(82 days)
The Cepheid Xpert Norovirus Assay, performed on the GeneXpert® Instrument Systems, is a qualitative in vitro diagnostic test for the identification and differentiation of norovirus genogroup I and genogroup II RNA from raw or unpreserved unformed stool specimens collected from individuals with symptoms of acute gastroenteritis. The test utilizes automated real-time reverse transcriptase polymerase chain reaction (RT-PCR) to detect norovirus RNA. The Xpert Norovirus Assay is intended to aid in the diagnosis of norovirus infections when used in conjunction with clinical evaluation, laboratory findings, and epidemiological information. The assay also aids in the detection and identification of norovirus infections in the context of outbreaks.
The Xpert Norovirus Assay is an automated in vitro diagnostic test for detection and differentiation of nucleic acid sequences for norovirus genogroup I and genogroup II from raw or unpreserved unformed (liquid or soft) stool specimens collected from individuals with symptoms of acute gastroenteritis. The test utilizes automated, multiplex real-time, reverse transcriptase polymerase chain reaction (RT-PCR) to detect specific viral gene sequences associated with norovirus genogroup I and genogroup II. The Xpert Norovirus Assay is intended to aid in the diagnosis of norovirus infections when used in conjunction with clinical evaluation, laboratory findings, and epidemiological information. The assay also aids in the detection and identification of norovirus infections in the context of outbreaks.
The Xpert Norovirus Assay is performed on the Cepheid GeneXpert Instrument Systems (GeneXpert Dx, GeneXpert Infinity-48, GeneXpert Infinity-48s, and GeneXpert Infinity-80 systems). The GeneXpert Instrument System platform automates sample preparation, amplification and real-time detection.
The GeneXpert Instrument Systems require the use of single-use, disposable cartridges (the Xpert Norovirus Cartridges) that hold the PCR reagents and host the PCR process. Because the cartridges are self-contained and specimens never come into contact with working parts of the instrument modules, cross-contamination between samples is minimized.
The Xpert Norovirus Assay includes reagents for the detection and differentiation of nucleic acid sequences for norovirus genogroup I and genogroup II from raw or unpreserved unformed human stool specimens collected from patients with signs and symptoms of acute gastroenteritis. All reagents except the Sample Reagent are contained pre-loaded in the cartridge. A Sample Processing Control (SPC) and a Probe Check Control (PCC) are also included in the cartridge. The SPC is present to control for adequate processing of the target viruses and to monitor the presence of inhibitors in the PCR reaction. The Probe Check Control (PCC) verifies reagent rehydration, PCR tube filling in the cartridge, probe integrity and dye stability.
The single-use, multi-chambered fluidic cartridges are designed to complete sample preparation and real-time RT-PCR for detection and differentiation of norovirus genogroup I and genogroup II viral RNA in 90 minutes or less. The GeneXpert Instrument Systems, comprised of the GeneXpert Dx Systems and the GeneXpert Infinity Systems, have 1 to 80 randomly accessible modules, depending upon the instrument, that are each capable of performing separate sample preparation and real-time PCR and RT-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 PCR and RT-PCR and detection.
Specimens are collected following the user's institution standard procedures for collecting stool specimens for norovirus testing and sent to the GeneXpert® testing area for processing. The specimen may be stored at 2-8 ℃ for up to two days prior to processing. When ready to process the specimen, a single-use disposable dry swab is used for transfer of the stool specimen to the Sample Reagent bottle that is provided with the Xpert Norovirus Assay kit. The user vortexes the capped Sample Reagent bottle for 10 seconds and transfers the entire contents to the sample chamber in the top of the disposable fluidic cartridge with a transfer pipette. The user initiates a test from the system user interface and places the cartridge into the GeneXpert instrument platform, which performs hands-off real-time, multiplex polymerase chain reaction (PCR) for detection of RNA. The results are automatically generated at the end of the process in a report that can be viewed and printed.
The document describes the Xpert Norovirus Assay, a qualitative in vitro diagnostic test for norovirus genogroup I and genogroup II RNA in stool specimens.
Here's an analysis of the acceptance criteria and the study that proves the device meets them:
1. A table of acceptance criteria and the reported device performance
The document does not explicitly state "acceptance criteria" for the clinical performance in a singular, consolidated table with pass/fail thresholds. Instead, it provides the observed performance metrics (PPA, NPA) with 95% confidence intervals from a clinical study, implying that these values were considered acceptable by the FDA for substantial equivalence. For analytical performance (LoD, specificity), the values obtained are presented as the device's performance without explicit numerical targets being stated beforehand.
