(85 days)
No
The description focuses on a Real-Time PCR assay for detecting viral RNA, which is a standard molecular diagnostic technique and does not mention any AI or ML components for data analysis or interpretation.
No.
The device is a diagnostic assay for detecting viral RNA, intended as an aid in diagnosis, not for treating or preventing disease.
Yes
The "Intended Use / Indications for Use" section explicitly states that the device is "intended for use as an aid in the differential diagnosis of parainfluenza virus types 1, 2, and 3."
No
The device is a Real-Time PCR assay, which involves physical reagents and laboratory procedures to detect viral RNA. It is not solely software.
Yes, this device is an IVD (In Vitro Diagnostic).
Here's why:
- Intended Use: The intended use explicitly states it is 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." This involves testing samples taken from the human body in vitro (outside the body) to provide information for diagnosis.
- Device Description: The description details a "Real-Time PCR assay" that detects "viral nucleic acids that have been extracted from a patient sample." This further confirms the in vitro nature of the testing.
- Aid in Diagnosis: The intended use states it is "intended for use as an aid in the differential diagnosis of parainfluenza virus types 1, 2 and 3." This is a key characteristic of an IVD.
- Specimen Type: The device uses "nasal and nasopharyngeal swab specimens," which are biological samples taken from a patient.
All these points align with the definition of an In Vitro Diagnostic device.
N/A
Device Name: Lyra™ Parainfluenza Virus Assay
Intended Use / Indications for Use
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.
Product codes
OOU
Device Description
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.
Mentions image processing
Not Found
Mentions AI, DNN, or ML
Not Found
Input Imaging Modality
Not Found
Anatomical Site
nasal and nasopharyngeal swab specimens
Indicated Patient Age Range
Not Found
Intended User / Care Setting
Not Found
Description of the training set, sample size, data source, and annotation protocol
Not Found
Description of the test set, sample size, data source, and annotation protocol
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Summary of Performance Studies (study type, sample size, AUC, MRMC, standalone performance, key results)
Precision/Reproducibility Study:
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.
Key results: The Lyra™ Parainfluenza Virus Assay produced highly reproducible results, with 100% positivity for positive controls, 5X LoD, and 2X LoD for all PIV types, and 0% positivity for negative controls. At 0.5X LoD, positivity ranged from 83% to 100%.
Reproducibility Study:
The reproducibility of the Lyra™ Parainfluenza Virus Assay was evaluated at three (3) laboratory sites 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).
Key results: For PIV-1, PIV-2, and PIV-3, Low Positive, Moderate Positive, Positive Control, and Negative samples showed 100% combined percent agreement across all sites. High Negative samples showed combined percent agreement of 60% for PIV-1, 64.4% for PIV-2, and 18.9% for PIV-3. The data indicates that the Lyra™ Parainfluenza Virus Assay generates reproducible results for the detection of parainfluenza virus types 1, 2, 3, and the internal control.
Limit of Detection (LoD) Study:
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.
Key results: LoD for Parainfluenza virus type 1 was 2.50 x 100 TCID50/mL, for type 2 was 2.50 x 102 TCID50/mL, and for type 3 was 8.00 x 101 TCID50/mL.
Analytical Reactivity (Inclusivity) Study:
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.
Key results: The study confirmed the detection of multiple strains of parainfluenza Type 1, Type 2, and Type 3.
Analytical Specificity/Cross-Reactivity Study:
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. Organisms were added to negative nasal matrix and tested in triplicate.
Key results: No cross-reactivity was seen with any of the organisms tested.
Microbial Interference Study:
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. Organisms were added to samples containing either parainfluenza virus types 1, 2, or 3 at 2 x LoD concentration and tested in triplicate.
Key results: No interference was seen with any of the organisms when the target viruses were tested at 2 x LoD concentrations.
Interfering Substances Study:
A study was performed to evaluate the performance of the Lyra™ Parainfluenza Virus Assay in the presence of eleven (11) potentially interfering/cross-reactive substances, at clinically relevant levels. Each substance was tested in the presence of 2X LoD parainfluenza virus types 1, 2, and 3 samples and with negative matrix.
Key results: None of the eleven (11) substances interfered with the detection of parainfluenza virus types 1, 2, and 3, nor did they cross-react with the assay.
Carry-Over and Cross Contamination Study:
Studies were performed using a 96-sample panel consisting of 48 high positives and 48 negative specimens, with high positive specimens containing 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 over a 5-day period.
Key results: Cross-contamination and amplicon carry-over did not occur.
Method Comparison (Prospective Study):
A prospective multi-center study using one thousand two hundred and forty-one (1241) fresh specimens from the upper respiratory tract. Specimens were processed for nucleic acid extraction and tested 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).
Key results:
PIV-1: Sensitivity 100% (95% CI: 72.2% to 100%), Specificity 99.8% (95% CI: 99.3% to 99.9%).
