DiagCORE Respiratory Panel 2 Instructions for use PL-013-05/2018-EN 210002
DiagCORE Respiratory Panel 2 Instructions for Use (CE) Cat # RP1: 210002 2018 May This document is to be used solely for the purpose of analyzing a DiagCORE Respiratory Panel 2 Cartridge on the DiagCORE Analyzer. No part of this document may be reproduced or transmitted by any means, whether electronic or mechanical, or for any purpose, without the express written permission of STAT-Dx Life, S.L. Copyright 2018, STAT-Dx Life, S.L. All rights reserved. A printed version of these instructions for use is available upon request. This Instructions for Use can be accessed at http.support.qiagen.com. STAT-Dx Life, S.L. Baldiri Reixac 4 08028 Barcelona, Spain Customer and technical support If assistance is required, contact Technical Support using the contact information below. Website: http.support.qiagen.com When contacting Technical Support about an error with the DiagCORE Analyzer or about an error with the DiagCORE Respiratory Panel 2 Cartridge, note the steps leading up to the error and any information appearing in any dialog boxes. This will help us solve the problem. When calling Technical Support about errors, please have the following information ready: Analyzer serial number, type and version (if applicable) Error code (if applicable) Time point when the error occurred for the first time Frequency of error occurrence (i.e., intermittent or persistent error) Photo of error, if possible Copy of support package 2 DiagCORE Respiratory Panel 2 Instructions for Use
Contents Customer and technical support... 2 Contents... 3 Table of symbols... 5 1 Information about the DiagCORE Respiratory Panel 2... 6 1.1 Product name and intended use... 6 1.2 Package contents... 7 1.3 Storage and expiration date... 7 2 Safety information... 8 3 General background... 9 3.1 DiagCORE Respiratory Panel 2 Cartridge description... 9 3.2 Detected pathogens... 10 3.3 Description of the procedure... 12 3.4 Sample collection and cartridge loading... 13 3.5 Sample preparation, nucleic acid amplification, and detection... 13 4 Required materials and equipment that are not provided... 15 5 Procedure for dry swab samples... 16 5.1 Sample collection, transport, and storage... 16 5.2 Loading a sample into the DiagCORE Respiratory Panel 2 Cartridge... 16 5.3 Starting the DiagCORE Analyzer... 19 5.4 Running a test... 19 6 Procedure for transport medium liquid samples... 25 6.1 Sample collection, transport, and storage... 25 6.2 Loading a sample into the DiagCORE Respiratory Panel 2 Cartridge... 25 6.3 Starting the DiagCORE Analyzer... 28 6.4 Running a test... 29 7 Internal control... 34 8 Interpretation of results... 35 8.1 Viewing results... 35 8.2 Result interpretation... 40 8.3 Internal Control interpretation... 41 DiagCORE Respiratory Panel 2 Instructions for Use 3
9 Installing the Assay Definition File... 42 10 Limitations of the procedure... 44 11 Performance characteristics. Clinical Performance... 46 12 Performance characteristics. Analytical Performance... 51 12.1 Sensitivity (Limit of Detection)... 51 12.2 Assay Robustness... 52 12.3 Exclusivity (Analytical Specificity)... 52 12.4 Inclusivity (Analytical Reactivity)... 54 12.5 Co-Infections... 57 12.6 Interfering Substances... 58 12.7 Carryover... 59 12.8 Reproducibility... 59 12.9 Sample Stability... 62 13 References... 63 14 Appendices... 64 14.1 Disposal information... 64 14.2 Declaration of conformity... 64 14.3 Glossary... 64 14.4 Trademarks and copyright... 65 14.5 Copyright, disclaimer, and warranty... 65 14.6 Patent statement... 65 14.7 Software license agreement... 65 4 DiagCORE Respiratory Panel 2 Instructions for Use
Table of symbols The following symbols can be found on the DiagCORE Respiratory Panel 2 Cartridge, packaging, and these instructions for use. Legal manufacturer Description In vitro diagnostic medical device CE marking for European Conformity Catalog number Storage temperature limitations Consult instructions for use Health hazard/hazardous to the ozone layer Expiration date (YYYY MM DD) Batch code Serial number Do not reuse Keep away from sunlight n Sufficient for <n> tests Do not use if package is damaged Corrosive DiagCORE Respiratory Panel 2 Instructions for Use 5
1 Information about the DiagCORE Respiratory Panel 2 1.1 Product name and intended use The DiagCORE Respiratory Panel 2 is a qualitative test intended for analyzing nasopharyngeal swab (NPS) samples taken from patients suspected of respiratory infection for the presence of viral or bacterial nucleic acids. The DiagCORE Respiratory Panel 2 is able to accept both dry swabs and transport medium liquid samples. The assay is designed for use with the DiagCORE Analyzer for integrated nucleic acid extraction and multiplex, RT-real-time PCR detection. The following pathogens can be detected and differentiated with the DiagCORE Respiratory Panel 2: Influenza A, Influenza A subtype H1N1/2009, Influenza A subtype H1, Influenza A subtype H3, Influenza B, Coronavirus 229E, Coronavirus HKU1, Coronavirus NL63, Coronavirus OC43, Parainfluenza virus 1, Parainfluenza virus 2, Parainfluenza virus 3, Parainfluenza virus 4, Respiratory Syncytial virus A/B, human Metapneumovirus A/B, Adenovirus, Bocavirus, Rhinovirus/Enterovirus, Mycoplasma pneumoniae, Legionella pneumophila and Bordetella pertussis. The results from the DiagCORE Respiratory Panel 2 must be interpreted within the context of all relevant clinical and laboratory findings. Assay performance characteristics have been established only for individuals who have shown respiratory symptoms. The DiagCORE Respiratory Panel 2 is intended for professional use only and is not intended for selftesting. For in vitro diagnostic use. 6 DiagCORE Respiratory Panel 2 Instructions for Use
