supplemental protocols for laboratory verification of ... … · performance specifications of...

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Technical Note BioFire Diagnostics, LLC www.biofiredx.com BFR0000-8659-01

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Supplemental Protocols for Laboratory Verification of Performance of the BioFire®

Respiratory Panel 2.1 (RP2.1)

Purpose

The Clinical Laboratory Improvement Amendments (CLIA), passed in 1988, establishes quality standards for all laboratory testing to ensure the accuracy and reliability of patient test results, regardless of where the test is performed. The CLIA regulations include a requirement for verifying the performance specifications of unmodified, moderate complexity tests cleared or approved by the FDA.

Verification of an FDA Emergency Use Authorized (EUA) Test Laboratories using an unmodified Emergency Use Authorization (EUA) diagnostic test must verify the test method performance specifications as applicable for their own laboratory prior to beginning patient testing. The laboratory may use information published in the manufacturer’s package insert and other published literature for some aspects of the study (eg, interferences). While the ultimate objective is to fully verify the method performance of the assay, the pandemic crisis, the urgent need for patient testing, and the possible lack of reagents and supplies make it difficult to fully evaluate the accuracy, precision, and reportable range, as stated in COM.40300. A more limited approach may be acceptable. Each laboratory, in coordination with the laboratory director, should determine the depth of verification needed to begin testing and the laboratory director (or qualified alternate designee) must approve the verification study prior to testing (COM.40475). Applicable checklist requirements include: COM.40300, COM.40475, and COM.40500.

For Analytic Interferences (COM.40500) please refer to the BioFire® Respiratory Panel 2.1 (RP2.1) Instructions for Use for a list of interfering

substances.

Note: EUA guidelines are frequently revised. Confirm that current regulatory guidelines are being followed prior to establishing performance verification for the BioFire RP2.1.

This document is intended to be used in conjunction with the document Protocols for Laboratory Verification of Performance of the BioFire® FilmArray® Respiratory Panel 2 (RP2) (FLM1-PRT-0232) and provides

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examples of verification procedures to assist your laboratory in developing a protocol for the verification of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) for the BioFire RP2.1 performance on BioFire® FilmArray® Systems as required by CLIA. Verification schemes, compatible with the BioFire RP2.1, have been designed using nonclinical specimens. This scheme provides positive and negative tests for SARS-CoV-2 detected by the BioFire RP2.1 and may be easily modified or expanded to meet specific criteria. Day-to-day variation is evaluated by testing each sample on two separate days. To evaluate user-to-user variation, multiple laboratory technicians may test the same sample. In addition, testing patient samples for verification of the performance of the BioFire RP2.1 should be done under the guidance of the Laboratory Director, but is not described here. As per the CLIA regulation, the Laboratory Director is ultimately responsible for ensuring that verification procedures meet the appropriate standards for CLIA and applicable laboratory accrediting agencies.

Intended Use

The BioFire RP2.1 is a multiplexed nucleic acid test intended for the simultaneous qualitative detection and differentiation of nucleic acids from multiple viral and bacterial respiratory organisms, including nucleic acids from Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), in nasopharyngeal swabs (NPS) obtained from individuals suspected of COVID-19 by their healthcare provider. Testing is limited to laboratories certified under the Clinical Laboratory Improvement Amendments of 1988 (CLIA), 42 U.S.C. §263a, to perform high complexity or moderate complexity tests. The BioFire RP2.1 is intended for the detection and differentiation of nucleic acid from SARS-CoV-2 and the following organism types and subtypes identified using the BioFire RP2.1.

Viruses Bacteria

Adenovirus Bordetella parapertussis

Coronavirus 229E Bordetella pertussis

Coronavirus HKU1 Chlamydia pneumoniae

Coronavirus NL63 Mycoplasma pneumoniae

Coronavirus OC43

Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2)

Human Metapneumovirus

Human Rhinovirus/Enterovirus

Influenza A, including subtypes

H1, H3, and H1-2009

Influenza B

Parainfluenza Virus 1




Respiratory Syncytial Virus

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The complete intended use statement and additional information about the use of the BioFire System can be found in the BioFire® Respiratory Panel 2.1 Instructions for Use.

