(180 days)
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
| Parameter | Acceptance Criteria (Implicit) | Reported Device Performance |
|---|---|---|
| Analytical Sensitivity (LoD) | Consistent detection at specified viral concentrations | NPS-UTM/VTM: 403 copies/mL (100% positive for both reagent lots) |
| NPS-eNAT: 403 copies/mL (100% positive for both reagent lots) | ||
| NS-UTM/VTM: 462 copies/mL (100% positive for both reagent lots) | ||
| WHO 1st International Standard (NS-UTM/VTM): 1000 IU/mL (100% positive for E/RdRP, 95% for N2) | ||
| Analytical Reactivity (Inclusivity) | Detection of all circulating SARS-CoV-2 variants/lineages | In silico: Predicted 100% inclusivity for E and RdRP amplicons and probes, ~99.95% for N2 amplicons and probes across various variants. Updated analysis (Aug 2022-Sep 2023) maintained similar high inclusivity (>97.8%). |
| Wet-testing: 61 SARS-CoV-2 strains (intact viral particles and RNA transcripts) tested positive in all 3 replicates. | ||
| Analytical Specificity (Exclusivity) | No cross-reactivity with common respiratory microorganisms | In silico: No expected cross-reactivity with listed organisms, except for known E-gene cross-reactivity with Human and Bat SARS-coronavirus. |
| Wet-testing: No false positives with 62 non-SARS-CoV-2 microorganisms, except for SARS-coronavirus Urbani (expected E gene cross-reactivity). | ||
| Microbial Interference | No inhibition of SARS-CoV-2 detection by commensal microorganisms | All 8/8 positive replicate samples correctly identified as SARS-CoV-2 POSITIVE in the presence of 18 common commensal viral and bacterial strains. |
| Potentially Interfering Substances | No interference with test performance by common nasal substances | 21 out of 23 substances showed no interference. |
| Fluticasone Propionate (5 µg/mL): 1/8 Invalid for negative & positive samples. No interference at 2.5 µg/mL. | ||
| Mucin type I-S (2.5 mg/mL): 1/8 Invalid for negative samples. No interference at 1.25 mg/mL. | ||
| Carryover Contamination | No contamination from high positive samples to negative samples | All 40 positive samples correctly reported POSITIVE and all 42 negative samples correctly reported NEGATIVE (tested immediately after high positive samples). |
| Reproducibility (Qualitative) | High agreement across operators, sites, and days for different panel members | Negative: 100% agreement |
| SARS-CoV-2 Low Pos: 100% agreement | ||
| SARS-CoV-2 Mod Pos: 100% agreement | ||
| (All with 95% CI of 95.9% - 100%) | ||
| Reproducibility (Quantitative - Ct values) | Low variability in Ct values across different factors | Coefficient of Variation (CV) for SPC, E, N2, and RdRP analytes generally low (ranging from 0.0% to 2.0%) across site, operator, day, and error. |
| Clinical Performance (NPS) | High Positive Percent Agreement (PPA) and Negative Percent Agreement (NPA) | PPA: 98.2% (95% CI: 93.8% - 99.5%) |
| NPA: 99.1% (95% CI: 98.1% - 99.6%) | ||
| Non-determinate rate: 0.7% (7/961) | ||
| Clinical Performance (NS) | High Positive Percent Agreement (PPA) and Negative Percent Agreement (NPA) | PPA: 99.0% (95% CI: 94.8% - 99.8%) |
| NPA: 99.1% (95% CI: 98.2% - 99.6%) | ||
| Non-determinate rate: 0.4% (4/973) |
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.
- Total specimens: 1783
-
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.
- Limit of Detection (LoD):
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.
§ 866.3981 Device to detect and identify nucleic acid targets in respiratory specimens from microbial agents that cause the SARS-CoV-2 respiratory infection and other microbial agents when in a multi-target test.
(a)
Identification. A device to detect and identify nucleic acid targets in respiratory specimens from microbial agents that cause the SARS-CoV-2 respiratory infection and other microbial agents when in a multi-target test is an in vitro diagnostic device intended for the detection and identification of SARS-CoV-2 and other microbial agents when in a multi-target test in human clinical respiratory specimens from patients suspected of respiratory infection who are at risk for exposure or who may have been exposed to these agents. The device is intended to aid in the diagnosis of respiratory infection in conjunction with other clinical, epidemiologic, and laboratory data or other risk factors.(b)
Classification. Class II (special controls). The special controls for this device are:(1) The intended use in the labeling required under § 809.10 of this chapter must include a description of the following: Analytes and targets the device detects and identifies, the specimen types tested, the results provided to the user, the clinical indications for which the test is to be used, the specific intended population(s), the intended use locations including testing location(s) where the device is to be used (if applicable), and other conditions of use as appropriate.