1.2 Package contents DiagCORE Respiratory Panel 2 Catalog No. Number of tests 210002 6 DiagCORE Respiratory Panel 2 cartridge 6 individually packaged cartridges containing all reagents needed for sample preparation and multiplex RT-real time PCR plus internal control Cartridge composition: The DiagCORE Respiratory Panel 2 Cartridge contents includes the following: Ethanol, isopropanol, enzymes, oligonucleotides, tris-edta, sodium azide, guanidine hydrochloride, guanidinium thiocyanate, guanidine chloride, propylene glycol, triton-x-100 and D-(+)-trehalose dihydrate. Transfer pipettes 6 individually packaged transfer pipettes for dispensing liquid sample into the DiagCORE Respiratory Panel 2 Cartridge 1.3 Storage and expiration date Store the DiagCORE Respiratory Panel 2 Cartridges in a dry, clean storage space at room temperature (15 25 C). Do not remove the DiagCORE Respiratory Panel 2 Cartridges or the transfer pipettes from their individual packaging until actual use. Under these conditions, DiagCORE cartridges can be stored until the expiration date printed on the individual packaging. The expiration date is also included in the cartridge barcode and is read by the DiagCORE Analyzer when the cartridge is inserted into the instrument to run a test. DiagCORE Respiratory Panel 2 Instructions for Use 7
2 Safety information Always wear appropriate personal protective equipment, including but not limited to disposable powder-free gloves, a lab coat, and protective eyewear. Protect skin, eyes, and mucus membranes. Change gloves often when handling samples. Handle all samples, used cartridges, and transfer pipettes as if they are capable of transmitting infectious agents. Always observe safety precautions as outlined in relevant guidelines, such as the Clinical and Laboratory Standards Institute (CLSI) Protection of Laboratory Workers from Occupationally Acquired Infections, Approved Guidelines M29, or other appropriate documents provided by: OSHA: Occupational Safety and Health Administration (United States of America) ACGIH: American Conference of Government Industrial Hygienists (United States of America) COSHH: Control of Substances Hazardous to Health (United Kingdom) Follow your institution s safety procedures for handling biological samples. Dispose of samples, DiagCORE cartridges, and transfer pipettes according to the appropriate regulations. The DiagCORE cartridge is a closed, single-use device that contains all reagents needed for sample preparation and multiplex RT- real time PCR within the DiagCORE Analyzer. Do not use a DiagCORE cartridge that is past its expiration date, appears damaged, or leaks fluid. Dispose of used or damaged cartridges in accordance with all national, state and local health and safety regulations and laws. Observe standard laboratory procedures for keeping the working area clean and contaminationfree. Guidelines are outlined in publications like the Biosafety in Microbiological and Biomedical Laboratories from the Centers for Disease Control and Prevention and the National Institutes of Health (www.cdc.gov/od/ohs/biosfty/biosfty.htm). 8 DiagCORE Respiratory Panel 2 Instructions for Use
3 General background 3.1 DiagCORE Respiratory Panel 2 Cartridge description The DiagCORE Respiratory Panel 2 Cartridge is a disposable plastic device that allows performance of fully automated molecular assays for the detection of respiratory pathogens. Main features of the DiagCORE Respiratory Panel 2 Cartridge include compatibility with the respiratory dry swabs (Copan FLOQSwabs, Ref. 503CS01) and transport medium liquid samples, hermetical containment of the pre-loaded reagents necessary for testing, and true walk-away operation. All sample preparation and assay testing steps are performed within the cartridge. All reagents required for the complete execution of a test run are pre-loaded and self-contained in the DiagCORE Respiratory Panel 2 Cartridge. The user does not need to come in contact with and/or manipulate any reagents. During the test, reagents are handled in the Analytical Module of the DiagCORE Analyzer by pneumatically-operated microfluidics and make no direct contact with the Analyzer actuators. The Analyzer houses air filters for both incoming and outgoing air, further safeguarding the environment. After testing, the cartridge stays hermetically closed at all times, greatly enhancing its safe disposal. Within the cartridge, multiple steps are automatically performed in sequence using pneumatic pressure to transfer samples and fluids via the transfer chamber to their intended destinations. After the DiagCORE Respiratory Panel 2 Cartridge containing the sample is introduced into the Analyzer, the following assay steps occur automatically: Resuspension of internal control Cell lysis using mechanical and/or chemical means Membrane-based nucleic acid purification Mixing of the purified nucleic acid with lyophilized master mix reagents Transfer of defined aliquots of eluate/master mix to different reaction chambers Performance of RT-real-time, multiplex PCR testing within each reaction chamber. An increase in fluorescence, indicating detection of the target analyte, is detected directly within each reaction chamber. DiagCORE Respiratory Panel 2 Instructions for Use 9
The layout of the DiagCORE Respiratory Panel 2 Cartridge and its features are illustrated below. DiagCORE Respiratory Panel 2 Cartridge. 3.2 Detected pathogens Acute respiratory infections can be caused by a variety of pathogens, including bacteria and viruses, and generally present with nearly indistinguishable clinical signs and symptoms. The rapid and accurate determination of the presence or absence of potential causative agent(s) helps make timely decisions regarding treatment, hospital admission, infection control, and return of the patient to work and family. It may also greatly support improved antimicrobial stewardship and other important public health initiatives. The DiagCORE Respiratory Panel 2 Cartridge is a single-use cartridge that includes all reagents needed for nucleic acid extraction, nucleic acid amplification, detection, and identification of 22 viral and bacterial pathogens that cause respiratory symptoms. Testing requires a small sample volume and minimal hands-on time, and the results are available in approximately one hour. Pathogens that can be detected and identified with the DiagCORE Respiratory Panel 2 are listed in Table 1. 10 DiagCORE Respiratory Panel 2 Instructions for Use
