(85 days)
The Lyra™ Parainfluenza Virus Assay is a Real-Time PCR assay for the qualitative detection and identification of human parainfluenza virus types 1, 2 and 3 viral RNA from nasal and nasopharyngeal swab specimens from symptomatic patients. It is intended for use as an aid in the differential diagnosis of parainfluenza virus types 1, 2 and 3. This test is not intended to detect Parainfluenza 4a or Parainfluenza 4b viruses.
Negative results do not preclude parainfluenza virus infection and should not be used as the sole basis for treatment or other patient management decisions.
The Lyra™ Parainfluenza Virus Assay is a Real-Time PCR assay for the qualitative detection and identification of human parainfluenza virus types 1, 2 and 3 viral RNA from nasal and nasopharyngeal swab specimens from symptomatic patients. The assay detects viral nucleic acids that have been extracted from a patient sample. A multiplex Real-time RT-PCR reaction is carried out under optimized conditions in a single tube generating amplicons for PIV-1, PIV-2, PIV-3 and the Process Control (PRC). Identification of PIV-1, PIV-2, PIV-3 and the PRC occurs by the use of target-specific primers and fluorescent-labeled probes that hybridize to conserved regions in the genomes of PIV-1. PIV-2. PIV-3 and the PRC.
Here's a summary of the acceptance criteria and study details for the Lyra™ Parainfluenza Virus Assay, based on the provided document:
1. Table of Acceptance Criteria and Reported Device Performance
The document does not explicitly state pre-defined acceptance criteria in terms of numerical thresholds for sensitivity or specificity. However, based on the conclusions regarding "good sensitivity and specificity" and "good positive and negative percent agreement," we can infer the expected performance. The reported performance is presented below:
| Performance Metric | PIV-1 | PIV-2 | PIV-3 |
|---|---|---|---|
| Prospective Study (vs. DSFA and CCFA) | |||
| Sensitivity | 100% (95% CI: 72.2% to 100%) | 100% (95% CI: 56.6% to 100%) | 100% (95% CI: 81.6% to 100%) |
| Specificity | 99.8% (95% CI: 99.3% to 99.9%) | 100% (95% CI: 99.7% to 100%) | 99.6% (95% CI: 99.0% to 99.8%) |
| Retrospective Study (vs. Prodesse ProParaFlu+ assay) | |||
| Positive Percent Agreement (PPA) | 100% (95% CI: 86.2% to 100%) | 100% (95% CI: 85.1% to 100%) | 100% (95% CI: 86.2% to 100%) |
| Negative Percent Agreement (NPA) | 98.8% (95% CI: 93.3% to 99.8%) | 94.0% (95% CI: 86.7% to 97.4%) | 100% (95% CI: 95.5% to 100%) |
2. Sample Size for Test Set and Data Provenance
- Prospective Study:
- Sample Size: 1241 fresh upper respiratory tract specimens.
- Data Provenance: Not explicitly stated, but the "Prospective multi-center study" suggests samples were collected from various clinical sites. The specimens were sent to a "central location" for comparative testing, implying multi-site collection.
- Retrospective Study:
- Sample Size: 105 frozen upper respiratory tract specimens.
- Data Provenance: Specimens "obtained from a pediatric hospital in the Southwest United States."
3. Number of Experts and Qualifications for Ground Truth
- Prospective Study: The ground truth was established using "direct specimen fluorescent antibody (DSFA) and cell culture with DFA (CCFA)." The document does not specify the number or qualifications of experts involved in performing or interpreting these reference methods.
- Retrospective Study: The ground truth was established using a legally marketed predicate device, the "Prodesse ProParaFlu+ assay (K091053)." The document does not mention experts establishing this ground truth, as it's a comparison against another device.
4. Adjudication Method for the Test Set
The document does not describe a formal adjudication method (e.g., 2+1, 3+1) for the test sets. For discrepant results in the prospective study, an "additional RT-PCR assay" was used for a subset of samples (e.g., 2 of 3 PIV-1 false positives, all 5 PIV-3 false positives). Similarly, for the retrospective study, an "additional RT-PCR assay" was used for 1 PIV-1 false positive and all 5 PIV-2 false positives. This implies a reference method approach, potentially with further molecular confirmation for outliers.
5. Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study
No multi-reader multi-case (MRMC) comparative effectiveness study was done. The document describes a standalone performance study of the device against reference methods and another legally marketed device; it does not involve human readers or assess improvement with AI assistance.
6. Standalone (Algorithm Only) Performance Study
Yes, a standalone performance study was done. The Lyra™ Parainfluenza Virus Assay, a Real-Time PCR assay (an algorithm-based diagnostic test, not requiring human interpretation of output beyond reading the results), was evaluated on its own against established reference methods (DSFA and CCFA in the prospective study, and the Prodesse ProParaFlu+ assay in the retrospective study).