(2) Any sample collection device used must be FDA-cleared, -approved, or -classified as 510(k) exempt (standalone or as part of a test system) for the collection of specimen types claimed by this device; alternatively, the sample collection device must be cleared in a premarket submission as a part of this device.
(3) The labeling required under § 809.10(b) of this chapter must include:
(i) A detailed device description, including reagents, instruments, ancillary materials, all control elements, and a detailed explanation of the methodology, including all pre-analytical methods for processing of specimens;
(ii) Detailed descriptions of the performance characteristics of the device for each specimen type claimed in the intended use based on analytical studies including the following, as applicable: Limit of Detection, inclusivity, cross-reactivity, interfering substances, competitive inhibition, carryover/cross contamination, specimen stability, precision, reproducibility, and clinical studies;
(iii) Detailed descriptions of the test procedure(s), the interpretation of test results for clinical specimens, and acceptance criteria for any quality control testing;
(iv) A warning statement that viral culture should not be attempted in cases of positive results for SARS-CoV-2 and/or any similar microbial agents unless a facility with an appropriate level of laboratory biosafety (
e.g., BSL 3 and BSL 3+, etc.) is available to receive and culture specimens; and(v) A prominent statement that device performance has not been established for specimens collected from individuals not identified in the intended use population (
e.g., when applicable, that device performance has not been established in individuals without signs or symptoms of respiratory infection).(vi) Limiting statements that indicate that:
(A) A negative test result does not preclude the possibility of infection;
(B) The test results should be interpreted in conjunction with other clinical and laboratory data available to the clinician;
(C) There is a risk of incorrect results due to the presence of nucleic acid sequence variants in the targeted pathogens;
(D) That positive and negative predictive values are highly dependent on prevalence;
(E) Accurate results are dependent on adequate specimen collection, transport, storage, and processing. Failure to observe proper procedures in any one of these steps can lead to incorrect results; and
(F) When applicable (
e.g., recommended by the Centers for Disease Control and Prevention, by current well-accepted clinical guidelines, or by published peer-reviewed literature), that the clinical performance may be affected by testing a specific clinical subpopulation or for a specific claimed specimen type.(4) Design verification and validation must include:
(i) Detailed documentation, including performance results, from a clinical study that includes prospective (sequential) samples for each claimed specimen type and, as appropriate, additional characterized clinical samples. The clinical study must be performed on a study population consistent with the intended use population and compare the device performance to results obtained using a comparator that FDA has determined is appropriate. Detailed documentation must include the clinical study protocol (including a predefined statistical analysis plan), study report, testing results, and results of all statistical analyses.
(ii) Risk analysis and documentation demonstrating how risk control measures are implemented to address device system hazards, such as Failure Modes Effects Analysis and/or Hazard Analysis. This documentation must include a detailed description of a protocol (including all procedures and methods) for the continuous monitoring, identification, and handling of genetic mutations and/or novel respiratory pathogen isolates or strains (
e.g., regular review of published literature and periodic in silico analysis of target sequences to detect possible mismatches). All results of this protocol, including any findings, must be documented and must include any additional data analysis that is requested by FDA in response to any performance concerns identified under this section or identified by FDA during routine evaluation. Additionally, if requested by FDA, these evaluations must be submitted to FDA for FDA review within 48 hours of the request. Results that are reasonably interpreted to support the conclusion that novel respiratory pathogen strains or isolates impact the stated expected performance of the device must be sent to FDA immediately.(iii) A detailed description of the identity, phylogenetic relationship, and other recognized characterization of the respiratory pathogen(s) that the device is designed to detect. In addition, detailed documentation describing how to interpret the device results and other measures that might be needed for a laboratory diagnosis of respiratory infection.
(iv) A detailed device description, including device components, ancillary reagents required but not provided, and a detailed explanation of the methodology, including molecular target(s) for each analyte, design of target detection reagents, rationale for target selection, limiting factors of the device (
e.g., saturation level of hybridization and maximum amplification and detection cycle number, etc.), internal and external controls, and computational path from collected raw data to reported result (e.g., how collected raw signals are converted into a reported signal and result), as applicable.(v) A detailed description of device software, including software applications and hardware-based devices that incorporate software. The detailed description must include documentation of verification, validation, and hazard analysis and risk assessment activities, including an assessment of the impact of threats and vulnerabilities on device functionality and end users/patients as part of cybersecurity review.