Table 1. Pathogens detected by the DiagCORE Respiratory Panel 2 Pathogen Classification (genome type) Influenza A Orthomyxovirus (RNA) Influenza A, subtype H1N1/2009 Orthomyxovirus (RNA) Influenza A subtype H1 Orthomyxovirus (RNA) Influenza A subtype H3 Orthomyxovirus (RNA) Influenza B Orthomyxovirus (RNA) Coronavirus 229E Coronavirus (RNA) Coronavirus HKU1 Coronavirus (RNA) Coronavirus NL63 Coronavirus (RNA) Coronavirus OC43 Coronavirus (RNA) Parainfluenza Virus 1 Paramyxovirus (RNA) Parainfluenza Virus 2 Paramyxovirus (RNA) Parainfluenza Virus 3 Paramyxovirus (RNA) Parainfluenza Virus 4 Paramyxovirus (RNA) Respiratory Syncytial Virus A/B Paramyxovirus (RNA) Human Metapneumovirus A/B Paramyxovirus (RNA) Adenovirus Adenovirus (DNA) Bocavirus Parvovirus (DNA) Rhinovirus/Enterovirus Picornavirus (RNA) Mycoplasma pneumoniae Bacterium (DNA) Legionella pneumophila Bacterium (DNA) Bordetella pertussis Bacterium (DNA) Note: Enterovirus and rhinovirus are both detected but not differentiated in the DiagCORE Respiratory Panel 2. DiagCORE Respiratory Panel 2 Instructions for Use 11
3.3 Description of the procedure Diagnostic tests with the DiagCORE Respiratory Panel 2 are performed on the DiagCORE Analyzer. Samples are collected and loaded manually into the DiagCORE cartridge: Option 1: Inserting the swab into the swab port in the case of dry swab sample type. Option 2: Inserting the liquid into the main port using a transfer pipette in the case of transport medium liquid sample type. All of the sample preparation and analysis steps are performed automatically by the DiagCORE Analyzer. 12 DiagCORE Respiratory Panel 2 Instructions for Use
3.4 Sample collection and cartridge loading The collection of samples and their subsequent loading into the DiagCORE cartridge should be performed by personnel trained in safe handling of biological samples. The following steps are involved and must be executed by the user: 1. A nasopharyngeal swab sample is collected. 2. The nasopharyngeal swab is placed into transport medium only in the case of transport medium liquid sample type. 3. The sample information is manually written on or a sample label is affixed to the top of a DiagCORE cartridge. 4. Sample is loaded manually into the DiagCORE cartridge: Dry swab sample type: The nasopharyngeal swab sample is inserted into the swab port of the DiagCORE cartridge. Transport medium liquid sample type: 300 µl of the sample is transferred into the DiagCORE cartridge using a transfer pipette. In the case of transport medium liquid sample loading, the user performs a visual check of the sample inspection window (see image below) to confirm that the liquid sample has been loaded. 5. The sample barcode and DiagCORE cartridge QR code are scanned in the DiagCORE Analyzer. 6. The DiagCORE cartridge is introduced into the DiagCORE Analyzer. 7. The test is started on the DiagCORE Analyzer. 3.5 Sample preparation, nucleic acid amplification, and detection The extraction, amplification, and detection of nucleic acids in the sample are performed automatically by the DiagCORE Analyzer. 1. The liquid sample is homogenized, and cells are lysed in the lysis chamber of the DiagCORE cartridge, which includes a rotor that turns at high speed. DiagCORE Respiratory Panel 2 Instructions for Use 13
2. Nucleic acids are purified from the lysed sample via binding to a silica membrane in the purification chamber of the DiagCORE cartridge in the presence of chaotropic salts and alcohol. 3. The purified nucleic acids are eluted from the membrane in the purification chamber and are mixed with the lyophilized PCR chemistry in the dried-chemistry chamber of the DiagCORE cartridge. 4. The mixture of sample and PCR reagents is dispensed into the DiagCORE cartridge PCR chambers, which contain lyophilized, assay-specific primers and probes. 5. The DiagCORE Analyzer creates the optimal temperature profiles to carry out effective RT-real time PCR and performs real-time fluorescence measurements to generate amplification curves. 6. The DiagCORE Analyzer Software interprets the resulting data and process controls and delivers a test report. 14 DiagCORE Respiratory Panel 2 Instructions for Use
4 Required materials and equipment that are not provided The DiagCORE Respiratory Panel 2 is designed for use with the DiagCORE Analyzer. Before beginning a test, make sure the following are available: DiagCORE Analyzer (at least one Operational module and one Analytical module) DiagCORE Analyzer User Manual DiagCORE Latest Assay Definition File software for Respiratory Panel 2 installed in the Operational module DiagCORE Respiratory Panel 2 Instructions for Use 15
5 Procedure for dry swab samples 5.1 Sample collection, transport, and storage 1. Collect nasopharyngeal swab samples according to the swab manufacturer s recommended procedures. 5.2 Loading a sample into the DiagCORE Respiratory Panel 2 Cartridge 1. Open the package of a DiagCORE Respiratory Panel 2 Cartridge using the tear notches on the sides of the packaging. After the package is open, sample should be introduced inside the DiagCORE Respiratory Panel 2 cartridge and loaded in the DiagCORE Analyser within 120 minutes. 2. Take out the cartridge and position it so that the QR code on the label faces you. 16 DiagCORE Respiratory Panel 2 Instructions for Use
3. Manually write the sample information or place a sample information label on the top of the DiagCORE cartridge. Make sure that the label is properly positioned and does not block the lid opening. 4. Open the sample lid of the swab port on the left side of the cartridge. 5. Insert the swab into the cartridge until the breakpoint is aligned with the access opening (the swab will go no further). DiagCORE Respiratory Panel 2 Instructions for Use 17
6. Break the swab shaft at the breakpoint, leaving the rest of the swab in the cartridge. 7. Firmly close the lid of the swab port until it clicks. 18 DiagCORE Respiratory Panel 2 Instructions for Use
