(201 days)
The Applied Biosystems TaqPath COVID-19, Flu A, Flu B, RSV Select Panel is a multiplex, real-time reverse transcription polymerase chain reaction (RT-PCR) in vitro diagnostic test for the qualitative detection and differentiation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza B virus, and respiratory syncytial virus (RSV). Nucleic acids are isolated and purified from nasopharyngeal (NP) swab and anterior nasal (AN) swab specimens obtained from individuals exhibiting signs and symptoms of a respiratory tract infection. Clinical signs and symptoms of respiratory viral infection due to SARS-CoV-2, influenza, and RSV can be similar. This test is intended to aid in the differential diagnosis of SARS-CoV-2, influenza B, and RSV A/B (undifferentiated) infections in humans and is not intended to detect influenza C virus infections.
Nucleic acids from the viral organisms identified by this test are generally detectable in NP and AN swab specimens during the acute phase of infection and identification of specific viral nucleic acids from individuals exhibiting signs and symptoms of respiratory tract infective of the presence of the identified virus and aids in diagnosis if used in conjunction with other clinical and epidemiological information, and laboratory findings.
The results of this test should not be used as the sole basis for diagnosis, treatment, or other patient management decisions. Positive results do not rule out coinfection with other organism(s) detected by the Applied Biosystems TaqPath COVID-19, Flu A, Flu B, RSV Select Panel may not be the definite cause of disease. Negative results do not preclude SARS-CoV-2, influenza A virus, influenza B virus, or RSV infections.
The Applied Biosystems TaqPath COVID-19, Flu A, Flu B, RSV Select Panel is intended for use by qualified and trained 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, Flu A, Flu B, RSV Select Panel is a multiplex, real-time reverse transcription polymerase chain reaction (RT-PCR) test. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A, influenza B, respiratory syncytial virus (RSV) A/B and RNase P primer and probe sets are designed to detect viral RNA in nasopharyngeal (NP) and anterior nasal (AN) swab specimens from individuals exhibiting signs and symptoms of a respiratory tract infection.
Each TaqPath™ COVID-19, Flu A, Flu B, RSV Select Panel includes the following components:
- TaqPath™ COVID-19, Flu A, Flu B, RSV Select Assay-Multiplex assays that contain . primer and probe sets specific to the following targets:
- Three SARS-CoV-2 targets (Orfla, Orf1b, and N genes) .
- . Two influenza A virus targets (PB1 & M genes)
- I Two influenza B virus targets (M & NS genes)
- . Three RSV targets (NP, M, and L protein genes)
- l RNase P (internal human sample collection control)
- TaqPath™ COVID-19, Flu A, Flu B, RSV Select Positive Control—Inactivated viral . control that contains SARS-CoV-2, influenza A, influenza B, and RSV.
- TaqPath™ COVID-19, Flu A, Flu B, RSV Select Negative Control—MS2 packaged RNA . control that contains targets specific to RNase P genomic regions targeted by the assay.
- TaqPath™ 1-Step Select Master Mix (No ROX)—Ready-to-use PCR mix, including . reverse transcriptase, polymerase, dNTPs, salts, and buffer.
- . Package Insert -- Provides the instructions and the link to download the instructions for use and other assets (including the ADF)
- An Assay Definition File (ADF) applicable to the instrument used in the workflow . (available via download).
In addition to the SARS-CoV-2, influenza A, influenza B and RSV viral assay targets, the assay portion of the panel includes RNase P, which serves as an endogenous internal process control to monitor extraction and amplification of each clinical sample. The TaqPath™ COVID-19, Flu A, Flu B, RSV Select Panel also contains external process positive and negative controls. The positive control (PC) component included is an inactivated viral control that contains SARS-CoV-2, influenza A, influenza B, and RSV viruses. The PC monitors extraction and real-time RT-PCR by demonstrating that each of the four viruses can be detected when present and that RNase P is not detected when absent. The negative control (NC) component included is an MS2 packaged RNA control that contains targets specific to RNase P genomic regions targeted by the assay. The NC also monitors extraction and real-time RT-PCR by demonstrating RNase P can be detected when present and that the four viruses are not detected when absent. The TaqPath™ 1-Step Select Master Mix (No ROX) included as a component of the kit is a ready-to-use PCR mix which contains a deoxyribonucleotide triphosphate mix (dNTPs), enzymes, and other components to permit reverse transcription and amplification of the assay targets. The TagPath™ 1-Step Select Master Mix (No ROX) also contains ribonuclease (RNase) inhibitors as well as deoxyuridine triphosphate (dUTP) and uracil N-glycosylase (known as UNG or UDG).
The TaqPath™ COVID-19, Flu A, Flu B, RSV Select Panel is provided in two overall kit configurations: either 200 reactions or 1.000 reactions.