7. Type of Ground Truth Used
- Prospective Study: Expert consensus, specifically a composite reference method of direct specimen fluorescent antibody (DSFA) and cell culture with DFA (CCFA).
- Retrospective Study: A legally marketed predicate device (Prodesse ProParaFlu+ assay).
8. Sample Size for the Training Set
The document does not provide information on the sample size for a training set. This is a diagnostic assay, and the studies described are performance evaluations, not specifically machine learning model training. The assay's design would have involved internal development and analytical verification, but the term "training set" as commonly used for machine learning is not applicable or detailed here.
9. How Ground Truth for the Training Set Was Established
As no specific "training set" is described in the context of machine learning, this information is not provided. The development of the assay would have been based on established molecular biology principles and analytical validation using known positive and negative controls/samples.
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Food and Drug Administration 10903 New Hampshire Avenue Document Control Center - WO66-G609 Silver Spring, MD 20993-0002
October 9, 2014
Quidel Corporation Ronald H. Lollar Senior Director, Clinical and Regulatory Affairs 2005 East State Street, Suite 100 Athens, OH 45701
Re: K141927
Trade/Device Name: Lyra™ Parainfluenza Virus Assay Regulation Number: 21 CFR 866.3980 Regulation Name: Respiratory viral panel multiplex nucleic acid assay Regulatory Class: II Product Code: OOU Dated: July 15, 2014 Received: July 16, 2014
Dear Mr. Lollar:
We have reviewed your Section 510(k) premarket notification of intent to market the device referenced above and have determined the device is substantially equivalent (for the indications for use stated in the enclosure) to legally marketed predicate devices marketed in interstate commerce prior to May 28, 1976, the enactment date of the Medical Device Amendments, or to devices that have been reclassified in accordance with the provisions of the Federal Food. Drug. and Cosmetic Act (Act) that do not require approval of a premarket approval application (PMA). You may, therefore, market the device, subject to the general controls provisions of the Act. The general controls provisions of the Act include requirements for annual registration, listing of devices, good manufacturing practice, labeling, and prohibitions against misbranding and adulteration. Please note: CDRH does not evaluate information related to contract liability warranties. We remind you, however, that device labeling must be truthful and not misleading.
If your device is classified (see above) into either class II (Special Controls) or class III (PMA), it may be subject to additional controls. Existing major regulations affecting your device can be found in the Code of Federal Regulations, Title 21. Parts 800 to 898. In addition, FDA may publish further announcements concerning your device in the Federal Register.
Please be advised that FDA's issuance of a substantial equivalence determination does not mean that FDA has made a determination that your device complies with other requirements of the Act or any Federal statutes and regulations administered by other Federal agencies. You must comply with all the Act's requirements, including, but not limited to: registration and listing (21 CFR Part 807); labeling (21 CFR Parts 801 and 809); medical device reporting (reporting of medical device-related adverse events) (21 CFR 803); good manufacturing practice requirements as set forth in the quality systems (QS) regulation (21 CFR Part 820); and if applicable, the electronic product radiation control provisions (Sections 531-542 of the Act); 21 CFR 1000-1050.
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If you desire specific advice for your device on our labeling regulations (21 CFR Parts 801 and 809), please contact the Division of Industry and Consumer Education at its toll-free number (800) 638 2041 or (301) 796-7100 or at its Internet address
http://www.fda.gov/MedicalDevices/Resourcesfor You/Industry/default.htm. Also, please note the regulation entitled, "Misbranding by reference to premarket notification" (21 CFR Part 807.97). For questions regarding the reporting of adverse events under the MDR regulation (21 CFR Part 803), please go to
http://www.fda.gov/MedicalDevices/Safety/ReportaProblem/default.htm for the CDRH's Office of Surveillance and Biometrics/Division of Postmarket Surveillance.
You may obtain other general information on your responsibilities under the Act from the Division of Industry and Consumer Education at its toll-free number (800) 638-2041 or (301) 796-7100 or at its Internet address
http://www.fda.gov/MedicalDevices/ResourcesforYou/Industry/default.htm.
Sincerely yours,
Tamara V. Feldblyum -S for
Sally A. Hojvat M.Sc., Ph.D. Director Division of Microbiology Devices Office of In Vitro Diagnostics and Radiological Health Center for Devices and Radiological Health
Enclosure
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Indications for Use
510(k) Number (if known) K141927
Device Name Lyra™ Parainfluenza Virus Assay
Indications for Use (Describe)
The Lyra™ Parainfluenza Virus Assay is a Real-Time PCR assay for the qualitative detection and identification of human parainfluenza virus types 1, 2 and 3 viral RNA from nasal and nasopharyngeal swab specimens from symptomatic patients. It is intended for use as an aid in the differential diagnosis of parainfluenza virus types 1, 2 and 3. This test is not intended to detect Parainfluenza 4a or Parainfluenza 4b viruses.