After sample is introduced inside the DiagCORE Respiratory Panel 2 cartridge, cartridge must be loaded in the DiagCORE Analyser within 90 minutes. 5.3 Starting the DiagCORE Analyzer 1. Press the On/Off button on the front of the Analyzer to start the unit. NOTE The power switch at the back of the Analytical Module must be set in the I position. The DiagCORE Analyzer status indicators turn blue in this case. 2. Wait until the Main screen appears and the DiagCORE Analyzer status indicators turn green and stop blinking. 3. Log in to the DiagCORE Analyzer by entering the user name and password. NOTE The Login screen will appear if User Access Control is activated. If the User Access Control is disabled, no user name/password will be required and the Main screen will appear. 4. In case the Assay Definition File software has not been installed in the Analyzer follow the instructions prior to running the test (See Section 9 of this document for additional information) 5.4 Running a test 1. Press the Run Test button at the top right corner of the touchscreen of the DiagCORE Analyzer. 2. When prompted, scan the sample ID barcode on the nasopharyngeal swab, or scan the specimen information barcode placed on the top of the DiagCORE cartridge, using the front barcode reader that is integrated into the DiagCORE Analyzer See figure below). DiagCORE Respiratory Panel 2 Instructions for Use 19
NOTE It is also possible to enter the sample ID using the virtual keyboard of the touchscreen by pressing on the Sample ID field. NOTE NOTE Depending on the chosen system configuration, entering the patient ID may also be required at this point. Instructions from the DiagCORE Analyzer appear in the Instructions Bar at the bottom of the touchscreen. 3. When prompted, scan the barcode of the DiagCORE Respiratory Panel 2 Cartridge to be used. The DiagCORE Analyzer automatically recognizes the assay to be run, based on the cartridge barcode. 20 DiagCORE Respiratory Panel 2 Instructions for Use
NOTE The DiagCORE Analyzer will not accept cartridges with elapsed expiration date, previously used cartridges or cartridges for assays that have not been installed on the unit. An error message will be shown in these cases and the cartridge will be rejected. Refer to the DiagCORE Analyzer User Manual for further details on how to install assays. 4. Select the appropriate sample type from the list (See image below). DiagCORE Respiratory Panel 2 Instructions for Use 21
5. The Confirm screen will appear. Review the data entered and make any necessary changes by pressing the relevant fields on the touchscreen and editing the information. 6. Press Confirm when all the displayed data are correct. If needed, press on the appropriate field to edit its content, or press Cancel to cancel the test. 7. Ensure that both sample lids of the cartridge are firmly closed. When the cartridge entrance port on the top of the DiagCORE Analyzer automatically opens, insert the cartridge with the barcode facing to the left and the reaction chambers facing down. There is no need to push the cartridge into the DiagCORE Analyzer. Position it correctly into the cartridge entrance port, and the DiagCORE Analyzer will automatically move the cartridge into the Analytical Module. 22 DiagCORE Respiratory Panel 2 Instructions for Use
8. Upon detecting the cartridge, the DiagCORE Analyzer will automatically close the lid of the cartridge entrance port and start the test run. No further action from the operator is required to start the run. NOTE NOTE NOTE The DiagCORE Analyzer will not accept a cartridge other than the one used and scanned during the test setup. If a cartridge other than the one scanned is inserted, an error will be generated and the cartridge will be automatically ejected. Up to this point, it is possible to cancel the test run by pushing the Cancel button in the bottom right corner of the screen. Depending on the system configuration, the operator may be required to re-type their user password to start the test run. NOTE The lid of the cartridge entrance port will close automatically after 30 seconds if no cartridge is positioned in the port. If this occurs, repeat the procedure starting with step 5. 9. While the test is running, the time remaining in the run is displayed on the screen. DiagCORE Respiratory Panel 2 Instructions for Use 23
10. After the test run is completed, the Eject screen will appear and the Module Status Bar will show the test result as one of the following options: TEST COMPLETED TEST FAILED TEST CANCELED The test was completed successfully. An error occurred during the test. The user canceled the test. NOTE If the test fails, refer to the DiagCORE Analyzer User Manual Troubleshooting section for possible reasons and instructions on how to proceed. 11. Press Eject to remove the cartridge and dispose of it as biohazardous waste in accordance with all national, state, and local health and safety regulations and laws. The cartridge should be removed when the cartridge entrance port opens and ejects the cartridge. If the cartridge is not removed after 30 seconds, it will be automatically moved back into the Analyzer, and the lid of the cartridge entrance port will close. If this occurs, press Eject to open the lid of the cartridge entrance port again and then remove the cartridge. NOTE Used cartridges must be discarded. It is not possible to re-use cartridges for tests for which the execution was started but then subsequently canceled by the operator, or for which an error was detected. 12. After the cartridge has been ejected, the Results Summary screen will appear. Please refer to section Interpretation of Results for further details. To run another test, press Run Test. NOTE For further information on the use of the instrument, refer to the DiagCORE Analyzer User Manual. 24 DiagCORE Respiratory Panel 2 Instructions for Use
6 Procedure for transport medium liquid samples 6.1 Sample collection, transport, and storage 1. Collect nasopharyngeal swab samples according to the swab manufacturer s recommended procedures, and place the swab into Universal Transport Medium. 6.2 Loading a sample into the DiagCORE Respiratory Panel 2 Cartridge 1. Open the package of a DiagCORE Respiratory Panel 2 Cartridge using the tear notches on the sides of the packaging. After the package is open, sample should be introduced inside the DiagCORE Respiratory Panel 2 cartridge and loaded in the DiagCORE Analyser within 120 minutes. 2. Take out the cartridge and position it so that the QR code on the label faces you. DiagCORE Respiratory Panel 2 Instructions for Use 25
3. Manually write the sample information or place a sample information label on the top of the DiagCORE cartridge. Make sure that the label is properly positioned and does not block the lid opening. 4. Open the sample lid of the main port on the front of the cartridge. 5. Open the tube with the sample to be tested. Use the supplied transfer pipette to draw up fluid to the third fill line on the pipette (300 µl). 26 DiagCORE Respiratory Panel 2 Instructions for Use
