molecular assays on NPS specimens.
• Analytical Performance:
  • Known concentrations of inactivated quantified SARS-CoV-2 virus (WHO International Standard) for LoD and reproducibility.
  • Known SARS-CoV-2 strains for inclusivity.
  • Known concentrations of various microorganisms or substances for analytical specificity and interference studies.

8. The Sample Size for the Training Set

The document describes a cobas SARS-CoV-2 Qualitative test, which is a real-time RT-PCR assay and not an AI/Machine Learning model. Therefore, the concept of a "training set" in the context of machine learning does not apply here. The document details validation studies for the assay, not the training of an algorithmic model.

9. How the Ground Truth for the Training Set Was Established

As stated above, this is an RT-PCR assay, not an AI/ML model. Therefore, there is no training set and consequently, no ground truth established for a training set. The performance is validated through various analytical and clinical studies as outlined in the document.

Ask a specific question about this device

The DiaSorin Molecular Simplexa™ COVID-19 Direct is real-time RT-PCR assay intended for use on the LIAISON® MDX instrument for the in vitro qualitative detection of nucleic acid from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in nasopharyngeal swabs (NPS) and nasal swabs (NS) from symptomatic individuals suspected of COVID 19 by their healthcare provider. The Simplexa™ COVID-19 Direct assay is an aid in the diagnosis of SARS-CoV-2 infection.

Positive results are indicative of the presence of SARS-CoV-2 RNA. Clinical correlation with patient history and other diagnostic information is necessary to determine patient infection status. Positive results do not rule out co-infection with other pathogens. Negative results do not preclude SARS-CoV-2 infection and should not be used as tor patient management decisions.

Results are meant to be used in conjunction with other clinical, epidemiologic, and laboratory data, in accordance with the guidelines provided by the relevant public health authorities.

The Simplexa COVID-19 Direct is a real-time RT-PCR (rRT-PCR) system that enables the direct amplification and detection of SARS-CoV-2 (COVID-19) RNA from nasopharyngeal swab or nasal swab that has not undergone nucleic acid extraction. The system consists of the Simplexa COVID-19 Direct reaction mix, the LIAISON MDX (with LIAISON MDX Studio Software), the Direct Amplification Disc and associated accessories. The assay uses forward and reverse primers and associated fluorescent probe(s) included in the reaction mix to amplify SARS-CoV-2 cDNA reverse transcribed from RNA. The primers and probe sets are designed to detect SARS-CoV-2 ORF 1ab and S gene from the viral RNA in nasopharyngeal swab or nasal swab. An RNA internal control, with associated primers and a fluorescent probe, is included in the reaction mix to detect RT-PCR failure and/or inhibition.

Here's a breakdown of the acceptance criteria and study proving the device meets them, based on the provided text:

Device: Simplexa™ COVID-19 Direct

1. Table of Acceptance Criteria and Reported Device Performance

For the Simplexa™ COVID-19 Direct assay, the primary acceptance criteria revolve around its accuracy in detecting SARS-CoV-2 (COVID-19) RNA in patient samples, as well as its reproducibility, analytical sensitivity (Limit of Detection), analytical reactivity (ability to detect various strains), and specificity (cross-reactivity and interference).

2. Sample Size Used for the Test Set and Data Provenance

• Clinical Agreement Test Set:

  • Total Samples: 1,150 prospective (fresh and/or frozen) samples collected.
  • Samples analyzed: 1,011 samples (114 excluded due to insufficient evidence for media types, 24 invalid results, 1 indeterminate CRM result).
  • Breakdown: 299 Nasopharyngeal Swabs (NPS) and 712 Nasal Swabs (NS).
  • Provenance: Collected from four (4) geographically diverse collection sites, one of which was outside the United States (OUS). Samples were prospective (fresh and/or frozen).
  • Timeframe: October 2020 to April 2021.

• Reproducibility Test Set:

  • Total replicates: 90 replicates per panel member (4 panel members), totaling 360 individual tests.
  • Panel members: 2 contrived low positive (LP), 2 contrived moderate positive (MP), 1 positive control, 1 negative (UTM).
  • Provenance: Tested at two (2) external clinical sites and one (1) internal site.
  • Study Design: Each panel member tested in triplicate per run, for 2 runs per day, for 5 non-consecutive testing days. Each site had two operators.