PIV-2: Sensitivity 100% (95% CI: 56.6% to 100%), Specificity 100% (95% CI: 99.7% to 100%).
PIV-3: Sensitivity 100% (95% CI: 81.6% to 100%), Specificity 99.6% (95% CI: 99.0% to 99.8%).
Method Comparison (Retrospective Study):
A retrospective study was conducted with one hundred five (105) frozen specimens from the upper respiratory tract, tested concurrently with the Lyra™ Parainfluenza Virus Assay and the Prodesse ProParaFlu+ assay (K091053).
Key results:
PIV-1: Positive Percent Agreement 100% (95% CI: 86.2% to 100%), Negative Percent Agreement 98.8% (95% CI: 93.3% to 99.8%).
PIV-2: Positive Percent Agreement 100% (95% CI: 85.1% to 100%), Negative Percent Agreement 94.0% (95% CI: 86.7% to 97.4%).
PIV-3: Positive Percent Agreement 100% (95% CI: 86.2% to 100%), Negative Percent Agreement 100% (95% CI: 95.5% to 100%).
Key Metrics (Sensitivity, Specificity, PPV, NPV, etc.)
Prospective Study (Comparator: DSFA and Culture with DFA):
PIV-1: Sensitivity 100%, Specificity 99.8%
PIV-2: Sensitivity 100%, Specificity 100%
PIV-3: Sensitivity 100%, Specificity 99.6%
Retrospective Study (Comparator: Prodesse ProParaFlu+ assay):
PIV-1: Positive Percent Agreement 100%, Negative Percent Agreement 98.8%
PIV-2: Positive Percent Agreement 100%, Negative Percent Agreement 94.0%
PIV-3: Positive Percent Agreement 100%, Negative Percent Agreement 100%
Predicate Device(s)
Reference Device(s)
Not Found
Predetermined Change Control Plan (PCCP) - All Relevant Information
Not Found
§ 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.
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Image /page/0/Picture/1 description: The image is a seal for the Department of Health & Human Services - USA. The seal is circular, with the text "DEPARTMENT OF HEALTH & HUMAN SERVICES - USA" arranged around the perimeter. In the center of the seal is a stylized image of three human profiles facing to the right, stacked on top of each other.
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.
1
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
2
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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3
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:
4
| Table 1. Comparison of New Device with Predicate Device | ||
|---|---|---|
| Item | Subject Device | |
| LyraTM Parainfluenza | ||
| Virus Assay | Predicate Device | |
| (K091053) | ||
| Prodesse | ||
| ProParafluTM+ Assay | ||
| Intended Use | The LyraTM | |
| Parainfluenza Virus | ||
| Assay is a Real-Time | ||
| PCR assay for the | ||
| qualitative detection and | ||
| identification of human | ||
| parainfluenza type 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 | ||
| infection and should not | ||
| be used as the sole basis | ||
| for treatment or other | ||
| patient management | ||
| decisions. | The ProParaflu+ Assay is | |
| a multiplex Real Time | ||
| RT-PCR in vitro | ||
| diagnostic test for the | ||
| qualitative detection and | ||
| discrimination of | ||
| Parainfluenza 1 Virus, | ||
| Parainfluenza 2 Virus | ||
| and | ||
| Parainfluenza 3 Virus | ||
| (HPIV-1, HPIV-2 and | ||
| HPIV-3) nucleic acids | ||
| isolated and purified | ||
| from nasopharyngeal | ||
| (NP) swab specimens | ||
| obtained from | ||
| individuals exhibiting | ||
| signs and symptoms of | ||
| respiratory tract | ||
| infections. This assay | ||
| targets the conserved | ||
| regions of the | ||
| Hemagglutinin- | ||
| Neuraminidase (HN) | ||
| gene of HPIV-1, HPIV-2 | ||
| and HPIV-3, | ||
| respectively. The | ||
| detection and | ||
| discrimination of HPIV- | ||
| I, HPIV-2 and HPIV-3 | ||
| nucleic acids from | ||
| symptomatic patients aid | ||
| in the diagnosis of | ||
| human respiratory tract | ||
| parainfluenza infections | ||
| if used in conjunction | ||
| with other clinical and | ||
| laboratory findings. This | ||
| test is not intended to |
5
| Comparison of New Device with Predicate Device
| Table 1. | ||||
|---|---|---|---|---|
| Item | Subject Device | |||
| Lyra™ Parainfluenza | ||||
| Virus Assay | Predicate Device | |||
| (K091053) | ||||
| Prodesse | ||||
| ProParaflu™+ Assay | ||||
| detect Parainfluenza 4a | ||||
| or Parainfluenza 4b | ||||
| Viruses. | ||||
| Negative test results are | ||||
| presumptive and should | ||||
| be confirmed by cell | ||||
| culture. Negative results | ||||
| do not preclude | ||||
| Parainfluenza 1, 2 or 3 | ||||
| virus infections and | ||||