IMPORTANT Take care to not draw air into the pipette. If COPAN UTM is used as transport medium, take care not to aspirate any of the beads present in the tube. If air or beads are drawn into the pipette, carefully expel the sample fluid in the pipette back into the sample tube, and draw up fluid again. 6. Carefully transfer 300 µl of sample volume into the main port of the DiagCORE Respiratory Panel 2 cartridge, using a supplied single-use transfer pipette. DiagCORE Respiratory Panel 2 Instructions for Use 27
7. Firmly close the lid of the main port until it clicks. 8. Confirm visually that the sample has been loaded by checking the sample inspection window in the cartridge (see the image below). After sample is introduced inside the DiagCORE Respiratory Panel 2 cartridge, cartridge must be loaded in the DiagCORE Analyser within 90 minutes. 6.3 Starting the DiagCORE Analyzer 1. Press the On/Off button on the front of the Analyzer to start the unit. 28 DiagCORE Respiratory Panel 2 Instructions for Use
NOTE The power switch at the back of the Analytical Module must be set in the I position. The DiagCORE Analyzer status indicators turn blue in this case. 2. Wait until the Main screen appears and the DiagCORE Analyzer status indicators turn green and stop blinking. 3. Log in to the DiagCORE Analyzer by entering the user name and password. NOTE The Login screen will appear if User Access Control is activated. If the User Access Control is disabled, no user name/password will be required and the Main screen will appear. 4. In case the Assay Definition File software has not been installed in the Analyzer follow the instructions prior to running the test (See Section 9 of this document for additional information). 6.4 Running a test 1. Press the Run Test button at the top right corner of the touchscreen of the DiagCORE Analyzer. 2. When prompted, scan the sample ID barcode on the UTM tube containing the sample, or scan the specimen information barcode placed on the top of the DiagCORE cartridge, using the front barcode reader that is integrated into the DiagCORE Analyzer. NOTE It is also possible to enter the sample ID using the virtual keyboard of the touchscreen by pressing on the Sample ID field. DiagCORE Respiratory Panel 2 Instructions for Use 29
NOTE NOTE Depending on the chosen system configuration, entering the patient ID may also be required at this point. Instructions from the DiagCORE Analyzer appear in the Instructions Bar at the bottom of the touchscreen. 3. When prompted, scan the barcode of the DiagCORE Respiratory Panel 2 Cartridge to be used. The DiagCORE Analyzer automatically recognizes the assay to be run, based on the cartridge barcode. NOTE The DiagCORE Analyzer will not accept cartridges with elapsed expiration date, previously used cartridges or cartridges for assays that are not installed on the unit. An error message will be shown in these cases and the cartridge will be rejected. Refer to the DiagCORE Analyzer User Manual for further details. 4. Select the appropriate sample type from the list. 5. The Confirm screen will appear. Review the data entered and make any necessary changes by pressing the relevant fields on the touchscreen and editing the information. 6. Press Confirm when all the displayed data are correct. If needed, press on the appropriate field to edit its content, or press Cancel to cancel the test. 30 DiagCORE Respiratory Panel 2 Instructions for Use
7. Ensure that both sample lids of the cartridge are firmly closed. When the cartridge entrance port on the top of the DiagCORE Analyzer automatically opens, insert the cartridge with the barcode facing to the left and the reaction chambers facing down. There is no need to push the cartridge into the DiagCORE Analyzer. Position it correctly into the cartridge entrance port, and the DiagCORE Analyzer will automatically move the cartridge into the Analytical Module. 8. Upon detecting the cartridge, the DiagCORE Analyzer will automatically close the lid of the cartridge entrance port and start the test run. No further action from the operator is required to start the run. NOTE NOTE NOTE The DiagCORE Analyzer will not accept a cartridge other than the one used and scanned during the test setup. If a cartridge other than the one scanned is inserted, an error will be generated and the cartridge will be automatically ejected. Up to this point, it is possible to cancel the test run by pushing the Cancel button in the bottom right corner of the screen. Depending on the system configuration, the operator may be required to re-type their user password to start the test run. DiagCORE Respiratory Panel 2 Instructions for Use 31
NOTE The lid of the cartridge entrance port will close automatically after 30 seconds if no cartridge is positioned in the port. If this occurs, repeat the procedure starting with step 5. 9. While the test is running, the time remaining in the run is displayed on the screen. 10. After the test run is completed, the Eject screen will appear and the Module Status Bar will show the test result as one of the following options: TEST COMPLETED TEST FAILED TEST CANCELED The test was completed successfully. An error occurred during the test. The user canceled the test. NOTE If the test fails, refer to the DiagCORE Analyzer User Manual Troubleshooting section for possible reasons and instructions on how to proceed. 11. Press Eject to remove the cartridge and dispose of it as biohazardous waste in accordance with all national, state, and local health and safety regulations and laws. The cartridge should be removed when the cartridge entrance port opens and ejects the cartridge. If the cartridge is not removed after 30 seconds, it will be automatically moved back into the Analyzer, and the lid of the cartridge entrance port will close. If this occurs, press Eject to open the lid of the cartridge entrance port again and then remove the cartridge. NOTE Used cartridges must be discarded. It is not possible to re-use cartridges for tests for which the execution was started but then subsequently canceled by the operator, or for which an error was detected. 12. After the cartridge has been ejected, the Results Summary screen will appear. Please refer to section Interpretation of Results for further details. To run another test, press Run Test. 32 DiagCORE Respiratory Panel 2 Instructions for Use