The provided text describes the analytical and clinical performance studies of the "Applied Biosystems TaqPath COVID-19, Flu A, Flu B, RSV Select Panel" (hereafter referred to as "the Device"). This device is an in vitro diagnostic test for the qualitative detection and differentiation of SARS-CoV-2, influenza A, influenza B, and respiratory syncytial virus (RSV).
Below is a breakdown of the acceptance criteria and study details based on the provided information, presented in the requested format.
Acceptance Criteria and Device Performance
The acceptance criteria for this diagnostic device are primarily demonstrated through various analytical performance evaluations (Limit of Detection, Inclusivity/Reactivity, Precision, Interfering Substances, Cross-Reactivity, Stability, Carryover) and clinical performance studies (PPA and NPA against a comparator device). The studies aim to show that the device performs as expected and is "substantially equivalent" to a legally marketed predicate device.
1. Table of Acceptance Criteria and Reported Device Performance
| Study Aspect / Performance Metric | Acceptance Criteria (Implied/Directly Stated where available) | Reported Device Performance (Summary) |
|---|---|---|
| Limit of Detection (LoD) | ≥ 95% positive detection at the determined LoD concentrations. | All viruses confirmed at ≥ 95% positive detection at the determined LoD concentrations (e.g., SARS-CoV-2 at 107 GCE/mL; Flu A H1N1 at 340 GCE/mL). WHO Standard LoD for SARS-CoV-2 confirmed at 150.36 IU/mL. |
| Inclusivity (in silico) | Less than 1% (SARS-CoV-2) and less than 5% (Flu A, Flu B, and RSV) of publicly available sequences have mutations that reduce melting temperature below annealing temperature for all gene targets. | > 99.99% of SARS-CoV-2, 99.9% of Flu B, and 99.49% of RSV strains met the criteria. For Flu A, 95.27% of strains were considered reactive after wet testing. |
| Reactivity (wet-lab) | 100% detection at approximately 3x LoD. | Most tested strains showed 100% detection at approximately 3x LoD. Strains not at 100% initially were further tested until 100% detection was achieved at higher concentrations. |
| Precision (Within-Laboratory) | N/A (Statistical measures like %CV and %PPA are reported). | Positivity Rate (Negative Sample): 0%. |
| Overall PPA (1x LoD, 3x LoD): 100.00% for all targets. | ||
| Observed Precision and Repeatability %CV (1x and 3x LoD): 85-90%). | ||
| Flu A: NP Overall PPA 94.9%, NPA 99.36%; AN Overall PPA 97.8%, NPA 99.06%. | ||
| Flu B: NP Overall PPA 98.0%, NPA 99.87%; AN Overall PPA 100.0%, NPA 99.87%. | ||
| RSV: NP Overall PPA 93.8%, NPA 99.75%; AN Overall PPA 100.0%, NPA 99.6%. | ||
| Clinical Performance (Enrichment Study) | Maintain high PPA/NPA for Flu A, Flu B, RSV (where prospective numbers might be low). | Flu A: NP Overall PPA 97.9%, NPA 100.0%; AN Overall PPA 100.0%, NPA 95.5%. |
| Flu B: NP Overall PPA 92.3%, NPA 98.2%; AN Overall PPA 92.3%, NPA 100.0%. | ||
| RSV: NP Overall PPA 100.0%, NPA 94.9%; AN Overall PPA 100.0%, NPA 96.6%. |
2. Sample Size Used for the Test Set and Data Provenance
-
Clinical Performance Study (Prospective Cohort):
- Subjects: 1,909 subjects enrolled (1,840 prospectively, 69 enrichment).
- Test Set (Evaluable Specimens): 1,620 Nasopharyngeal (NP) swabs and 1,541 Anterior Nasal (AN) swabs were included in the final data analysis for the prospective cohort. (Minor adjustments for inconclusive comparator results in Flu A, specifically 1,539 AN and 1,616 NP for Flu A analysis).
- Enrichment Study: 69 subjects, yielding 69 NP swabs and 68 AN swabs for analysis.
- Data Provenance:
- Country of Origin: Not explicitly stated as a single country, but "14 different collection sites across the U.S." indicate United States data.
- Retrospective or Prospective: Primarily prospective data, with an "enrichment phase" also involving prospective collection from subjects with confirmed positive PCR results for Flu A, Flu B, and/or RSV.
- Specimen Handling: Specimens were tested either fresh (Category I) or frozen (Category II).
-
Analytical Studies (Test Sets):
- LoD Confirmation: At least 24 replicates per virus strain/specimen type.
- Precision (within-lab): 96 replicates for each panel member.