• Analytical Sensitivity (LoD) Test Set:

  • NPS: 40 replicates for confirmation.
  • NS: 20 replicates for confirmation.
  • WHO International Standard: 40 replicates for confirmation.

• Analytical Reactivity (Wet testing) Test Set:

  • 3 replicates per strain for 5 SARS-CoV-2 strains.

• Cross-Reactivity Test Set:

  • 3 replicates per organism for 47 different viruses, bacteria, and fungi (some 6 replicates for Leptospira interrogans).

• Potential Interfering Substances Test Set:

  • 3 replicates per substance (some 6 replicates for saliva and Zanamivir).

• Interference by Other Microorganisms Test Set:

  • 3 replicates per organism (some 6 replicates for Lactobacillus plantarum 17-5).

3. Number of Experts Used to Establish the Ground Truth for the Test Set and Qualifications of Those Experts

The ground truth for the clinical agreement test set was established using a "Composite Reference Method (CRM)" based on three (3) COVID-19 EUA approved NAAT assays. The rule for CRM agreement was: "Two out of three positive results determined 'Detected' CRM and two out of three negative results determined 'Not Detected' CRM."

The document does not specify the number or qualifications of experts (e.g., medical technologists, clinical lab scientists, or physicians) who performed these NAAT assays or interpreted their results for the CRM. It's implied that these were standard laboratory personnel qualified to run EUA-approved molecular diagnostic tests.

For analytical studies (LoD, reproducibility, reactivity, cross-reactivity, interference), the ground truth was based on the known composition and concentration of the samples (e.g., spiked RNA, cultured organisms, negative matrix). No external experts beyond the study design team would have been needed for this type of ground truth establishment.

4. Adjudication Method for the Test Set

For the clinical agreement test set, the adjudication method for the ground truth (CRM) was clearly defined: "Two out of three positive results determined 'Detected' CRM and two out of three negative results determined 'Not Detected' CRM." This is a form of consensus-based adjudication, specifically a majority rule.

For other analytical studies, adjudication was not described as it involved pre-defined positive/negative samples rather than interpretive human judgment.

5. If a Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study Was Done

No, a Multi-Reader Multi-Case (MRMC) comparative effectiveness study was not done. This study focuses on the in vitro diagnostic performance of a molecular assay (RT-PCR) in a laboratory setting, not on the interpretative performance of human readers (e.g., radiologists) with or without AI assistance. Therefore, there is no discussion of human readers or an effect size of AI assistance.

6. If a Standalone (i.e. algorithm only without human-in-the loop performance) Was Done

Yes, the primary clinical performance and analytical studies are standalone (algorithm only) performance. The Simplexa™ COVID-19 Direct is an RT-PCR assay. Its "performance" refers to its ability to detect SARS-CoV-2 RNA based on its set algorithms for signal detection (Ct values for S gene and ORF1ab targets) and interpretation. The results (detected/not detected) are determined directly by the instrument and its software, not by a human interpreting images or complex patterns. The human involvement is in sample preparation and loading, and reviewing the qualitative output from the instrument.

7. The Type of Ground Truth Used

• Clinical Agreement Test Set: Composite Reference Method (CRM) using results from three (3) COVID-19 EUA approved NAAT assays, with a "two out of three" majority rule for determining "Detected" or "Not Detected." This is a form of expert consensus based on other validated diagnostic tests.
• Analytical Studies (Reproducibility, LoD, Reactivity, Cross-Reactivity, Interference): Known analytical truth established by spiking known concentrations of inactivated viral particles or other organisms into negative matrices. This is a laboratory-controlled ground truth.

8. The Sample Size for the Training Set

The provided document describes a premarket notification (510(k)) for an in vitro diagnostic device. For such devices, particularly RT-PCR assays, the "training set" typically refers to internal development and optimization data, rather than a distinct, formally defined "training set" for machine learning algorithms that would be tested on a separate "test set."

The document does not specify a numerical sample size for a training set. The assay's design (primers, probes, conditions) would have been developed and optimized internally by DiaSorin Molecular using various samples and experiments, but these are not enumerated as a specific "training set" in this regulatory submission. The "in silico inclusivity analysis" section points to the use of GISAID databases (millions of sequences) which could be considered a form of "training data" for validating the generalizability of the primer/probe design, but not as a conventional, labeled "training set" in a machine learning context.

