(104 days)
The BioCode Respiratory Pathogen Panel (RPP) is a qualitative multiplexed nucleic acid-based in vitro diagnostic test intended for use with BioCode MDx 3000 Instrument. The BioCode of the simultaneous detection and identification of nucleic acids from multiple viruses and bacteria extracted from nasopharyngeal swab (NPS) samples obtained from individuals with signs and/or symptoms of respiratory tract infection. The following pathogens and subtypes are identified using the BioCode RPP:
- Adenovirus
- · Coronavirus (229E, OC43, HKU1, and NL63)
- Human Metapneumovirus A/B
- · Influenza A, including subtypes H1, H1 2009 Pandemic, and H3
- Influenza B
- Parainfluenza Virus 1
- Parainfluenza Virus 2
- · Parainfluenza Virus 3
- · Parainfluenza Virus 4
- · Respiratory Syncytial Virus A/B
- Rhinovirus/Enterovirus
- · Bordetella pertussis
- Chlamydia pneumoniae
- Mycoplasma pneumoniae
The detection and identification of specific viral and bacterial nucleic acids from individuals exhibiting signs and/or symptoms of a respiratory infection aids in the diagnosis of respiratory infection if used in conjunction with other clinical and epidemiological information. The results of this test should not be used as the sole basis for diagnosis, treatment, or other patient management decisions.
Negative results in the setting of a respiratory illness may be due to infection with pathogens that are not detected by this test, or lower respiratory tract infection that may not be detected by a nasopharyngeal swab specimen. Positive results do not rule out co-infection with other organisms: the agent(s) detected by the BioCode RPP may not be the definite cause of disease. Additional laboratory testing (e.g. bacterial and viral culture, immunofluorescence, and radiography) may be necessary when evaluating a patient with possible respiratory tract infection.
Due to the genetic similarity between Human Rhinovirus, the BioCode RPP cannot differentiate them. A positive BioCode RPP Rhinovirus/Enterovirus result should be followed up using an alternate method (e.g., cell culture or sequence analysis) if differentiation is required. The BioCode RPP detects Human Rhinovirus with reduced sensitivity. If a more accurate Rhinovirus result is required, it is recommended that specimens found to be negative for Human Rhinovirus/Enterovirus after examination using BioCode RPP be confirmed by an alternate method (e.g. FDA cleared molecular tests).
Performance characteristics for Influenza A were established when Influenza A H1 2009 Pandemic and A H3 were the predominant Influenza A viruses in circulation. Performance of detecting Influenza A may vary if other Influenza A strains are circulating or a novel Influenza A virus emerges.
The BioCode® Respiratory Pathogen Panel is a respiratory pathogen multiplex nucleic acid test designed for use with the BioCode® MDx-3000 system. The BioCode® MDx-3000 is an automated system that integrates PCR amplification, target capture, signal generation and optical detection for multiple viral and bacterial pathogens from a single nasopharyngeal swab specimen collected in transport media. Specimens are processed and nucleic acids extracted with the NucliSens easyMAG or Roche MagNA Pure 96 automated systems. Once the PCR plate is set up and sealed, all other operations are automated on MDx-3000. The BioCode® RPP simultaneously tests for 17 pathogens and/or subtypes (see table below) from nasopharyngeal swab specimens collected in UTM or VTM. Results from the BioCode RPP test are available within about 5 hours, including off-board nucleic acids extraction.
Here's a breakdown of the acceptance criteria and the study that proves the device meets them, based on the provided text.
Based on the provided text, the device is an in vitro diagnostic test (BioCode Respiratory Pathogen Panel - RPP). The primary evidence for meeting acceptance criteria comes from clinical performance studies and analytical performance studies. The document does not explicitly state pre-defined acceptance criteria values (e.g., "Positive Agreement must be > X%"), but rather presents the results achieved and implicitly confirms they meet regulatory expectations for substantial equivalence.
Acceptance Criteria and Reported Device Performance
Since explicit numerical acceptance criteria were not stated, I'll present the reported performance, which implicitly met the necessary thresholds for FDA clearance. The document focuses on Positive Percent Agreement (PA) and Negative Percent Agreement (NA) compared to an FDA-cleared molecular multiplexed respiratory pathogen panel (the "comparator test").