Negative results do not preclude parainfluenza virus infection and should not be used as the sole basis for treatment or other patient management decisions.
| Type of Use (Select one or both, as applicable) | |
|---|---|
| ☑ Prescription Use (Part 21 CFR 801 Subpart D) | ☐ Over-The-Counter Use (21 CFR 801 Subpart C) |
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Applicant:
Quidel Corporation 12544 High Bluff Drive, Suite 200 San Diego, California 92130 Telephone: 858-552-7910 Fax: 858-646-8045
Contact Information:
Ronald H. Lollar, Senior Director Clinical and Regulatory Affairs 2005 East State Street Suite 100 Athens, Ohio 45701 740-589-3300 – Corporate number 740-589-3373 – Desk phone 740-593-8437 - Fax lollar@dhiusa.com
Date of preparation of 510(k) summary:
July 15, 2014
Device Name:
Trade name - Lyra™ Parainfluenza Virus Assay Classification name - Respiratory viral panel multiplex nucleic acid assay Product Code - OOU Regulation Section - 21CFR 866.3980
Substantial Equivalency
The Lyra™ Parainfluenza Virus Assay used direct specimen DFA and viral tissue culture with DFA as the reference comparator. The predicate device for the assay is the Prodesse ProParaflu™+ Assay. The characteristics of the Lyra™ Parainfluenza Virus Assay ("Subject Device") and the legally marketed device is described in the Table below:
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| Table 1. Comparison of New Device with Predicate Device | ||
|---|---|---|
| Item | Subject DeviceLyraTM ParainfluenzaVirus Assay | Predicate Device(K091053)ProdesseProParafluTM+ Assay |
| Intended Use | The LyraTMParainfluenza VirusAssay is a Real-TimePCR assay for thequalitative detection andidentification of humanparainfluenza type 1, 2and 3 viral RNA fromnasal andnasopharyngeal swabspecimens fromsymptomatic patients.It is intended for use asan aid in the differentialdiagnosis ofparainfluenza virustypes 1, 2 and 3.Thistest is not intended todetect Parainfluenza 4aor Parainfluenza 4bViruses.Negative results do notpreclude parainfluenzainfection and should notbe used as the sole basisfor treatment or otherpatient managementdecisions. | The ProParaflu+ Assay isa multiplex Real TimeRT-PCR in vitrodiagnostic test for thequalitative detection anddiscrimination ofParainfluenza 1 Virus,Parainfluenza 2 VirusandParainfluenza 3 Virus(HPIV-1, HPIV-2 andHPIV-3) nucleic acidsisolated and purifiedfrom nasopharyngeal(NP) swab specimensobtained fromindividuals exhibitingsigns and symptoms ofrespiratory tractinfections. This assaytargets the conservedregions of theHemagglutinin-Neuraminidase (HN)gene of HPIV-1, HPIV-2and HPIV-3,respectively. Thedetection anddiscrimination of HPIV-I, HPIV-2 and HPIV-3nucleic acids fromsymptomatic patients aidin the diagnosis ofhuman respiratory tractparainfluenza infectionsif used in conjunctionwith other clinical andlaboratory findings. Thistest is not intended to |
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| Comparison of New Device with Predicate DeviceTable 1. | ||||
|---|---|---|---|---|
| Item | Subject DeviceLyra™ ParainfluenzaVirus Assay | Predicate Device(K091053)ProdesseProParaflu™+ Assay | ||
| detect Parainfluenza 4aor Parainfluenza 4bViruses.Negative test results arepresumptive and shouldbe confirmed by cellculture. Negative resultsdo not precludeParainfluenza 1, 2 or 3virus infections andshould not be used as thesole basis for treatmentor other managementdecisions. | ||||
| DNA AmplificationTechnology | Real time polymerasechain reaction | Same | ||
| Target Sequence Detected | Parainfluenza type 1nuclear protein geneParainfluenza type 2phosphate protein geneParainfluenza type 3phosphate protein gene | Conserved regions of theHemagglutinin-Neuraminidase (HN)gene of HPIV-1, HPIV-2and HPIV-3 | ||
| Sample Types | Nasal andNasopharyngeal swabs | Nasopharyngeal swabs | ||
| Extraction | NucliSENS®easyMAGTM(bioMérieux) | MagNA Pure LC System(Roche)NucliSENS®easyMAGTM(bioMérieux ) | ||
| Amplification | Applied Biosystems7500 Fast Dx | Cepheid SmartCycler II | ||
| Detection Techniques | Applied Biosystems7500 Fast Dx | Cepheid SmartCycler II |
Intended Use
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The Lyra™ Parainfluenza Virus Assay is a Real-Time PCR assay for the qualitative detection and identification of human parainfluenza virus types 1, 2 and 3 viral RNA from nasal and nasopharyngeal swab specimens from symptomatic patients. It is intended for use as an aid in the differential diagnosis of parainfluenza virus types 1, 2 and 3. This test is not intended to detect Parainfluenza 4a or Parainfluenza 4b viruses.