NOTE For further information on the use of the instrument, refer to the DiagCORE Analyzer User Manual. DiagCORE Respiratory Panel 2 Instructions for Use 33
7 Internal control The DiagCORE Respiratory Panel 2 Cartridge includes a full process Internal Control which is titered MS2 bacteriophage. The MS2 bacteriophage is a single-stranded RNA virus, and it is included in the cartridge in dried form and is rehydrated upon sample loading. This internal control material verifies all steps of the analysis process, including sample resuspension/homogenization, lysis, nucleic acid purification, reverse transcription, and PCR. A positive signal for the internal control indicates that all processing steps performed by the DiagCORE Respiratory Panel 2 Cartridge were successful. A negative signal of the internal control does not negate any positive results for detected and identified targets, but it does invalidate all negative results in the analysis. Therefore, the test should be repeated if the internal control signal is negative. 34 DiagCORE Respiratory Panel 2 Instructions for Use
8 Interpretation of results 8.1 Viewing results The DiagCORE Analyzer automatically interprets and saves test results. After ejecting the cartridge, the Results Summary screen is automatically displayed. Example screen showing Test Data on the left panel and Test Summary in the main panel. The main part of the screen provides the following two lists and uses color-coding and symbols to indicate the results: The first list includes all pathogens detected and identified in the sample, preceded by a sign and are colored red. The second list includes all pathogens tested in the sample. Pathogens detected and identified in the sample are preceded by a not detected are preceded by a sign and are colored red. Pathogens that were tested but sign and are colored green. Note that the pathogens detected and identified in the sample are shown in both lists. In case the test failed to complete successfully, a message will indicate Failed followed by the specific Error Code. The following Test Data is shown on the left side of the screen: Sample ID Assay Type Sample Type DiagCORE Respiratory Panel 2 Instructions for Use 35
Further data about the assay is available, depending on the operator s access rights, through the tabs at the bottom of the screen (e.g., amplification plots and test details). A report with the assay data can be exported to an external USB storage device. Insert the USB storage device into one of the USB ports of the DiagCORE Analyzer and press Save Report in the bottom bar of the screen. This report can be exported later at any time by selecting the test from the View Result List. The report can also be sent to the printer by pressing Print Report in the bottom bar of the screen. 8.1.1 Viewing amplification curves To view test amplification curves of pathogens detected, press the Amplification Curves tab. Amplification Curves screen (Pathogens). Details about the tested pathogens and controls are shown on the left, and the amplification curves are shown in the center. NOTE If User Access Control is enabled on the DiagCORE Analyzer the Amplification Curves screen is only available for operators who have access rights. Press the Pathogens tab on the left side to display the plots corresponding to the tested pathogens. Press on the pathogen name to select which pathogens are shown in the amplification plot. It is possible to select single, multiple, or no pathogens. Each pathogen in the selected list will be assigned a color corresponding to the amplification curve associated with this pathogen. Unselected pathogens will be shown in gray. The corresponding CT and endpoint fluorescence values are shown below each pathogen name. Press the Controls tab on the left side to view the controls and select which controls are shown in the amplification plot. Press the circle next to the control name to select or deselect it. 36 DiagCORE Respiratory Panel 2 Instructions for Use
Amplification Curves screen (Pathogens and Controls). The amplification plot displays the data curve for the selected pathogens or controls. To alternate between logarithmic or linear scale for the Y-axis, press the Lin or Log button at the bottom left corner of the plot. The scale of the X-axis and Y-axis can be adjusted using the gray pickers on each axis. Press and hold a picker and then move it to the desired location on the axis. Move a picker to the axis origin to return to the default values. 8.1.2 Viewing test details Press Test Details in the Tab Menu Bar at the bottom of the touchscreen to review the results in more detail. Scroll down to see the complete report. The following Test Details are shown in the center of the screen: User ID Cartridge serial number Cartridge expiration date Analytical Module serial number Test status (completed, failed, canceled by operator) Error code if applicable Test start date and time Test execution time Assay name Test ID Test Result: Positive (in case at least one respiratory pathogen is detected/identified), negative (in case no respiratory pathogen is detected) or failed (an error occurred or the test was canceled by the user) DiagCORE Respiratory Panel 2 Instructions for Use 37
List of analytes tested in the assay, with CT and endpoint fluorescence in case of a positive signal Internal Control, with CT and endpoint fluorescence Example screen showing Test Data on the left panel and Test Details in the main panel. 8.1.3 Browsing results from previous tests To view results from previous tests that are stored in the results repository, press the Main Menu bar. View Results from Example of View Results List. 38 DiagCORE Respiratory Panel 2 Instructions for Use