Performance Verification of SARS-CoV-2 for Labs That Have Established Verification of Performance for the BioFire®

FilmArray® Respiratory Panel 2 (RP2)

The BioFire RP2.1 is an expansion of the BioFire RP2 and includes the addition of assays targeting the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19. For laboratories that have previously established performance verification for the BioFire RP2, the protocol(s) below describe an efficient procedure for establishing performance verification for SARS-CoV-2 using non-clinical specimens.

This verification when used in conjunction with the results from the Performance Verification of the BioFire RP2 will allow reporting of all analytes on the panel.

Performance Verification of SARS-CoV-2 for Labs That Have NOT Established Verification of Performance for BioFire RP2

Laboratories that have not established performance verification for the BioFire RP2 will be able to report only the SARS-CoV-2 detections reported by the BioFire RP2.1 after completion of a performance verification using guidelines described here.

All other analytes must have established performance verification prior to reporting. Guidance for establishing performance verification for the other analytes on the BioFire RP2.1 is provided in Protocols for Laboratory Verification of Performance of the BioFire® FilmArray® Respiratory Panel 2 (RP2) (FLM1-PRT-0232).

Performance Verification: Overview

Two different examples of performance verification procedures are described: (1) a Simple Protocol for the verification of SARS-CoV-2 performance on the BioFire RP2.1 and (2) a Transport Media Protocol that evaluates SARS-CoV-2 performance on the BioFire RP2.1 in a transport media sample matrix. These protocols are examples of procedures to assist your laboratory in developing a protocol for the verification of SARS-CoV-2 performance on the BioFire RP2.1 on BioFire® FilmArray® 2.0 and BioFire® FilmArray® Torch Systems. The verification procedures described here may be used to evaluate the performance of the SARS-CoV-2 assays on the BioFire RP2.1. The

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procedures were developed using NATtrol™ SARS-Related Coronavirus 2 (SARS-CoV-2) External Run Control and the NATtrol™ SARS-Related Coronavirus 2 (SARS-CoV-2) Negative Control available from ZeptoMetrix™ Corporation, Buffalo, NY (part numbers NATSARS(COV2)-ERC and NATSARS(COV2)-NEG).

Note: If ZeptoMetrix NATtrol™ SARS-COV-2 control materials are unavailable, or if the laboratory director chooses to use alternate control materials, please use guidance provided in the Appendix.

A BioFire System is defined as all BioFire Instrument modules that are connected to and controlled by a single computer system. If the laboratory director chooses not to perform the verification protocol on each individual module, it is advised that test replicates are evenly distributed among the modules. An example of a performance verification workflow using 2, or 4 modules is provided in Figure 2. Clinical/patient samples may be used in place of, or in addition to the verification schemes described here in order to assess clinical sensitivity/specificity and sample matrix effects as part of the performance verification of SARS-CoV-2 on the BioFire RP2.1. Table 1. Overview of Verification Protocol

Verification Protocol

Organisms per Pool

Number of

Sample Pools

Replicates per Sample

Pool

Pouches Required

Expected Positive Results

Expected Negative Results

Approximate Days of Testing

Example 1: Simple

Protocol 1 4 4 8

4 per organism

4 per organism

2

Example 2: Transport

Media Protocol

1 4 4 8 4 per

organism 4 per

organism 2

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Performance Verification: Materials

The following materials may be used to perform the verification procedure:

Table 2. Recommended materials for the verification protocols

Material EUA Part Number IVD Part Number

BioFire® Respiratory Panel 2.1 (RP2.1) Kit (30 tests)

BioFire Diagnostics, LLC 423738


BioFire® Respiratory Panel 2.1 (RP2.1) Instructions for Use

BioFire Diagnostics, LLC BFR0000-8303


BioFire® Respiratory Panel 2.1 (RP2.1) Quick Guide



Control Organisma

Positive Control: NATtrol™ SARS-Related Coronavirus 2 (SARS-CoV-2) External Run Control, ZeptoMetrix NATSARS(COV2)-ERC

Negative Control: NATtrol™ SARS-Related Coronavirus 2 (SARS-CoV-2) Negative Control, ZeptoMetrix NATSARS(COV2)-NEG

Transport Media (e.g. Remel M4 Viral Transport Media)

Various media are appropriate

2 mL or 5 mL Sample Tubes

Various manufacturers

Disposable Transfer pipets, graduated

VWR, 414004-024 (or equivalent)

aAny appropriate source of organism may be used for verification of any or all of the assays in the BioFire RP2.1. However, when alternate organism sources are used (i.e. not the ZeptoMetrix NATSARS(COV2)-ERC and NATSARS(COV2)-NEG material), the sample volumes or pooling

schemes suggested in the examples below may need to be adjusted. Please refer to the appendix for further guidance.

