(234 days)
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.
| Acceptance Criterion (Test Type) | Reported Device Performance |
|---|---|
| Analytical Sensitivity (LoD) - Clinical NPS-UTM/VTM Matrix | 403 copies/mL (N2 target) |
| Analytical Sensitivity (LoD) - Clinical NS-UTM/VTM Matrix | 462 copies/mL (N2 target) |
| Analytical Sensitivity (LoD) - WHO First International Standard SARS-CoV-2 RNA in clinical NS-UTM/VTM Matrix | 1000 IU/mL |
| Analytical Inclusivity (Primers E, N2, RdRP amplicons) | E: 100%, N2: 99.95%, RdRP: 100% (Predicted) |
| Analytical Inclusivity (Probes E, N2, RdRP) | E: 100%, N2: 100%, RdRP: 99.6% (Predicted) |
| Analytical Inclusivity (Wet-Testing, 61 strains) | 100% detection of all 61 SARS-CoV-2 strains tested (3/3 replicates positive for all) |
| Analytical Exclusivity (In silico) | No potential unintended cross-reactivity with listed organisms (E gene cross-reactivity with SARS-CoV, Human and Bat SARS-coronavirus expected) |
| Analytical Exclusivity (Wet-Testing) | No cross-reactivity with 62 non-SARS-CoV-2 microorganisms (except expected E gene cross-reactivity with SARS-coronavirus Urbani) |
| Microbial Interference | No interference from 18 commensal microorganisms at tested concentrations (8/8 correct results) |
| Potentially Interfering Substances | No interference from 21 of 23 substances at tested concentrations. Fluticasone propionate nasal spray and mucin type I-S interfered at higher concentrations, but not at half the concentration. |
| Carryover Contamination | 0% carryover contamination (40/40 positive, 42/42 negative correctly identified) |
| Reproducibility (Qualitative Agreement - Negative) | 99.3% (142/143) [96.1% - 99.9% CI] |
| Reproducibility (Qualitative Agreement - Low Positive) | 100% (144/144) [97.4% - 100% CI] |
| Reproducibility (Qualitative Agreement - Moderate Positive) | 100% (144/144) [97.4% - 100% CI] |
| Single-Site Precision (Qualitative Agreement - Negative) | 100% (80/80) [95.4%-100.0% CI] |
| Single-Site Precision (Qualitative Agreement - Low Positive) | 100% (80/80) [95.4%-100.0% CI] |
| Single-Site Precision (Qualitative Agreement - Moderate Positive) | 100% (80/80) [95.4%-100.0% CI] |
| Clinical Performance (Overall PPA) | 98.1% (95% CI: 96.7% - 98.9%) |
| Clinical Performance (Overall NPA) | 98.3% (95% CI: 97.7% - 98.7%) |
| Clinical Performance (NPS PPA) | 97.0% (95% CI: 94.4% - 98.4%) |
| Clinical Performance (NPS NPA) | 98.2% (95% CI: 97.4% - 98.8%) |
| Clinical Performance (NS PPA) | 99.3% (95% CI: 97.5% - 99.8%) |
| Clinical Performance (NS NPA) | 98.3% (95% CI: 97.5% - 98.8%) |
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.
§ 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.