The following information is available for every executed test: Sample ID Assay Name Operator ID Analytical Module on which the test was executed Date and time when the test was finished Outcome of the test (positive (pos), negative (neg), failed (fail) or successful (suc)) NOTE When User Access Control is enabled on the DiagCORE Analyzer, the data for which the user has no access rights will be hidden with asterisks. Select one or more test results by pressing the circle to left of the sample ID. A checkmark will appear next to selected results. Unselect test results by pressing this checkmark. The entire list of results can be selected by pressing the button in the top row. Example of selecting test results in the View Results list. Press anywhere in the test row to view the result for a particular test. Press a column headline (e.g., Sample ID) to sort the list in ascending or descending order according to that parameter. The list can be sorted according to only one column at a time. The Result column shows the outcome of each test: Name Button Description Positive pos At least one pathogen is positive. Negative neg No analytes were detected. DiagCORE Respiratory Panel 2 Instructions for Use 39
Name Button Description Failed fail The test failed, either because an error occurred or the test was cancelled by the user. Successful suc The test is either positive or negative, but the user does not have the access rights to view the test results. Please make sure a printer is connected to DiagCORE system and proper driver is installed. Press Print Report to print the report(s) for the selected result(s). Press Save Report to save the report(s) for the selected result(s) in PDF format to an external USB storage device. Select the report type: List of Tests or Test Reports. Press the Search button to search the test results by Sample ID, Assay and Operator ID. Enter the search string using the virtual keyboard, and press Enter to start the search. Only the records containing the search text will be displayed in the search results. If the results list has been filtered, the search will only apply to the filtered list. Press and hold a column headline to apply a filter based on that parameter. For some parameters, such as Sample ID, the virtual keyboard will appear so the search string for the filter can be entered. For other parameters, such as Assay, a dialog will open with a list of assays stored in the repository. Select one or more assays to filter only the tests that were performed with the selected assays. The symbol to the left of a column headline indicates that the column s filter is active. A filter can be removed by pressing the Remove Filter button in the submenu bar. 8.1.4 Exporting results to a USB drive From any tab of the test results screen, select Save Report to export and save a copy of the test results in PDF format to a USB drive. The USB port is located on the front of the instrument. 8.1.5 Printing results Please make sure a printer is connected to DiagCORE system and proper driver is installed. Select Print Report to send a copy of the test results to the printer. 8.2 Result interpretation A result for a respiratory organism is interpreted as Positive when the corresponding PCR assay is positive, except for Influenza A. The Influenza A assay in the DiagCORE Respiratory Panel 2 is designed to detect Influenza A as well as Influenza A subtype H1N1/2009, Influenza A subtype H1or Influenza A subtype H3, respectively. In particular, this means: In case seasonal Influenza A H1 strain is detected by the DiagCORE Respiratory Panel 2 assay, two signals will be generated, one for Influenza A and a second one for H1 strain and shown on the DiagCORE Analyzer screen. 40 DiagCORE Respiratory Panel 2 Instructions for Use
In case seasonal Influenza A H3 strain is detected by the DiagCORE Respiratory Panel 2 assay, two signals will be generated, one for Influenza A and a second one for H3 strain and shown on the DiagCORE Analyzer screen. In case a pandemic Influenza A/H1N1/2009 strain is detected, two signals will be generated, one for Influenza A and a second one for H1N1/2009 and shown on the DiagCORE Analyzer screen. For every other pathogen that can be detected with the DiagCORE Respiratory Panel 2, only one signal will be generated if the pathogen is present in the sample. 8.3 Internal Control interpretation Controls result Explanation Action Passed The internal control amplified successfully. The run was completed with success, and all results are validated and can be reported. Detected pathogens are reported as positive, and not detected pathogens are reported as negative. Failed The internal control failed. Positively detected pathogen(s) are reported, but all negative results (tested but not detected pathogen(s)) are invalid. Repeat the testing using a new DiagCORE Respiratory Panel 2 Cartridge. DiagCORE Respiratory Panel 2 Instructions for Use 41
9 Installing the Assay Definition File The Assay Definition File of the DiagCORE Respiratory Panel 2 has to be installed in the DiagCORE Analyzer previously to execute tests with the DiagCORE Respiratory Panel 2 cartridges. The same procedure has to be applied when a new version of the DiagCORE Respiratory Panel 2 assay is released. NOTE Assay Definition Files are available on the STAT-Dx web site and also through the STAT-Dx sellers/distributors. The Assay Definition File (extension.asy) must be saved into a USB Drive previously to the installation on the DiagCORE Analyzer. This USB Drive must be formatted with a FAT32 file system. To import new assays from the USB to the DiagCORE Analyzer proceed with the following steps: 1. Insert the USB stick with the Assay Definition File on one of the USB ports of the DiagCORE Analyzer. 2. Press the Options button and then the Assay Management button. The Assay Management screen appears on the content area of the display (See screenshot below). 42 DiagCORE Respiratory Panel 2 Instructions for Use
3. Press the Import icon in the bottom left of the screen. 4. Select the file from the USB drive corresponding to the assay to be imported. 5. A dialog will appear to confirm upload of the file. 6. A dialog may appear to override current version by a new one. Press yes to override. 7. The assay becomes active by pressing the Assay Active button (See screenshot below). DiagCORE Respiratory Panel 2 Instructions for Use 43