9. How the Ground Truth for the Training Set Was Established

Since a formal "training set" with established ground truth is not explicitly detailed in the way a machine learning model's training data would be, we can infer the following:

• Assay Development & Optimization: The ground truth for the development phase would have been based on known positive and negative samples, viral loads, and various SARS-CoV-2 strains or synthetic genetic material. This involves standard molecular biology techniques where the presence or absence of the target nucleic acid, and its concentration, are experimentally determined and controlled.
• In Silico Inclusivity: For the evaluation of primer/probe design against genetic variants, the "ground truth" is the published, annotated SARS-CoV-2 genome sequences available in the GISAID database. This involves bioinformatic analysis to determine sequence homology and potential binding efficacy.

Ask a specific question about this device

The BioFire® COVID-19 Test 2 is a qualitative nested multiplexed RT-PCR in vitro diagnostic test intended for use with the BioFire® FilmArray® 2.0 and BioFire® FilmArray® Torch Systems. The BioFire COVID-19 Test 2 detects nucleic acids from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in nasopharyngeal swabs (NPS) from symptomatic individuals suspected of COVID-19 by their healthcare provider.

Results are for the identification of SARS-CoV-2 RNA. The SARS-CoV-2 RNA is generally detectable in NPS specimens during the acute phase of infection. Positive results are indicative of the presence of SARS-CoV-2 RNA; clinical correlation with patient history and other diagnostic information is necessary to determine patient infection status. Positive results do not rule out co-infection with other pathogens.

Results are meant to be used in conjunction with other clinical, epidemiologic, and laboratory data, in accordance with the guidelines provided by the relevant public health authorities. The BioFire COVID-19 Test 2 is intended for use by trained medical and laboratory professionals in a laboratory setting or under the supervision of a trained laboratory professional.

For In Vitro Diagnostic Use.

The BioFire COVID-19 Test 2 is a multiplexed nucleic acid-based test for the detection of SARS-CoV-2 RNA from nasopharyngeal swabs (NPS) eluted in either transport medium or saline. The test was originally described and cleared in K211079. The BioFire COVID-19 Test 2 uses BioFire FilmArray technology and is for use with BioFire FilmArray 2.0 and BioFire FilmArray Torch instruments. Once the sample is injected into the FilmArray pouch is loaded into the Film Array instrument which performs all aspects of testing including nucleic acid extraction, reverse-transcription, and nested PCR with melt analysis. The currently cleared version of the test uses three SARS-CoV-2 assays and returns a 'SARS-CoV-2 Detected' call if one or more of the SARS-CoV-2 assays are positive.

The purpose of this submission is to display results for four additional SARS-CoV-2 assays which are currently present on the test, but for which results are masked through software. The assays are being unmasked as a mitigation against the risk of future SARS-CoV-2 variants affecting the sensitivity of the BioFire COVID-19 Test 2 due to mutations in assay primer regions. Note that to date BioFire Defense has not identified any variants that are predicted to affect the performance of the three-assay version of BioFire COVID-19 Test 2 described in K211079. These changes are being requested preemptively. The calling scheme when using the seven total SARS-CoV-2 assays will remain unchanged: one or more positive SARS-CoV-2 assay results will return an overall 'SARS-CoV-2 Detected' result.

Here's a breakdown of the acceptance criteria and the study details for the BioFire COVID-19 Test 2 based on the provided document:

1. Table of Acceptance Criteria and Reported Device Performance

The provided document describes a Special 510(k) submission where the primary change is the unmasking of four additional SARS-CoV-2 assays within an already cleared device (BioFire COVID-19 Test 2, K211079). Therefore, the "acceptance criteria" are implied by demonstrating equivalence to the predicate device's performance. The re-analysis of prior studies with the modified software is used to show this equivalence.

Since this is a submission for a software modification to unmask existing assays and not a de novo submission establishing new performance benchmarks, the acceptance criteria are largely defined by matching or showing no significant degradation from the predicate device's performance.

2. Sample Size Used for the Test Set and Data Provenance

The document states that no additional testing was performed for this submission. Instead, all study data previously submitted in K211079 were re-analyzed using the updated software.

Therefore, the "test set" for this specific submission is the re-analysis of data from the original K211079 (and potentially EUA200044) studies.