Negative results do not preclude parainfluenza virus infection and should not be used as the sole basis for treatment or other patient management decisions.
Methodology
The assay detects viral nucleic acids that have been extracted from a patient sample. A multiplex Real-time RT-PCR reaction is carried out under optimized conditions in a single tube generating amplicons for PIV-1, PIV-2, PIV-3 and the Process Control (PRC). Identification of PIV-1, PIV-2, PIV-3 and the PRC occurs by the use of target-specific primers and fluorescent-labeled probes that hybridize to conserved regions in the genomes of PIV-1. PIV-2. PIV-3 and the PRC.
| Table 2. Lyra™ Probe Labels | |
|---|---|
| Target | Dye |
| PIV-1 | FAM |
| PIV-2 | JOE |
| PIV-3 | Tex Red |
| PRC | CY5 |
Performance Data
Precision/Reproducibility
Precision
For the Precision/Within Laboratory Repeatability study, a panel of four (4) simulated samples that include medium positive and low positive, high negative PIV-1, PIV-2, PIV-3 and negative samples was tested by two (2) operators, in triplicate for twelve (12) days.
| Table 3. Applied Biosystems® 7500 Fast Dx Results Summary | |||||||
|---|---|---|---|---|---|---|---|
| Ct Values and Percent Positive (%) | |||||||
| Virus | Target | Pos.Control | 5XLoD | 2XLoD | 0.5XLoD | Neg.Matrix | Neg.Control |
| PIV-1 | Operator 1 Avg Ct | 29.1 | 33.0 | 35.1 | 40.1 | Neg | Neg |
| Operator 2 Avg Ct | 28.6 | 33.1 | 35.0 | 40.0 | Neg | Neg | |
| Positivity | 100% | 100% | 100% | 83% | 0% | 0% | |
| PIV-2 | Operator 1 Avg Ct | 29.6 | 32.6 | 34.6 | 40.2 | Neg | Neg |
| Operator 2 Avg Ct | 29.1 | 32.6 | 34.6 | 40.5 | Neg | Neg | |
| Positivity | 100% | 100% | 100% | 83% | 0% | 0% | |
| PIV-3 | Operator 1 Avg Ct | 31.6 | 32.3 | 34.3 | 38.8 | Neg | Neg |
| Operator 2 Avg Ct | 31.2 | 32.8 | 34.7 | 38.8 | Neg | Neg | |
| Positivity | 100% | 100% | 100% | 100% | 0% | 0% |
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The Lyra™ Parainfluenza Virus Assay produces results that are highly reproducible.
Reproducibility
The reproducibility of the Lyra™ Parainfluenza Virus Assay was evaluated at three (3) laboratory sites. Reproducibility was assessed using a panel of four (4) simulated samples that include medium positive and low positive, high negative PIV-1, PIV-2, PIV-3 and negative samples. Panels and controls were tested at each site by two (2) operators for 5-days (triplicate testing x 2 operators x 5 days x 3 sites = 90 results per level for each virus). The LoD values were based on the values obtained in the LoD study. The panels and controls were extracted using the bioMérieux easyMAG system and tested on the Applied Biosystems 7500 Fast DX.