Table of Acceptance Criteria (Implicit) and Reported Device Performance (Clinical Study - Total Specimens)
| Target | Implicit Acceptance Criterion (Threshold for Clearance) | Reported Device Performance (Positive Agreement (PA) % (95% CI)) | Reported Device Performance (Negative Agreement (NA) % (95% CI)) |
|---|---|---|---|
| Adenovirus | (Not explicitly defined, but achieved values were acceptable) | 87.2% (78.0%, 92.9%) | 98.4% (97.8%, 98.8%) |
| Bordetella pertussis | (Not explicitly defined, but achieved values were acceptable) | 100% (34.2%, 100%) | 99.3% (98.9%, 99.5%) |
| Chlamydia pneumoniae | (Not explicitly defined, but achieved values were acceptable) | 100% (51.0%, 100%) | 100% (99.8%, 100%) |
| Coronavirus | (Not explicitly defined, but achieved values were acceptable) | 83.5% (76.2%, 88.8%) | 99.1% (98.7%, 99.4%) |
| Human Metapneumovirus | (Not explicitly defined, but achieved values were acceptable) | 95.1% (90.2%, 97.6%) | 99.3% (98.9%, 99.6%) |
| Human Rhinovirus/Enterovirus | (Not explicitly defined, but achieved values were acceptable) | 80.8% (77.0%, 84.1%) | 98.4% (97.8%, 98.9%) |
| Influenza A | (Not explicitly defined, but achieved values were acceptable) | 96.4% (93.0%, 98.2%) | 99.0% (98.5%, 99.3%) |
| Influenza A H1 | No positive reference results for this subtype | N/A | 100% (99.9%, 100%) |
| Influenza A H1 2009pdm | (Not explicitly defined, but achieved values were acceptable) | 98.1% (90.1%, 99.7%) | 99.7% (99.3%, 99.8%) |
| Influenza A H3 | (Not explicitly defined, but achieved values were acceptable) | 93.6% (88.7%, 96.5%) | 99.6% (99.3%, 99.8%) |
| Influenza B | (Not explicitly defined, but achieved values were acceptable) | 94.4% (84.9%, 98.1%) | 99.5% (99.1%, 99.7%) |
| Mycoplasma pneumoniae | (Not explicitly defined, but achieved values were acceptable) | 100% (82.4%, 100%) | 99.2% (98.8%, 99.5%) |
| Parainfluenza Virus 1 | (Not explicitly defined, but achieved values were acceptable) | 88.2% (65.7%, 96.7%) | 100% (99.9%, 100%) |
| Parainfluenza Virus 2 | (Not explicitly defined, but achieved values were acceptable) | 83.3% (55.2%, 95.3%) | 99.9% (99.7%, 100%) |
| Parainfluenza Virus 3 | (Not explicitly defined, but achieved values were acceptable) | 96.7% (91.9%, 98.7%) | 99.3% (98.9%, 99.6%) |
| Parainfluenza Virus 4 | (Not explicitly defined, but achieved values were acceptable) | 88.9% (67.2%, 96.9%) | 99.9% (99.7%, 100%) |
| Respiratory Syncytial Virus | (Not explicitly defined, but achieved values were acceptable) | 98.0% (95.1%, 99.2%) | 99.1% (98.7%, 99.4%) |
Study Details:
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Sample Size and Data Provenance:
- Clinical Test Set (Prospective Study):
- Sample Size: 2649 residual nasopharyngeal swab (NPS) specimens in VTM or UTM.
- Data Provenance: Prospectively collected from patients suspected of respiratory tract infections at five geographically diverse clinical sites in the U.S. (August 2017 to May 2019). Specimens were either tested freshly (stored 2-8°C for no more than 7 days) or stored frozen and thawed later.
- Clinical Test Set (Archived Specimens - Retrospective Study):
- Sample Size: 165 clinical specimens (archived NPS in VTM or UTM).
- Data Provenance: Retrospective, preselected archives from source laboratories, chosen because they had previously tested positive for low-prevalence pathogens or were negative. These specimens were then randomized and blinded.
- Contrived Specimens (Analytical Performance):
- Chlamydia pneumoniae & Influenza A H1: 50 unique negative natural NPS in VTM or UTM specimens were spiked to create 100 positive samples (2X LOD or greater) and interspersed with negative samples. A total of 110 samples were tested.
- Reproducibility Study: 6 contrived positive samples and 1 negative sample, each extracted in triplicate, each assayed in singlet. This translates to 90 samples per concentration level per extraction type (easyMAG, MagNA Pure 96) across multiple sites/runs, total 90 (3x LoD) + 90 (1.5x LoD) + 450 (no analyte) = 630 for each virus/bacteria category listed (e.g., Adenovirus, Coronavirus, Human Metapneumovirus).
- Limit of Detection (LoD): 20 replicates for each target at or near the presumptive LoD.
- Analytical Reactivity/Inclusivity: Triplicate extractions for each strain/serotype.
- Analytical Specificity/Cross Reactivity: Triplicate extractions for each off-panel and on-panel organism.
- Interfering Substances/Microbes: Triplicate extractions for each sample/substance combination.
- Competitive Inhibition: Triplicate extractions for each pooled sample.
- Specimen Stability: Triplicate extractions for each time point and storage condition.
- Matrix Equivalency: Quadruplicate extractions for each pool/matrix combination.
- Clinical Test Set (Prospective Study):
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Number of Experts and Qualifications for Ground Truth:
- The document states that the BioCode RPP test results were compared against those from an "FDA-cleared molecular multiplexed respiratory pathogen panel" (Standard of Care/Comparator Test). This FDA-cleared comparator test serves as the primary "ground truth" for the clinical studies.