10 Limitations of the procedure Results from the DiagCORE Respiratory Panel 2 are not intended to be used as the sole basis for the diagnosis, treatment, or other patient management decisions. Positive results do not rule out co-infection with organisms not included in the DiagCORE Respiratory Panel 2. The agent detected may not be the definitive cause of the disease. Negative results do not preclude infection of the upper respiratory tract. Not all agents of acute respiratory infection are detected by this assay, and sensitivity in some clinical settings may differ from that described in the package insert. A negative result with the DiagCORE Respiratory Panel 2 does not exclude the infectious nature of the syndrome. Negative assay results may originate from several factors and their combinations, including sample handling mistakes, variation in the nucleic acid sequences targeted by the assay, infection by organisms not included in the assay, organism levels of included organisms that are below the limit of detection for the assay, and use of certain medications, therapies, or agents. The DiagCORE Respiratory Panel 2 is not intended for testing of samples other than those described in these instructions for use. Test performance characteristics have been established only with nasopharyngeal swab samples collected in transport medium, from individuals with acute respiratory symptoms. The DiagCORE Respiratory Panel 2 is intended to be used in conjunction with standard of care culture for organism recovery, serotyping, and/or antimicrobial susceptibility testing where applicable. The results from the DiagCORE Respiratory Panel 2 must be interpreted by a trained healthcare professional within the context of all relevant clinical, laboratory, and epidemiological findings. The DiagCORE Respiratory Panel 2 can be used only with the DiagCORE Analyzer. The DiagCORE Respiratory Panel 2 is a qualitative assay and does not provide a quantitative value for detected organisms. Viral and bacterial nucleic acids may persist in vivo, even if the organism is not viable or infectious. Detection of a target marker does not imply that the corresponding organism is the causative agent of the infection or the clinical symptoms. Detection of viral and material nucleic acids depends on proper sample collection, handling, transportation, storage, and loading into the DiagCORE Respiratory Panel 2 Cartridge. Improper operations for any of the aforementioned can cause incorrect results, including falsepositive or false-negative results. 44 DiagCORE Respiratory Panel 2 Instructions for Use
The assay sensitivity and specificity, for the specific organisms and for all organisms combined, are intrinsic performance parameters of a given assay and do not vary depending on prevalence. In contrast, both the negative and positive predictive values of a test result are dependent on the disease/organism prevalence. Please note that a higher prevalence favors the positive predictive value of a test results, while a lower prevalence favors the negative predictive value of a test result. DiagCORE Respiratory Panel 2 Instructions for Use 45
11 Performance characteristics. Clinical Performance The performance characteristics of the DiagCORE Respiratory Panel 2 assay were assessed in a multicenter clinical trial. Both the performance of the universal transport medium of nasopharyngeal swab specimen ( UTM ), and of a dry nasopharyngeal swab specimen (FLOQSwabs, Copan ref 503CS01) ( SWAB ) were assessed. In the latter case, a swab is directly entered in the DiagCORE cartridge after collection avoiding the transfer into a liquid medium. This testing approach may greatly support safe and error-free sample managment, especially at the point of care settting. The study was designed as observational, prospective-retrospective, using left-over samples obtained from subjects with signs and symptoms of an acute respiratory infection. Participating sites were asked to test fresh and/or frozen clinical samples, according to a protocol and site/specific instructions. Three (3) hospital laboratories, located in Copenhagen (Denmark), Bonn, (Germany) and Paris, (France) participated in the study. Samples tested by the DiagCORE Respiratory Panel 2 were compared with the results of the standard of care (SOC) method(s) at the sites, as wells as with a range of validated and commercially available molecular methods. This approach provided results for pathogens not detected by SOC and/or allowed for final discrepancy resolution of discordant results. As such the DiagCORE Respiratory Panel 2 assay results were compared against Filmarray Respiratory Panel 1.7 & 2 and the Allplex Respiratory Panel assay. A total of 578 clinical UTM patient samples were enrolled into the study. One (1) sample was excluded from the analysis due to the sample being misplaced between DiagCORE and comparator testing. Seven (7) of 577 samples failed initial testing, resulting in a first testing success rate of 98.8%. The failure rate includes the failure rate of the internal control, which was 0.17% (1/577). Two (2) samples could not be retested due to insufficient remaining specimen volume. The sample that showed an initial internal control failure was successful upon retesting. Fifteen (15) pathogen results could not be resolved because there was no SOC result (10 results) or no resolution method result available (5 results). This resulted in the loss of 2 samples, the remaining unresolvable results were in samples with multiple pathogens detected (coinfection samples). Clinical sensitivity or Positive Percent Agreement (PPA) was calculated as 100% x (TP / TP + FN). True positive (TP) indicates that both the DiagCORE Respiratory Panel 2 and comparator(s) methods had a positive result for the organism, and false negative (FN) indicates that the DiagCORE Respiratory Panel 2 result was negative while the comparator resolution methods results were positive. Specificity or Negative Percent Agreement (NPA) was calculated as 100% x (TN / TN + FP). True negative (TN) indicates that both the DiagCORE Respiratory Panel 2 and the comparator method had negative results, and a false positive (FP) indicates that the DiagCORE Respiratory Panel 2 result was positive but the comparator methods results were negative. For the calculation of the clincial specificity of the individual pathogens the total available results were used, with the 46 DiagCORE Respiratory Panel 2 Instructions for Use