| Table 4.Reproducibility Data | ||||
|---|---|---|---|---|
| Percent Agreement(CI95)Site 1 | Percent Agreement(CI95)Site 2 | Percent Agreement(CI95)Site 3 | Percent Agreement(CI95)Combined | |
| PIV-1 HighNegative | 40%(CI95 24.6% to 57.7%) | 76.6%(CI95 59.1% to88.2%) | 63.3%(CI95 45.5% to78.1%) | 60%(CI95 49.7% to 69.5%) |
| PIV-1 LowPositive | 100%(CI95 88.6% to 100%) | 100%(CI95 88.6% to 100%) | 100%(CI95 88.6% to 100%) | 100%(CI95 95.6% to 100%) |
| PIV-1 ModeratePositive | 100%(CI95 88.6% to 100%) | 100%(CI95 88.6% to 100%) | 100%(CI95 88.6% to 100%) | 100%(CI95 95.6% to 100%) |
| PIV-1 Negative | 100%(CI95 88.6% to 100%) | 100%(CI95 88.6% to 100%) | 100%*(CI95 88.3% to 100%) | 100%(CI95 95.6% to 100%) |
| PIV-2 HighNegative | 20%(CI95 9.5% to 37.3%) | 93.3%(CI95 78.7% to98.2%) | 80%(CI95 62.7% to90.5%) | 64.4%(CI95 54.1% to 73.6%) |
| PIV-2 LowPositive | 100%(CI95 88.6% to 100%) | 100%(CI95 88.6% to 100%) | 100%(CI95 88.6% to 100%) | 100%(CI95 95.6% to 100%) |
| PIV-2 ModeratePositive | 100%(CI95 88.6% to 100%) | 100%(CI95 88.6% to 100%) | 100%(CI95 88.6% to 100%) | 100%(CI95 95.6% to 100%) |
| PIV-2 Negative | 100%(CI95 88.6% to 100%) | 100%(CI95 88.6% to 100%) | 100%*(CI95 88.3% to 100%) | 100%(CI95 95.6% to 100%) |
| PIV-3 HighNegative | 0%(CI95 0% to 11.4%) | 3.3%(CI95 0.6% to 16.7%) | 53.3%(CI95 36.1% to69.8%) | 18.9%(CI95 12.1% to 28.2%) |
| PIV-3 LowPositive | 100%(CI95 88.6% to 100%) | 100%(CI95 88.6% to 100%) | 100%(CI95 88.6% to 100%) | 100%(CI95 95.6% to 100%) |
| PIV-3 ModeratePositive | 100%(CI95 88.6% to 100%) | 100%(CI95 88.6% to 100%) | 100%(CI95 88.6% to 100%) | 100%(CI95 95.6% to 100%) |
| PIV-3 Negative | 100%(CI95 88.6% to 100%) | 100%(CI95 88.6% to 100%) | 100%*(CI95 88.3% to 100%) | 100%(CI95 95.6% to 100%) |
| PIV-1 PositiveControl | 100%(CI95 88.6% to 100%) | 100%(CI95 88.6% to 100%) | 100%(CI95 88.6% to 100%) | 100%(CI95 95.6% to 100%) |
| PIV-2 PositiveControl | 100%(CI95 88.6% to 100%) | 100%(CI95 88.6% to 100%) | 100%(CI95 88.6% to 100%) | 100%(CI95 95.6% to 100%) |
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| Table 4. Reproducibility Data | ||||
|---|---|---|---|---|
| Percent Agreement (CI95) | Percent Agreement (CI95) | Percent Agreement (CI95) | Percent Agreement (CI95) | |
| Site 1 | Site 2 | Site 3 | Combined | |
| PIV-3 Positive | 100% | 100% | 100% | 100% |
| Control | (CI95 88.6% to 100%) | (CI95 88.6% to 100%) | (CI95 88.6% to 100%) | (CI95 95.6% to 100%) |
| Negative Control | 100% | 100% | 100% | 100% |
| (CI95 88.6% to 100%) | (CI95 88.6% to 100%) | (CI95 88.6% to 100%) | (CI95 95.6% to 100%) |
- One (1) replicate had an invalid PRC value and was removed for analysis.
The data from the combined sites indicates that the Lyra™ Parainfluenza Virus Assay, on the Applied Biosystems® 7500 Fast Dx, generates reproducible results for the detection of parainfluenza virus types 1, 2, 3, and the internal control.
Limit of Detection (LoD)
The analytical sensitivity (limit of detection or LoD) of the Lyra™ Parainfluenza Virus Assay was determined using quantified (TCID50/mL) stocks of parainfluenza virus types 1, 2, and 3 diluted in a negative matrix. Analytical sensitivity (LoD) is defined as the lowest concentration at which 95% of all replicates tested positive.
| Table 5. Limit of Detection | TCID50/mL |
|---|---|
| Parainfluenza virus type 1 (C-35 strain) | 2.50 x 100 |
| Parainfluenza virus type 2 (Greer strain) | 2.50 x 102 |
| Parainfluenza virus type 3 (C-243 strain) | 8.00 x 101 |
Analytical Reactivity (Inclusivity)
To verify the Lyra™ Parainfluenza Virus Assay detects multiple strains of parainfluenza Type 1 (HPIV-1), Type 2 (HPIV-2) and Type 3 (HPIV-3). The number of characterized strains of parainfluenza is very limited. In silico analysis was performed to demonstrate that primers are representative of the genetic diversity in the chosen target region for each parainfluenza virus type identified by the assay.