- For discrepant results in the clinical studies, further investigation was conducted by "performing independent molecular tests, including analytically validated PCR followed by bi-directional sequencing assays and alternate NAATs." This implies the use of specialized laboratory personnel with expertise in molecular diagnostics, but the exact number or specific qualifications (e.g., "radiologist with 10 years of experience") are not specified as this is a molecular diagnostic device, not an imaging device typically read by radiologists. The ground truth for presence/absence of pathogens is established by these comparator and confirmatory molecular tests.
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Adjudication Method for the Test Set:
- For the clinical studies (prospective and archived), the method for addressing discrepancies between the BioCode RPP and the comparator test was to perform "independent molecular tests, including analytically validated PCR followed by bi-directional sequencing assays and alternate NAATs." This serves as an adjudication method, where an orthogonal, high-accuracy method is used to determine the true positivity or negativity of discrepant samples. The specific "2+1" or "3+1" concensus type is not explicitly mentioned, but the retesting with confirmatory methods acts as a form of adjudication.
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Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study:
- No, an MRMC study was not done. This type of study (comparative effectiveness with human readers) is typical for AI-powered imaging devices where human interpretation is a key component. The BioCode RPP is an in vitro diagnostic (IVD) molecular test where the output is directly from the instrument analysis, not reliant on human interpretation of complex images. The study focuses on comparing the device's accuracy against a legally marketed predicate device/standard of care, not on improving human reader performance.
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Standalone Performance (Algorithm Only):
- Yes, the primary performance evaluation is standalone. The device ("BioCode RPP") is a qualitative multiplexed nucleic acid-based in vitro diagnostic test for use with the "BioCode MDx-3000 Instrument." The instrument integrates PCR, target capture, signal generation, and optical detection. The results are generated by the system (the "algorithm" in this context refers to the instrument's processing logic and interpretation algorithm), and the performance metrics (PA, NA) are reported for this system. There is no human interpretation component in the direct testing process that could be "assisted" by the algorithm.
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Type of Ground Truth Used:
- The ground truth for the clinical test sets (prospective and archived) was established by an FDA-cleared molecular multiplexed respiratory pathogen panel (Standard of Care).
- For discrepant results, expert molecular laboratory retesting using analytically validated PCR followed by bi-directional sequencing assays and alternate NAATs served as the confirmatory ground truth. This is a form of expert consensus/confirmatory testing using highly accurate molecular methods.
- For the analytical studies (e.g., LoD, inclusivity, specificity, inhibition), the ground truth was based on known concentrations of purified organisms/nucleic acids or genetically characterized strains (e.g., ATCC strains, Zeptometrix controls). This is a form of analytical ground truth where the content is precisely controlled and known.
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Sample Size for the Training Set:
- The document does not specify a separate "training set" sample size. For IVD devices, especially those based on molecular assays, a distinct "training set" as understood in machine learning (where an algorithm learns from labeled data) is not typically described in the same way. The device's underlying "algorithm" is the biochemical and optical detection system itself, and its performance characteristics are established through extensive analytical and clinical validation, not by training on a large dataset of patient samples in the AI sense. The design and validation are based on principles of molecular biology and traditional assay development.
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How the Ground Truth for the Training Set Was Established:
- As there isn't a "training set" in the machine learning sense, this question isn't directly applicable for this type of IVD device. The development of the assay (e.g., primer and probe design) would rely on known genetic sequences of the target pathogens. The validation data (clinical and analytical studies) demonstrate that the final, developed assay meets its intended performance, rather than being used to train a model in an iterative machine learning manner.
§ 866.3980 Respiratory viral panel multiplex nucleic acid assay.
(a)
Identification. A respiratory viral panel multiplex nucleic acid assay is a qualitative in vitro diagnostic device intended to simultaneously detect and identify multiple viral nucleic acids extracted from human respiratory specimens or viral culture. The detection and identification of a specific viral nucleic acid from individuals exhibiting signs and symptoms of respiratory infection aids in the diagnosis of respiratory viral infection when used in conjunction with other clinical and laboratory findings. The device is intended for detection and identification of a combination of the following viruses:(1) Influenza A and Influenza B;
(2) Influenza A subtype H1 and Influenza A subtype H3;
(3) Respiratory Syncytial Virus subtype A and Respiratory Syncytial Virus subtype B;
(4) Parainfluenza 1, Parainfluenza 2, and Parainfluenza 3 virus;
(5) Human Metapneumovirus;
(6) Rhinovirus; and
(7) Adenovirus.
(b)
Classification. Class II (special controls). The special controls are:(1) FDA's guidance document entitled “Class II Special Controls Guidance Document: Respiratory Viral Panel Multiplex Nucleic Acid Assay;”
(2) For a device that detects and identifies Human Metapneumovirus, FDA's guidance document entitled “Class II Special Controls Guidance Document: Testing for Human Metapneumovirus (hMPV) Using Nucleic Acid Assays;” and
(3) For a device that detects and differentiates Influenza A subtype H1 and subtype H3, FDA's guidance document entitled “Class II Special Controls Guidance Document: Testing for Detection and Differentiation of Influenza A Virus Subtypes Using Multiplex Nucleic Acid Assays.” See § 866.1(e) for the availability of these guidance documents.