Performance Verification: Protocols

A simple protocol and a transport media protocol are described below. Each protocol and workflow scheme (Figures 1 and 2) illustrates testing 4 positive replicates and 4 negative replicates over 2 days. This produces a total of 8 verification sample test runs and provides 4 positive results and 4 negative results for the SARS-CoV-2 analyte. The number of samples tested per day should be determined by the individual laboratory. This testing scheme can be modified to run more samples per day based on the number of modules in the BioFire System.

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Simple Protocol The Simple Protocol evaluates the BioFire RP2.1 SARS-CoV-2 performance when the verification materials (ZeptoMetrix NATtrol™ SARS-CoV-2 External Run Control and NATtrol™ SARS-CoV-2 Negative Control) are tested in the absence of clinical matrix. The proposed organism pooling scheme (Table 3) should be followed to obtain the expected number of positive and negative results for the SARS-CoV-2 assay in a time and resource-efficient manner.

Note: Dilution of ZeptoMetrix Verification material beyond levels proposed in these guidelines may lead to inconsistent results and is not recommended.

Table 3. Proposed Organism Pooling Scheme for Simple Protocol

Verification Material Approximate

Organism Volume Approximate Pool

Volume

Positive Control

SARS-C0V-2 External Run Control 1.5 mL 1.5 mL

Negative Control

SARS-CoV-2 Negative Control 1.5 mL 1.5 mL

Day 1………………………………………………………………………………

1. Organize materials needed (Table 2).

2. Prepare the positive control sample from the ZeptoMetrix NATtrol™

SARS-CoV-2 External Run Control material. Organism vials should be well mixed prior to preparing each pool. Refer to Table 3 for details.

a. Use a transfer pipette (or other suitable pipette) to remove the entire contents of the SARS-CoV-2 External Run Control vial (approximately 0.5 mL) and transfer to a sterile 2 mL tube.

b. Repeat step 2a with an additional two SARS-CoV-2 External Run Control vials so that the final volume is approximately 1.5 mL (Table 3).

c. Ensure the pooled sample is well mixed prior to removing a sample for testing.

3. Prepare the Negative control sample from the SARS-CoV-2 Negative Control material by repeating Step 2 above.

4. Test 2 replicates from each control pool (i.e. positive and negative). The replicate samples should be tested in a single day by different users.

Note: For each sample, follow instructions in the BioFire® Respiratory Panel 2.1 (RP2.1) Instructions for Use and the BioFire® Respiratory Panel 2.1 (RP2.1) Quick Guide for pouch preparation, pouch hydration, sample loading, and sample testing.

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5. Refrigerate samples (2–8°C) for up to 3 days for the evaluation of day-to-day variation.

Day 2………………………………………………………………………………

To evaluate day-to-day variation, test replicates from the positive and negative pools prepared on Day 1 by repeating Step 4 above.

Note: A SARS-CoV-2 Supplemental Verification Record for the BioFire RP2.1 is provided and may serve as a template for recording your results. Figure 1. Workflow for the Simplified or the Transport Media Protocols

Figure 2. Example of a Verification workflow for use with multiple BioFire Modules

2 modules Module 1 Module 2

Day 1 Positive/ User 1

Negative/ User 2

Positive/ User 2

Negative/ User 1


Negative/ User 1

Positive/ User 1

Negative/ User 2

4 modules Module 1 Module 2 Module 3 Module 4


Positive/ User 2

Negative/ User 1

Negative/ User 2

Day 2 Negative/ User 2

Negative/ User 1

Positive/ User 2

Positive/ User 1

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Transport Media Protocol The Transport Media Protocol evaluates the BioFire RP2.1 SARS-CoV-2 performance when verification material (ZeptoMetrix NATtrol™ SARS-CoV-2 External Run Control and NATtrol™ SARS-CoV-2 Negative Control) are tested in a transport media sample matrix. Sample material is added to an equal volume of Transport Media. The proposed organism pooling scheme (Table 4) should be followed to obtain the expected number of positive and negative results for the SARS-CoV-2 assay in a time and resource-efficient manner.