All full-genome Genbank annotation files for Human Parainfluenza virus Types 1, 2, and 3 were downloaded from NCBI. A summary of the number of sequences evaluated for each virus type is in the table below.
| Table 6. | Summary of Parainfluenza Sequences Evaluated | |
|---|---|---|
| HPIV Type | Subtyping HPIV Type | Total Number of Sequences |
| HPIV1 | HPIV2 | 308 |
| HPIV3 | ||
| HPIV4 |
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| HPIV1 | ||
|---|---|---|
| HPIV2 | HPIV3 | 458 |
| HPIV4 | ||
| HPIV1 | ||
| HPIV3 | HPIV2 | 509 |
| HPIV4 |
Analytical Specificity/Cross-Reactivity
The analytical specificity with potentially cross-reactive organisms was evaluated by testing a panel consisting of 28 viral, 26 bacterial, and 1 yeast strains representing common respiratory pathogens or flora commonly present in the nasopharynx. The organisms were added to negative nasal matrix. The bacteria and yeast were tested at concentrations of 104 to 10° CFU/mL. Viruses were tested at concentrations of 104 to 10° TCID50/mL. Samples were extracted using the NucliSens easyMAG instrument and tested in triplicate.
| Table 7. | Organisms Evaluated for Cross-Reactivity | |
|---|---|---|
| Bordetella pertussis | Candida albicans | RSV A (Long) |
| Bordetella bronchiseptica | Adenovirus 1 | RSV B (Wash/18537/62) |
| Chlamydophila pneumonia | Coronavirus 229E | Varicella Zoster Virus |
| Chlamydia trachomatis | Coronavirus NL63 | |
| Legionella pneumophila | Coronavirus OC43 | |
| Mycobacterium intracellualre | Coxsackievirus B4 | |
| Mycobacterium tuberculosis | Coxsackievirus B5/10/2006 | |
| Mycobacterium avium | Cytomegalovirus | |
| Mycoplasma pneumoniae | Echovirus 6 | |
| Haemophilus influenzae | Echovirus 7 | |
| Pseudomonas aeruginosa | Echovirus 9 | |
| Proteus vulgaris | Echovirus 11 | |
| Proteus mirabilis | Enterovirus 70 | |
| Neisseria gonorrhoeae | Enterovirus 71 | |
| Neisseria meningitidis | Epstein Barr Virus | |
| Neisseria mucosa | HSV Type 1 MacIntyre | |
| Strain | ||
| Klebsiella pneumoniae | HSV Type 2 Strain G | |
| Escherichia coli | Human Metapneumovirus | |
| (A1) | ||
| Moraxella catarrhalis | Human Rhinovirus 45 | |
| Corynebacterium diptheriae | Human Rhinovirus 52 | |
| Lactobacillus plantarum | Influenza | |
| A/Mexico/4108/2009 | ||
| Streptococcus pneumoniae | Influenza A/Port Chalmers | |
| Streptococcus pyogenes | Influenza B/Florida/04/2006 |
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| Table 7. Organisms Evaluated for Cross-Reactivity | ||
|---|---|---|
| Streptococcus salivarius | Measles/7/2000 | |
| Staphylococcus epidermidis | Mumps Virus | |
| Staphylococcus aureus | Parainfluenza Type 4A |
No cross-reactivity was seen with any of the organisms tested.
Microbial Interference
The analytical specificity with interfering organisms of the Lyra™ Parainfluenza Virus Assay was evaluated by testing a panel consisting of 28 viral, 26 bacterial, and 1 yeast strains representing common respiratory pathogens or flora commonly present in the nasopharynx. The organisms were added to samples containing either parainfluenza virus types 1, 2, or 3 at 2 x LoD concentration. The bacteria and yeast were tested at concentrations of 10 to 10° CFU/mL. Viruses were tested at concentrations of 10t to 10° TCIDs(/mL. Samples were extracted using the NucliSens easyMAG instrument and tested in triplicate.
| Table 8. Organisms Evaluated for Interference | ||
|---|---|---|
| Bordetella pertussis | Candida albicans | RSV A (Long) |
| Bordetella bronchiseptica | Adenovirus 1 | RSV B (Wash/18537/62) |
| Chlamydophila pneumonia | Coronavirus 229E | Varicella Zoster Virus |
| Chlamydia trachomatis | Coronavirus NL63 | |
| Legionella pneumophila | Coronavirus OC43 | |
| Mycobacterium intracellualre | Coxsackievirus B4 | |
| Mycobacterium tuberculosis | Coxsackievirus B5/10/2006 | |
| Mycobacterium avium | Cytomegalovirus | |
| Mycoplasma pneumoniae | Echovirus 6 | |
| Haemophilus influenzae | Echovirus 7 | |
| Pseudomonas aeruginosa | Echovirus 9 | |
| Proteus vulgaris | Echovirus 11 | |
| Proteus mirabilis | Enterovirus 70 | |
| Neisseria gonorrhoeae | Enterovirus 71 | |
| Neisseria meningitidis | Epstein Barr Virus | |
| Neisseria mucosa | HSV Type 1 MacIntyreStrain | |
| Klebsiella pneumoniae | HSV Type 2 Strain G | |
| Escherichia coli | Human Metapneumovirus(A1) | |
| Moraxella catarrhalis | Human Rhinovirus 45 | |
| Corynebacterium diptheriae | Human Rhinovirus 52 | |
| Lactobacillus plantarum | InfluenzaA/Mexico/4108/2009 | |
| Streptococcus pneumoniae | Influenza A/Port Chalmers | |
| Streptococcus pyogenes | Influenza B/Florida/04/2006 | |
| Streptococcus salivarius | Measles/7/2000 | |
| Staphylococcus epidermidis | Mumps Virus | |
| Staphylococcus aureus | Parainfluenza Type 4A |
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No interference was seen with any of the organisms when the target viruses were tested at 2 x LoD concentrations.