| should not be used as the | ||||
| sole basis for treatment | ||||
| or other management | ||||
| decisions. | ||||
| DNA Amplification | ||||
| Technology | Real time polymerase | |||
| chain reaction | Same | |||
| Target Sequence Detected | Parainfluenza type 1 | |||
| nuclear protein gene | ||||
| Parainfluenza type 2 | ||||
| phosphate protein gene | ||||
| Parainfluenza type 3 | ||||
| phosphate protein gene | Conserved regions of the | |||
| Hemagglutinin- | ||||
| Neuraminidase (HN) | ||||
| gene of HPIV-1, HPIV-2 | ||||
| and HPIV-3 | ||||
| Sample Types | Nasal and | |||
| Nasopharyngeal swabs | Nasopharyngeal swabs | |||
| Extraction | NucliSENS® | |||
| easyMAGTM | ||||
| (bioMérieux) | MagNA Pure LC System | |||
| (Roche) | ||||
| NucliSENS® | ||||
| easyMAGTM | ||||
| (bioMérieux ) | ||||
| Amplification | Applied Biosystems | |||
| 7500 Fast Dx | Cepheid SmartCycler II | |||
| Detection Techniques | Applied Biosystems | |||
| 7500 Fast Dx | Cepheid SmartCycler II |
Intended Use
6
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 | 5X | ||||||
| LoD | 2X | ||||||
| LoD | 0.5X | ||||||
| LoD | 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 High | ||||
| Negative | 40% | |||
| (CI95 24.6% to 57.7%) | 76.6% | |||
| (CI95 59.1% to | ||||
| 88.2%) | 63.3% | |||
| (CI95 45.5% to | ||||
| 78.1%) | 60% | |||
| (CI95 49.7% to 69.5%) | ||||
| PIV-1 Low | ||||
| Positive | 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 Moderate | ||||
| Positive | 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 High | ||||
| Negative | 20% | |||
| (CI95 9.5% to 37.3%) | 93.3% | |||
| (CI95 78.7% to | ||||
| 98.2%) | 80% | |||
| (CI95 62.7% to | ||||
| 90.5%) | 64.4% | |||
| (CI95 54.1% to 73.6%) | ||||
| PIV-2 Low | ||||
| Positive | 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 Moderate | ||||
| Positive | 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 High | ||||
| Negative | 0% | |||
| (CI95 0% to 11.4%) | 3.3% | |||
| (CI95 0.6% to 16.7%) | 53.3% | |||
| (CI95 36.1% to | ||||
| 69.8%) | 18.9% | |||
| (CI95 12.1% to 28.2%) | ||||
| PIV-3 Low | ||||
| Positive | 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 Moderate | ||||
| Positive | 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 Positive | ||||
| Control | 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 Positive | ||||
| Control | 100% | |||
| (CI95 88.6% to 100%) | 100% | |||
| (CI95 88.6% to 100%) | 100% | |||
| (CI95 88.6% to 100%) | 100% | |||
| (CI95 95.6% to 100%) |
8
| 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 |
9
| 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 |
10
| 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 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 | |
| Streptococcus salivarius | Measles/7/2000 | |
| Staphylococcus epidermidis | Mumps Virus | |
| Staphylococcus aureus | Parainfluenza Type 4A |
11
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-1 | ||||||||
| Ct Avg. | PIV-1 | ||||||||
| SD | PIV-2 | ||||||||
| Ct Avg. | PIV-2 | ||||||||
| SD | PIV-3 | ||||||||
| Ct Avg. | PIV-3 | ||||||||
| SD | 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 (Bovine | |||||||||
| Submaxillary Gland, | |||||||||
| type I-S) | 35.8 | 0.4 | 35.6 | 0.7 | 34.4 | 0.3 | Neg | N/A | No |
| Blood (human), | |||||||||
| EDTA | |||||||||
| anticoagulated | 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 Homeopathic | |||||||||
| Non-Drowsy Allergy | |||||||||
| Relief No Drip | |||||||||
| Liquid 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 Throat | |||||||||
| Lozenges: Ricola | |||||||||
| Action 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 |
| Oseltamivir | |||||||||
| phosphate | 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.
12
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.
13
| Table 10. PIV-1 | Comparator: DSFA and Culture with DFA | ||
|---|---|---|---|
| LyraTM | |||
| Parainfluenza Virus | |||
| Assay | 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 | |||
|---|---|---|---|
| LyraTM | |||
| Parainfluenza Virus | |||
| Assay | 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 | |||
|---|---|---|---|
| LyraTM | |||
| Parainfluenza Virus | |||
| Assay | 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.
14
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 Virus | |||
| Assay | 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
15
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.