Note: Dilution of ZeptoMetrix Verification material beyond levels proposed in these guidelines may lead to inconsistent results and is not recommended.

Table 4. Proposed Organism Pooling Scheme for the Transport Media Protocol


Organism Volume

Volume Transport

Media

Approximate Pool Volume

Positive Control

SARS-C0V-2 External Run Control

1.0 mL 1.0 mL 2.0 mL

Negative Control

SARS-CoV-2 Negative Control 1.0 mL 1.0 mL 2.0 mL

Day 1………………………………………………………………………………

1. Organize materials needed (Table 2). 2. Transfer 1.0 mL of transport media (as described in Table 4) into a

sterile 2 mL tube.

3. Prepare the positive control sample from ZeptoMetrix NATtrol™ SARS-CoV-2 External Run Control material. Organism vials should be well mixed prior to preparing each pool. Refer to Table 4 for details.

a. Use a transfer pipette (or other suitable pipette) to remove

the entire contents of the SARS-CoV-2 External Run Control vial (approximately 0.5 mL) and transfer to the tube containing transport media.

b. Repeat step 3a with a second SARS-CoV-2 External Run Control vial so that the total volume is approximately 2.0 mL (Table 4).

c. Ensure the pooled sample is well mixed prior to removing a sample for testing.

4. Prepare the Negative control sample from the SARS-CoV-2

Negative Control material by repeating Step 2-3.

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5. Test 2 replicates from each control pool (i.e. positive and negative). The replicate samples should be tested in a single day by different users.


6. Refrigerate samples (2–8°C) for up to 3 days for the evaluation of

day-to-day variation.

Day 2………………………………………………………………………………

To evaluate day-to-day variation, test replicates from the control pools prepared on Day 1 by repeating Step 5 above.

Note: A SARS-CoV-2 Supplemental Verification Record for the BioFire RP2.1 is provided and may serve as a template for recording your results.

Expanding the protocols

The protocols described above can be expanded by increasing the number of tests from each of the control pools. Each pool contains sufficient volume for testing additional replicates.

Verification of Loaner, Repaired, and Permanent Replacement Instruments

If it becomes necessary to verify the performance of a loaner, repaired, or permanent replacement instrument, the following protocol may serve as a guideline but should be verified by the Laboratory Director. 1. Select a few specimens and/or proficiency samples (any combination

of positives and negatives) previously tested on the BioFire RP2.1. The Laboratory Director should determine the appropriate number of samples to test. Proficiency samples should not be pooled or diluted.

2. Select a set of controls that verify detection of all targets on the BioFire RP2.1.

3. Test the selected samples on the loaner, repaired, or permanent replacement instrument and document the results.

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Supplemental Verification Record for the BioFire RP2.1

Module Serial # Module Serial #

Module Serial # Module Serial #

Lot #

1-A

1-B

1-C

1-D

2-A

2-B

2-C

2-D

# P

osit

ives

# N

eg

ati

ves

# U

sers

# D

ays

# M

od

ule

s

Pati

en

t

Sam

ple

s?

PositiveSevere Acute Respiratory Syndrome

Coronavirus 2 (SARS-CoV-2)

Negative Negative

Signature Date

Reviewed by:

Kit Part #

SummaryReplicate Testing

Organism and Resistance Genes

SARS-CoV-2 Supplemental Verification Record for the

BioFire® Respiratory Panel 2.1 (RP2.1)

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Technical Support Contact Information

BioFire is dedicated to providing the best customer support available. If you have any questions or concerns about this process, please contact the BioFire Technical Support team for assistance. BioFire Technical Support Email: [email protected] Phone: +1-801-736-6354, select Option 5

mailto:[email protected]