(vi) For devices intended for the detection and identification of microbial agents for which an FDA recommended reference panel is available, design verification and validation must include the performance results of an analytical study testing the FDA recommended reference panel of characterized samples. Detailed documentation must be kept of that study and its results, including the study protocol, study report for the proposed intended use, testing results, and results of all statistical analyses.
(vii) For devices with an intended use that includes detection of Influenza A and Influenza B viruses and/or detection and differentiation between the Influenza A virus subtypes in human clinical specimens, the design verification and validation must include a detailed description of the identity, phylogenetic relationship, or other recognized characterization of the Influenza A and B viruses that the device is designed to detect, a description of how the device results might be used in a diagnostic algorithm and other measures that might be needed for a laboratory identification of Influenza A or B virus and of specific Influenza A virus subtypes, and a description of the clinical and epidemiological parameters that are relevant to a patient case diagnosis of Influenza A or B and of specific Influenza A virus subtypes. An evaluation of the device compared to a currently appropriate and FDA accepted comparator method. Detailed documentation must be kept of that study and its results, including the study protocol, study report for the proposed intended use, testing results, and results of all statistical analyses.
(5) When applicable, performance results of the analytical study testing the FDA recommended reference panel described in paragraph (b)(4)(vi) of this section must be included in the device's labeling under § 809.10(b) of this chapter.
(6) For devices with an intended use that includes detection of Influenza A and Influenza B viruses and/or detection and differentiation between the Influenza A virus subtypes in human clinical specimens in addition to detection of SARS-CoV-2 and similar microbial agents, the required labeling under § 809.10(b) of this chapter must include the following:
(i) Where applicable, a limiting statement that performance characteristics for Influenza A were established when Influenza A/H3 and A/H1-2009 (or other pertinent Influenza A subtypes) were the predominant Influenza A viruses in circulation.
(ii) Where applicable, a warning statement that reads if infection with a novel Influenza A virus is suspected based on current clinical and epidemiological screening criteria recommended by public health authorities, specimens should be collected with appropriate infection control precautions for novel virulent influenza viruses and sent to State or local health departments for testing. Viral culture should not be attempted in these cases unless a BSL 3+ facility is available to receive and culture specimens.
(iii) Where the device results interpretation involves combining the outputs of several targets to get the final results, such as a device that both detects Influenza A and differentiates all known Influenza A subtypes that are currently circulating, the device's labeling must include a clear interpretation instruction for all valid and invalid output combinations, and recommendations for any required followup actions or retesting in the case of an unusual or unexpected device result.
(iv) A limiting statement that if a specimen yields a positive result for Influenza A, but produces negative test results for all specific influenza A subtypes intended to be differentiated (
i.e., H1-2009 and H3), this result requires notification of appropriate local, State, or Federal public health authorities to determine necessary measures for verification and to further determine whether the specimen represents a novel strain of Influenza A.(7) If one of the actions listed at section 564(b)(1)(A) through (D) of the Federal Food, Drug, and Cosmetic Act occurs with respect to an influenza viral strain, or if the Secretary of Health and Human Services determines, under section 319(a) of the Public Health Service Act, that a disease or disorder presents a public health emergency, or that a public health emergency otherwise exists, with respect to an influenza viral strain:
(i) Within 30 days from the date that FDA notifies manufacturers that characterized viral samples are available for test evaluation, the manufacturer must have testing performed on the device with those influenza viral samples in accordance with a standardized protocol considered and determined by FDA to be acceptable and appropriate.
(ii) Within 60 days from the date that FDA notifies manufacturers that characterized influenza viral samples are available for test evaluation and continuing until 3 years from that date, the results of the influenza emergency analytical reactivity testing, including the detailed information for the virus tested as described in the certificate of authentication, must be included as part of the device's labeling in a tabular format, either by:
(A) Placing the results directly in the device's labeling required under § 809.10(b) of this chapter that accompanies the device in a separate section of the labeling where analytical reactivity testing data can be found, but separate from the annual analytical reactivity testing results; or
(B) In a section of the device's label or in other labeling that accompanies the device, prominently providing a hyperlink to the manufacturer's public website where the analytical reactivity testing data can be found. The manufacturer's website, as well as the primary part of the manufacturer's website that discusses the device, must provide a prominently placed hyperlink to the website containing this information and must allow unrestricted viewing access.