Interfering Substances
A study was performed on the Applied Biosystems 7500 Fast Dx to evaluate the performance of the Lyra™ Parainfluenza Virus Assay in the presence of eleven (11) of potentially interfering/cross-reactive substances, at clinically relevant levels, that might be present in specimens. Each substance was tested in the presence of 2X LoD parainfluenza virus types 1, 2, and 3 samples and with negative matrix.
| Table 9. Interfering/Cross-reactive Substances Summary | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Substance Name | PIV-1Ct Avg. | PIV-1SD | PIV-2Ct Avg. | PIV-2SD | PIV-3Ct Avg. | PIV-3SD | No Analyte Ct Avg. | No Analyte SD | Inhibition (yes/no) |
| Controls | 35.1 | 0.3 | 36.8 | 2.9 | 33.4 | 0.6 | Neg | N/A | N/A |
| Mucin (BovineSubmaxillary Gland,type I-S) | 35.8 | 0.4 | 35.6 | 0.7 | 34.4 | 0.3 | Neg | N/A | No |
| Blood (human),EDTAanticoagulated | 34.9 | 0.2 | 34.0 | 0.3 | 32.2 | 0.6 | Neg | N/A | No |
| Neo-Synephrine | 34.8 | 0.5 | 34.2 | 0.7 | 33.1 | 0.4 | Neg | N/A | No |
| Afrin Nasal Spray | 35.2 | 0.6 | 34.1 | 0.2 | 33.5 | 0.1 | Neg | N/A | No |
| Zicam HomeopathicNon-Drowsy AllergyRelief No DripLiquid Nasal Gel | 34.9 | 0.8 | 34.2 | 0.1 | 34.0 | 0.4 | Neg | N/A | No |
| Saline Nasal Spray | 34.8 | 0.2 | 34.5 | 0.2 | 33.4 | 0.2 | Neg | N/A | No |
| OTC ThroatLozenges: RicolaAction Cherry | 34.7 | 0.2 | 34.2 | 0.4 | 34.0 | 0.2 | Neg | N/A | No |
| Zanamivir | 34.6 | 0.2 | 34.2 | 0.5 | 33.9 | 0.2 | Neg | N/A | No |
| Tobramycin | 34.9 | 0.3 | 34.1 | 0.5 | 34.5 | 1.6 | Neg | N/A | No |
| Mupirocin | 35.2 | 0.4 | 35.2 | 0.5 | 34.0 | 0.3 | Neg | N/A | No |
| Oseltamivirphosphate | 35.1 | 0.2 | 35.3 | 0.8 | 34.1 | 0.2 | Neg | N/A | No |
None of the eleven (11) of substances interferes with the detection of parainfluenza virus types 1, 2, and 3.
None of the eleven (11) of substances tested cross-reacts with the Lyra™ Parainfluenza Virus Assay.
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Carry-Over and Cross Contamination
Studies were performed on the Applied Biosystems® 7500 Fast Dx using a 96-sample panel consisting of 48 high positives and 48 negative specimens. Each high positive specimen contained a concentration of 1.0 x 10 TCID50/mL parainfluenza-1, parainfluenza-2, and parainfluenza-3 combined into one sample. The high positive samples were extracted and analyzed in series alternating with the negative samples. The negative samples were comprised of negative matrix. The testing was repeated over a 5day period.
Over the course of 5 days, cross-contamination and amplicon carry-over did not occur with the Lyra™ Parainfluenza Virus Assay when extracted the NucliSens easyMAG automated nucleic acid extraction instrument and analyzed on the Applied Biosystems® 7500 Fast Dx.
Method Comparison
Prospective Study
The evaluation of the Lyra™™ Parainfluenza Virus Assay occurred in two separate studies: a prospective multi-center study using one thousand two hundred and forty-one (1241) fresh specimens from the upper respiratory tract; and a retrospective study using one hundred five (105) frozen specimens from the upper respiratory tract. In both studies the specimens were processed the bioMérieux NucliSENS® easyMag® at all sites for the extraction of nucleic acids from the clinical specimens. The Applied Biosystems 7500 Fast Dx Real-Time PCR Instrument was used with the Quidel assay for the amplification and detection of the target nucleic acids with the Lyra™ Parainfluenza Virus Assay. The prospective specimens were also processed and tested with direct specimen fluorescent antibody (DSFA) and cell culture with DFA (CCFA). The retrospective specimens were extracted and tested with an additional FDAcleared molecular assay.