• Clinical Testing (DF-SDY-030617):
  • Sample Size: 69 positive samples, 454 negative samples. (Total = 523 samples)
  • Data Provenance: Prospective Clinical Evaluation. The document does not explicitly state the country of origin, but generally, FDA submissions for predicate devices are expected to include data from diverse geographic regions within the US, or from regions with comparable patient populations.
• Bench Testing: Sample sizes vary per study. For example:
  • LoD studies (DF-SDY-029904, DF-SDY-030331) involve serial dilutions and replicates.
  • Specificity/Exclusivity (DF-SDY-029903, DF-SDY-030333) involve testing a panel of organisms/viruses.
  • Reproducibility (DF-SDY-030398) involves testing replicates across multiple sites.

3. Number of Experts Used to Establish the Ground Truth for the Test Set and Qualifications of Those Experts

The ground truth for the clinical samples (DF-SDY-030617) would typically be established by a reference method, most commonly another FDA-authorized RT-PCR assay. The document does not specify the number or qualifications of experts involved in determining the ground truth for the clinical samples. For molecular diagnostics, "expert consensus" is less common for ground truth than established reference tests.

For bench testing studies (e.g., LoD, inclusivity, exclusivity), the ground truth is based on the known concentration of spiked analytes or the known identity of the assayed organisms/viruses, which does not typically involve human experts establishing ground truth in the same way as clinical image interpretation.

4. Adjudication Method for the Test Set

The document does not describe an adjudication method for the test set regarding human interpretation, as the device is an in vitro diagnostic (IVD) molecular test for direct detection of SARS-CoV-2 RNA. Results are determined by the instrument and its software.

For the clinical study, the reference method used to establish positive/negative status for the clinical samples would be the "adjudication." However, the method (e.g., comparison to a composite reference standard, or another cleared test) is not detailed here.

5. If a Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study was Done

No, an MRMC comparative effectiveness study was not done. This device is an in vitro diagnostic (IVD) device that performs a laboratory test. It does not involve human readers interpreting images or data with or without AI assistance. The output is a "SARS-CoV-2 Detected" or "SARS-CoV-2 Not Detected" result.

6. If a Standalone (Algorithm Only Without Human-in-the-Loop Performance) was done

Yes, the performance presented is standalone/algorithm only. The BioFire COVID-19 Test 2 is an IVD automated system. The results are generated directly by the device's software based on its internal processes (nucleic acid extraction, RT-PCR, melt analysis) without human interpretation of raw data. The study validates the device's ability to detect SARS-CoV-2 RNA independently. The phrasing "Software uses results from 7 assays" further confirms this.

7. The Type of Ground Truth Used

• Clinical Testing (DF-SDY-030617): The ground truth for the prospective clinical evaluation samples would most commonly be established by a highly sensitive and specific reference molecular assay (e.g., another FDA-cleared or EUA RT-PCR test for SARS-CoV-2), possibly combined with clinical diagnosis, but the document does not explicitly state this.
• Bench Testing:
  • LoD, Reactivity (Inclusivity): Ground truth is based on the known concentration and identity of specific SARS-CoV-2 strains/genomic material spiked into negative matrix.
  • Specificity (Exclusivity): Ground truth is based on the known identity of other respiratory pathogens or commensals tested.
  • Interfering Substances: Ground truth is based on the known presence of potential interfering substances without SARS-CoV-2.
• In Silico Analysis: Ground truth is based on publicly available genetic sequence databases (e.g., GISAID for SARS-CoV-2 variants).

8. The Sample Size for the Training Set

The document does not mention a separate training set for this submission. The purpose of this submission is to unmask existing assays on an already established device. The performance data presented are from validation and verification studies (effectively "test sets") previously conducted for the predicate device. For the original development of the BioFire COVID-19 Test 2 assays, various internal optimization and calibration steps (which could be considered analogous to "training") would have occurred, but these details are not part of this 510(k) summary.

9. How the Ground Truth for the Training Set was Established

As no specific "training set" is described for this 510(k) modification, this question is not directly applicable. For the initial development of the assays, the ground truth would have been established through a combination of:

• Bioinformatics: Designing primers and probes based on known SARS-CoV-2 sequences.
• Analytical studies: Testing synthetic targets and cultured virus at known concentrations.
• Clinical studies: Initial evaluation with patient samples where SARS-CoV-2 status was determined by a reference method.

Ask a specific question about this device