Below is a table summarizing the reported device performance, with implied acceptance based on FDA clearance.
| Test Parameter / Criteria | Acceptance Criteria (Implied) | Reported Device Performance (Xpert Norovirus Assay) |
|---|---|---|
| Analytical Performance | ||
| Limit of Detection (LoD) Norovirus GI.3 | Reproducibly distinguished from negative samples with 95% confidence | 5.7 x 105 copies/mL (95% CI: 4.64 x 105 – 6.67 x 105) |
| Limit of Detection (LoD) Norovirus GII.4 | Reproducibly distinguished from negative samples with 95% confidence | 3.0 x 105 copies/mL (95% CI: 1.25 x 105 – 1.78 x 105) |
| Analytical Specificity (Cross-reactivity) | 100% specificity (no false positives for other organisms) | 100% (All 68 organisms tested were correctly reported as NORO GI NOT DETECTED; NORO GII NOT DETECTED) |
| Analytical Reactivity (Inclusivity) | Detect all 31 tested norovirus genotypes (GI and GII) | All 31 norovirus strains (representing GI and GII genotypes) tested near LoD concentration resulted in POS for the correct genogroup and NEG for the other. |
| Potential Interfering Substances (Inhibition/False-Negatives) | No significant inhibition or false negatives | Inhibition observed with Benzalkonium chloride (1% w/v, 0.2% w/v, 0.04% w/v), false negatives for Norovirus GII at 1% w/v. Statistically significant inhibitory effect on Norovirus GII Ct with Barium sulfate (5% w/w). No other substances found inhibitory or causing false negatives. (Note: These are findings, not direct "pass" criteria, but inform proper use instructions). |
| Carry-Over Contamination | No carry-over contamination | 19/20 positive samples correctly detected, 1 reported as ERROR. All 22 negative samples correctly reported. (Demonstrates acceptable control of carry-over for the claimed self-contained system). |
| Clinical Performance (Fresh, Prospective Specimens) | ||
| Norovirus GI: Positive Percent Agreement (PPA) | Sufficiently high agreement with reference method | 100% (95% CI: 73.5-100) |
| Norovirus GI: Negative Percent Agreement (NPA) | Sufficiently high agreement with reference method | 99.6% (95% CI: 98.9-99.9) |
| Norovirus GII: Positive Percent Agreement (PPA) | Sufficiently high agreement with reference method | 98.5% (95% CI: 91.7-100) |
| Norovirus GII: Negative Percent Agreement (NPA) | Sufficiently high agreement with reference method | 98.8% (95% CI: 97.8-99.4) |
| Clinical Performance (Frozen, Archived Specimens) | ||
| Norovirus GI: Positive Percent Agreement (PPA) | Sufficiently high agreement with reference method | 98.1% (95% CI: 93.2-99.8) |
| Norovirus GI: Negative Percent Agreement (NPA) | Sufficiently high agreement with reference method | 94.6% (95% CI: 91.8-96.6) |
| Norovirus GII: Positive Percent Agreement (PPA) | Sufficiently high agreement with reference method | 100% (95% CI: 96.7-100) |
| Norovirus GII: Negative Percent Agreement (NPA) | Sufficiently high agreement with reference method | 96.8% (95% CI: 94.5-98.3) |
| Reproducibility | High agreement between sites, days, operators | Overall agreement for Neg (100%), GI-Low Pos (93.3%), GI-Mod Pos (100%), GII-Low Pos (95.0%), GII-Mod Pos (98.3%). High Neg samples showed lower agreement (GI: 25.0%, GII: 30.0%) as expected due to being near LoD. Ct values showed low CVs across sites, days, and operators. |
| Instrument System Precision | High agreement between GeneXpert Dx and Infinity systems | Overall agreement for Neg (100%), GI-Low Pos (98.4%), GI-Mod Pos (100%), GII-Low Pos (88.5%), GII-Mod Pos (100%). High Neg samples showed lower agreement (GI: 16.2%, GII: 28.7%). Ct values showed low CVs across instruments, lots, days, and operators. |
2. Sample size used for the test set and the data provenance (e.g. country of origin of the data, retrospective or prospective)
- Clinical Study Test Set Sample Size:
- Norovirus GI: 1403 total specimens (914 fresh, prospectively collected; 489 frozen, archived).