One thousand two hundred and forty-one (1241) fresh specimens were collected and transported to each laboratory for testing with the Lyra™ Parainfluenza Virus Assay. The specimens shipped daily with cold packs for DSFA and CCFA to the central location and were tested within 72-hours of collection. The table below details the PIV-1 results for the specimens.
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| Table 10. PIV-1 | Comparator: DSFA and Culture with DFA | ||
|---|---|---|---|
| LyraTMParainfluenza VirusAssay | Positive | Negative | Total |
| Positive | 10 | 3* | 13 |
| Negative | 0 | 1228 | 1228 |
| Total | 10 | 1231 | 1241 |
| 95% CI | |||
| Sensitivity | 10/10 | 100% | 72.2% to 100% |
| Specificity | 1228/1231 | 99.8% | 99.3 % to 99.9% |
- Two (2) of the three (3) positives were positive by an additional RT-PCR assay.
The table below details the PIV-2 results for the specimens.
| Table 11. PIV-2 | |||
|---|---|---|---|
| LyraTMParainfluenza VirusAssay | Comparator: DSFA and Culture with DFA | ||
| Positive | Negative | Total | |
| Positive | 5 | 0 | 5 |
| Negative | 0 | 1236 | 1241 |
| Total | 5 | 1236 | 1246 |
| 95% CI | |||
| Sensitivity | 5/5 | 100% | 56.6% to 100% |
| Specificity | 1236/1236 | 100% | 99.7% to 100% |
The table below details the PIV-3 results for the specimens.
| Table 12. PIV-3 | |||
|---|---|---|---|
| LyraTMParainfluenza VirusAssay | Comparator: DSFA and Culture with DFA | ||
| Positive | Negative | Total | |
| Positive | 17 | 5* | 22 |
| Negative | 0 | 1219 | 1219 |
| Total | 17 | 1224 | 1241 |
| 95% CI | |||
| Sensitivity | 17/17 | 100% | 81.6% to 100% |
| Specificity | 1219/1224 | 99.6% | 99.0% to 99.8% |
- Five (5) of the five (5) positives were positive by an additional RT-PCR assay.
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Retrospective Study
Due to the low prevalence of parainfluenza virus at the clinical sites during the study period, a retrospective study was conducted with specimens obtained from a pediatric hospital in the Southwest United States. One hundred five (105) frozen specimens from the upper respiratory tract were tested concurrently with the Lyra™ Parainfluenza Virus Assay and the Prodesse ProParaFlu+ assay (K091053).
| Table 13. PIV-1 | |||
|---|---|---|---|
| Comparator: Prodesse ProParaFlu+ assay | |||
| Lyra™ Parainfluenza Virus Assay | Positive | Negative | Total |
| Positive | 24 | 1* | 25 |
| Negative | 0 | 80 | 80 |
| Total | 24 | 81 | 105 |
| 95% CI | |||
| Positive Percent Agreement | 24/24 | 100% | 86.2% to 100% |
| Negative Percent Agreement | 80/81 | 98.8% | 93.3% to 99.8% |
- One (1) of one (1) positive was positive by an additional RT-PCR assay.
| Table 14. PIV-2 | |||
|---|---|---|---|
| Comparator: Prodesse ProParaFlu+ assay | |||
| Lyra™ Parainfluenza Virus Assay | Positive | Negative | Total |
| Positive | 22 | 5* | 27 |
| Negative | 0 | 78 | 78 |
| Total | 22 | 83 | 105 |
| 95% CI | |||
| Positive Percent Agreement | 22/22 | 100% | 85.1% to 100% |
| Negative Percent Agreement | 78/83 | 94.0% | 86.7% to 97.4% |
- Five (5) of five (5) positives were positive by an additional RT-PCR assay.
| Table 15. PIV-3 | Comparator: Prodesse ProParaFlu+ assay | ||
|---|---|---|---|
| Lyra™ Parainfluenza VirusAssay | Positive | Negative | Total |
| Positive | 24 | 0 | 24 |
| Negative | 0 | 81 | 81 |
| Total | 24 | 81 | 105 |
| 95% CI | |||
| Positive Percent Agreement | 24/24 | 100% | 86.2% to 100% |
| Negative Percent Agreement | 81/81 | 100% | 95.5% to 100% |
Statement of Safety and Effectiveness
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When performed on the Applied Biosystems® 7500 Fast Dx, the Lyra™ Parainfluenza Virus Assay yielded good sensitivity and specificity when compared to the composite reference method of direct specimen fluorescent antibody (DSFA) and cell culture with DFA (CCFA).
When performed on the Applied Biosystems® 7500 Fast Dx, the Lyra™ Parainfluenza Virus Assay yielded good positive and negative percent agreement when compared to and FDAcleared molecular device.
§ 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.