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Appendix

Performance Verification Guidance When Using Alternate Control Materials If ZeptoMetrix NATtrol™ SARS-Related Coronavirus 2 (SARS-CoV-2) External Run Control material is unavailable, or if the laboratory director chooses to use alternate control materials, the protocols below may serve as examples of procedures to assist your laboratory in developing a protocol for the verification of SARS-CoV-2 performance on the BioFire RP2.1 on BioFire 2.0 and BioFire Torch Systems. This document is intended to be used in conjunction with the document: Protocols for Laboratory Verification of Performance of the BioFire® FilmArray® Respiratory Panel 2 (RP2) (FLM1-PRT-0232) and provides

examples of verification procedures to assist your laboratory in developing protocols for the verification of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) for the BioFire Respiratory Panel 2.1 (RP2.1) performance on BioFire Systems as required by CLIA. The BioFire RP2.1 is an expansion of the BioFire RP2 and includes the addition of assays targeting the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19. The verification procedures described here may be used to evaluate the performance of the SARS-CoV-2 assays on the BioFire RP2.1. The procedures were developed using control materials described in Table 5. Two different examples of performance verification procedures are described: (1) a Simple Protocol for the verification of SARS-CoV-2 performance on the BioFire RP2.1 and (2) a transport media Protocol that evaluates SARS-CoV-2 performance on the BioFire RP2.1 in a transport media sample matrix. A BioFire System is defined as all BioFire Instrument modules that are connected to and controlled by a single computer system. If the laboratory director chooses not to perform the verification protocol on each individual module, it is advised that test replicates are evenly distributed among the modules. An example of a performance verification workflow using 2, or 4 modules is provided in Figure 3. Clinical/patient samples may be used in place of, or in addition to the verification schemes described here in order to assess clinical sensitivity/specificity and sample matrix effects as part of the performance verification of SARS-CoV-2 on the BioFire RP2.1.

Note: Refer to pages 1-4 of this document for complete information on Purpose, Intended Use, and Performance Verification.

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Performance Verification Using Alternate Control Materials A simple protocol and a transport media protocol are described below. Each protocol and workflow scheme (Figures 3 and 4) illustrates testing 4 positive replicates and 4 negative replicates over 2 days. This produces a total of 8 verification sample test runs and provides 4 positive results and 4 negative results for the SARS-CoV-2 analyte.

The following materials may be used to perform the verification procedure using alternate control materials:

Table 5. Recommended materials for the verification protocols using alternate control materials:

Material EUA Part Number IVD Part Number

BioFire® Respiratory Panel 2.1 (RP2.1) Kit (30 tests)



BioFire® Respiratory Panel 2.1 (RP2.1) Instructions for Use



BioFire® Respiratory Panel 2.1 (RP2.1) Quick Guide



Control Organism*

Heat inactivated SARS-CoV-2, ATCC® VR-1986HK™ (1:10,000)

Genomic RNA from Severe acute respiratory syndrome-related coronavirus 2, ATCC® VR-1986D (1:1000)

Genomic RNA from SARS-Related Coronavirus 2, Isolate USA-WA1/2020, BEI NR-52285 (1:10,000)

Heat inactivated, SARS-Related Coronavirus 2, USA-WA1/20, ZeptoMetrix 0810587CFHI-0.5mL (1:10,000)

Transport Media (e.g. Remel M4 Viral Transport Media)


Sample Tubes; 2 mL, 5 mL, or 50 mL may be needed


Disposable Transfer pipets, graduated

VWR, 414004-024 (or equivalent)

* Dilution of the control organism may be needed

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Simple Protocol Using Alternate Control Materials The Simple Protocol evaluates the BioFire RP2.1 SARS-CoV-2 performance when verification material (see Table 5) is tested in the absence of clinical matrix. The proposed organism pooling scheme (Table 6) should be followed to obtain the expected number of positive and negative results for the SARS-CoV-2 assay in a time and resource-efficient manner.

Table 6. Proposed Organism Pooling Scheme for Simple Protocol Using Alternate Control Materials


Organism Volume Approximate Pool

Volume

Positive Control

Dilute Control material 1.5 mL 1.5 mL

Negative Control

Transport Media 1.5 mL 1.5 mL

Day 1………………………………………………………………………………

1. Organize materials needed (Table 5). 2. Materials listed in Table 5 are at a high concentration and should be

diluted prior to preparing a positive control pool. A 1:1000 or 1:10,000 dilution (Table 5) should provide robust detections and may reduce the risk of environmental contamination. Consult the organism vendor for instructions on handling and diluting of control materials listed in Table 5.