- Reproducibility (site-to-site): 9 replicates per panel member (3 sites x 3 reagent lots x 1 replicate/lot). Total ~270 replicates per analyte level across 3 sites.
- Interfering Substances: 3 replicates per substance/condition.
- Competitive Interference: 3 replicates per condition.
- Cross-Reactivity & Microbial Interference: 3 replicates per organism/condition.
- Specimen Stability: Multiple replicates per time point/storage condition.
- Eluate Stability: Multiple replicates per time point/storage condition.
- Fresh vs Frozen Equivalency: Multiple replicates per F/T cycle and concentration.
- In-Use and Hold Time Stability: Multiple replicates per time point/F/T cycle.
- Carryover Cross-Contamination: 492 replicates (negative wells).
- RNase P Internal Control Cutoff Confirmation: Individually collected NP and AN swabs (specific number not given for the initial confirmation, but the follow-up AN study used 138 AN samples).
- Matrix Equivalency: Multiple replicates per matrix and concentration.
3. Number of Experts Used to Establish the Ground Truth for the Test Set and Qualifications of Those Experts
- For the clinical performance study, the ground truth appears to be established by a comparator FDA-cleared molecular test.
- The document does not specify the number or qualifications of human experts (e.g., radiologists, pathologists) involved in establishing the ground truth for any of the studies. This is typical for molecular diagnostic assays where the "ground truth" is often defined by the results of a highly sensitive and specific reference method (e.g., another molecular test or a composite reference method incorporating multiple tests or clinical findings).
4. Adjudication Method for the Test Set
- For the clinical performance study, samples that produced a discordant call between the Device and the comparator test were further tested with "another FDA cleared molecular assay" (a resolver assay). This implies a reconciliation method where a third test acts as an adjudicator for discordant results between the device under evaluation and the primary comparator.
- The specific rules for how the resolver assay's result determined the final ground truth (e.g., 2+1 majority rule, or if the resolver result was the final truth) are not explicitly detailed but are common in diagnostic test evaluation.
5. If a Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study was done
- No, an MRMC comparative effectiveness study was not done. The evaluated device is a molecular diagnostic test (RT-PCR kit), not an imaging AI algorithm that typically involves human readers. The performance is assessed based on the device's ability to detect viral nucleic acids against a comparator molecular test, not on improvements in human reader performance.
6. If a Standalone (i.e., algorithm only without human-in-the-loop performance) was done
- Yes, the primary evaluation of this device is a standalone performance study. The "TaqPath™ COVID-19, Flu A, Flu B, RSV Select Panel" is a laboratory-based RT-PCR diagnostic kit. Its performance, as detailed in the analytical and clinical studies, is measured by its output (detection/differentiation of viral targets) directly from patient samples, independent of human interpretation or "human-in-the-loop" assistance for the test result itself. The Diomni™ Software provides automated interpretation, making it an algorithm-only result at the interpretation stage.
7. The Type of Ground Truth Used
- For analytical studies (e.g., LoD, Inclusivity, Precision, Interference, Cross-Reactivity, Stability), the ground truth was established by contrived samples with known concentrations of viral material or known presence/absence of interfering/cross-reactive substances. This is a common and appropriate method for analytical validation.
- For the clinical performance study, the ground truth was established by an FDA-cleared molecular test (comparator device), supplemented by a resolver FDA-cleared molecular assay for discordant results. This constitutes a form of "composite reference standard" where the truth is determined by a highly reliable, already approved diagnostic method.
8. The Sample Size for the Training Set
- The document describes the validation of a diagnostic kit, not an AI model requiring a separate "training set" in the machine learning sense. The information provided heavily details the test set performance (analytical and clinical validation).
- While the "Diomni™ Software" performs data analysis and interpretation based on "assay-specific parameters from the Assay Definition File (ADF)," the document does not specify a distinct training set size typically associated with machine learning model development. The "training" of such a system would typically involve internal development data used to establish parameters like Cq cutoffs, but this is not detailed as a separate "training set" with specific sample numbers. The development study that determined the RNase P IC cutoff of Cq = 33.0 could be considered part of the "training" or parameter establishment phase, but no sample size is given for it.
9. How the Ground Truth for the Training Set Was Established
- As noted above, a distinct "training set" for an AI/algorithm is not explicitly described in the context of this diagnostic kit's submission. The "ground truth" for establishing device parameters (like Cq cutoffs) would generally come from extensive analytical experiments and internal validation studies using characterized samples (e.g., known concentrations of viruses, negative controls).
- For example, the preliminary LoD determined by probit analysis and the RNase P IC cutoff determined in a development study are examples of how internal parameters were established. These processes rely on highly controlled experiments with well-defined inputs (the "ground truth" being the known composition of the contrived samples).
§ 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.