- Norovirus GII: 1401 total specimens (914 fresh, prospectively collected; 487 frozen, archived).
- Data Provenance:
- Origin: The clinical studies were evaluated at seven institutions in the U.S. and the E.U.
- Retrospective or Prospective:
- Prospective: 914 fresh, prospectively collected specimens.
- Retrospective (Archived): 489 frozen, archived specimens for GI and 487 for GII.
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 document states that the performance of the Xpert Norovirus Assay was compared to a composite reference test method performed at the CDC (Atlanta, GA). It does not specify the number of individual experts, their specific qualifications (e.g., radiologist with 10 years of experience), or if multiple experts were involved in interpreting the results of the composite reference test. The "composite reference test" itself acts as the ground truth.
4. Adjudication method (e.g. 2+1, 3+1, none) for the test set
The document does not describe an explicit adjudication method (like 2+1 or 3+1) involving multiple human readers for establishing the ground truth. The ground truth was established by a "composite comparator method that consisted of a combination of Center for Disease Control and Prevention (CDC) RT-PCR assays and bi-directional sequencing for norovirus". This implies a definitive laboratory-based method rather than a consensus among human interpreters.
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
No, a multi-reader multi-case (MRMC) comparative effectiveness study was not performed. This device is a diagnostic assay (an in-vitro diagnostic test), not an AI-assisted imaging device or a decision support system for human readers. Therefore, the concept of "human readers improve with AI vs without AI assistance" is not applicable to this submission.
6. If a standalone (i.e. algorithm only without human-in-the-loop performance) was done
Yes, the primary clinical performance evaluation (PPA and NPA) presented for the Xpert Norovirus Assay is a standalone (algorithm only) performance measure. The assay processes the sample and provides a result ("NORO GI DETECTED," "NORO GII DETECTED," or "NOT DETECTED") without human interpretive input into the test result itself. The test is stated to be "intended to aid in the diagnosis... when used in conjunction with clinical evaluation, laboratory findings, and epidemiological information," implying that clinicians use the standalone result in their overall patient management, but the device performance metrics themselves are standalone.
7. The type of ground truth used (expert consensus, pathology, outcomes data, etc.)
The ground truth used was a composite reference method. Specifically, it consisted of:
- Center for Disease Control and Prevention (CDC) RT-PCR assays
- Bi-directional sequencing for norovirus
This is a laboratory-based, molecular diagnostic ground truth, considered highly authoritative for viral detection.
8. The sample size for the training set
This document describes a premarket notification for an IVD device, which typically involves analytical and clinical verification/validation studies. It does not explicitly mention a "training set" in the context of machine learning, as the device is a molecular diagnostic assay based on RT-PCR, not an AI/ML algorithm that requires training data in the same way. The studies outlined are for evaluating the device's performance against established methods.
9. How the ground truth for the training set was established
As there is no "training set" described for a machine learning algorithm, this question is not applicable in the context of this IVD device submission. The described studies are validation studies against a composite reference method.
§ 866.3990 Gastrointestinal microorganism multiplex nucleic acid-based assay.
(a)
Identification. A gastrointestinal microorganism multiplex nucleic acid-based assay is a qualitativein vitro diagnostic device intended to simultaneously detect and identify multiple gastrointestinal microbial nucleic acids extracted from human stool specimens. The device detects specific nucleic acid sequences for organism identification as well as for determining the presence of toxin genes. The detection and identification of a specific gastrointestinal microbial nucleic acid from individuals exhibiting signs and symptoms of gastrointestinal infection aids in the diagnosis of gastrointestinal infection when used in conjunction with clinical evaluation and other laboratory findings. A gastrointestinal microorganism multiplex nucleic acid-based assay also aids in the detection and identification of acute gastroenteritis in the context of outbreaks.(b)
Classification. Class II (special controls). The special controls are set forth in FDA's guideline document entitled: “Class II Special Controls Guideline: Gastrointestinal Microorganism Multiplex Nucleic Acid-Based Assays for Detection and Identification of Microorganisms and Toxin Genes from Human Stool Specimens.” For availability of the guideline document, see § 866.1(e).