3. Transport media, or a suitable alternative, may be used as a negative control material.

4. Test 2 replicates from each control pool (i.e. positive and negative). The replicate samples should be tested in a single day by different users. Ensure that the sample is well mixed prior to testing.

5. Table 6 illustrates the approximate volume of material needed for 4 positive and 4 negative tests on the BioFire RP2.1.


Day 2………………………………………………………………………………

To evaluate day-to-day variation, test replicates from the sample pools prepared on Day 1 by repeating Step 4 above.

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Note: A SARS-CoV-2 Supplemental Verification Record for the BioFire RP2.1 is provided and may serve as a template for recording your results. Figure 3. Workflow for the Simplified or the Transport Media Protocols

Figure 4. Example of a Verification workflow for use with multiple BioFire Modules

2 modules Module 1 Module 2


Negative/ User 2

Positive/ User 2

Negative/ User 1


Negative/ User 1

Positive/ User 1

Negative/ User 2

4 modules Module 1 Module 2 Module 3 Module 4


Positive/ User 2

Negative/ User 1

Negative/ User 2

Day 2 Negative/ User 2

Negative/ User 1

Positive/ User 2

Positive/ User 1

Transport Media Protocol Using Alternate Control Materials The Transport Media Protocol evaluates the BioFire RP2.1 SARS-CoV-2 performance when verification material (see Table 5) is tested in a transport

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media sample matrix. Dilute control material is added to an equal volume of Transport Media matrix. The proposed organism pooling scheme (Table 7) should be followed to obtain the expected number of positive and negative results for the SARS-CoV-2 assay in a time and resource-efficient manner.

Table 7. Proposed Organism Pooling Scheme for the Transport Media Protocol Using Alternate Control Materials


Organism Volume

Volume Transport

Media

Approximate Pool Volume

Positive Control

Dilute Control Material 1.0 mL 1.0 mL 2.0 mL

Negative Control

Transport media 1.0 mL 1.0 mL 2.0 mL

Day 1………………………………………………………………………………

1. Organize materials needed (Table 5). Refer to Table 7 for volumes for each pool.

2. Materials listed in Table 5 are at a high concentration and should be

diluted prior to preparing a positive control pool. A 1:000 or 1:10,000 dilution (Table 5) should provide robust detections and may reduce the risk of environmental contamination. Consult the organism vendor for instructions on handling and diluting of control materials listed in Table 5.

3. Transfer 1.0 mL of transport media into a sterile 2 mL tube (as described in Table 7).

4. Add 1.0 mL of dilute positive control material from Step 2 into the tube, for a total volume of approximately 2 mL.

6. Transport media, or a suitable alternative, may be used as a negative

control material.

7. Test 2 replicates from each control pool (i.e. positive and negative). The replicate samples should be tested in a single day by different users. Ensure that the sample is well mixed prior to testing.


Day 2………………………………………………………………………………

To evaluate day-to-day variation, test replicates from the control pools prepared on Day 1 by repeating Step 5 above.

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Note: A SARS-CoV-2 Supplemental Verification Record for the BioFire RP2.1 is provided and may serve as a template for recording your results.

Expanding the protocols

The protocols described above can be expanded by increasing the number of tests from each of the control pools. Each pool contains sufficient volume for testing additional replicates.

Verification of Loaner, Repaired, and Permanent Replacement Instruments

If it becomes necessary to verify the performance of a loaner, repaired, or permanent replacement instrument, the following protocol may serve as a guideline but should be verified by the Laboratory Director. 4. Select a few specimens and/or proficiency samples (any combination

of positives and negatives) previously tested on the BioFire RP2.1. The Laboratory Director should determine the appropriate number of samples to test. Proficiency samples should not be pooled or diluted.

5. Select a set of controls that verify detection of all targets on the BioFire RP2.1.

6. Test the selected samples on the loaner, repaired, or permanent replacement instrument and document the results.

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