XPERT FLU, GENEXPERT DX SYSTEMS, GENEXPERT INFINITY SYSTEM, GENEXPERT SYSTEM SOFTWARE VERISIONS 2.1 AND 4.0

• K Number: K103766
• Device Name: XPERT FLU, GENEXPERT DX SYSTEMS, GENEXPERT INFINITY SYSTEM, GENEXPERT SYSTEM SOFTWARE VERISIONS 2.1 AND 4.0
• Manufacturer: CEPHEID
• Date Cleared: 2011-04-21 ( 119 days)
• Product Code: OQW OCC OOI
• Regulation Number: 866.3332

Intended Use

The Cepheid® Xpert Flu Assay is an automated, multiplex real-time RT-PCR assay intended for the in vitro qualitative detection and differentiation of influenza B and 2009 H1N1 influenza viral RNA. The Xpert Flu Assay uses nasal aspirates/washes and nasopharyngeal swab specimens collected from patients with signs and symptoms of respiratory infection in conjunction with clinical and epidemiological risk factors. The Xpert Flu Assay is intended as an aid in the diagnosis of influenza. Negative results do not preclude influenza virus infection and should not be used as the sole basis for treatment or other patient management decisions. Performance characteristics for influenza A were established during the 2009-2010 influenza season when 2009 H1N1 influenza was the predominant influenza A virus in circulation. When other influenza A viruses are emerging, performance characteristics may vary. If infection with a novel influenza A virus is suspected based on current clinical and epidemiological screening criteria recommended by public health authorities, specimens should be collected with appropriate infection control precautions for novel virulent influenza viruses and sent to state or local health department for testing. Viral culture should not be attempted in these cases unless a BSL 3+ facility is available to receive and culture specimens.

Device Description

The Xpert Flu Assay is a rapid, automated in vitro diagnostic test for qualitative detection and differentiation of influenza A, influenza B and influenza A, subtype 2009 HINI. The assay is performed on the Cepheid GeneXpert Instrument Systems. The GeneXpert Instrument Systems automate and integrate sample purification, nucleic acid amplification, and detection of the target sequence in simple or complex samples using real-time PCR and RT-PCR assays. The systems require the use of single-use disposable cartridges that hold the PCR reagents and host the PCR process. Because the cartridges are self-contained and specimens never come into contact with working parts of the instrument modules, cross-contamination between samples is eliminated. The Xpert Flu Assay includes reagents for the detection and differentiation of influenza A, influenza B and influenza A, subtype 2009 H1N1 directly from nasal aspirates/washes (NA/W) and nasopharyngeal (NP) swab specimens from patients with signs and symptoms of respiratory infection. A Sample Processing Control (SPC) and a Probe Check Control (PCC) are also included. The SPC is present to control for adequate processing of the target viruses and to monitor the presence of inhibitors in the PCR reaction. The Probe Check Control (PCC) verifies reagent rehydration, PCR tube filling in the cartridge, probe integrity and dye stability. The liquid specimen (NA/W) or swab specimen (NP) is collected according to the institution's standard procedures and placed into Universal Transport Medium (3mL UTM tubes). Following a brief mixing by inverting the UTM tube five times, the eluted material and one single-use reagent (Reagent 1), that is provided with the assay, are transferred to different, uniquely-labeled chambers of the disposable fluidic cartridge (the Xpert Flu cartridge). The user initiates a test from the system user interface and places the cartridge into the GeneXpert instrument platform, which performs hands-off reverse transcription and real-time, multiplex polymerase chain reaction (PCR) for detection of DNA. In this platform, additional sample preparation, amplification, and real-time detection are all fully-automated and completely integrated. The single-use, multi-chambered fluidic cartridges are designed to complete sample preparation and real-time RT-PCR for detection and differentiation of influenza A, influenza B and influenza A, subtype 2009 H1N1 in 75 minutes. The GeneXpert Instrument Systems have 1 to 48 randomly accessible modules that are each capable of performing separate sample preparation and real-time PCR tests. Each module contains a syringe drive for dispensing fluids (i.e., the syringe drive activates the plunger that works in concert with the rotary valve in the cartridge to move fluids between chambers), an ultrasonic horn for lysing cells or spores, and a proprietary I-CORE® thermocycler for performing real-time PCR and detection.

Predicate Devices

K073029, K100148

Reference Devices

K073029, K100148

AI/ML (Artificial Intelligence / Machine Learning)

No
The description focuses on automated sample preparation, real-time PCR, and detection of specific nucleic acid sequences. There is no mention of AI or ML algorithms being used for analysis or interpretation.

Therapeutic

No
The device is an in vitro diagnostic test intended for the qualitative detection and differentiation of influenza A and B viral RNA. It is used as an aid in diagnosis, not for treatment or therapy.

Diagnostic

Yes

The device's "Intended Use / Indications for Use" states that the Xpert Flu Assay "is intended as an aid in the diagnosis of influenza."

SaMD (Software as a Medical Device)

No

The device description clearly outlines hardware components including the Cepheid GeneXpert Instrument Systems, single-use disposable cartridges, syringe drives, ultrasonic horns, and thermocyclers, in addition to the software that controls these components and processes the data.

IVD (In Vitro Diagnostic)

Yes, this device is an IVD (In Vitro Diagnostic).

Here's why:

• Intended Use: The "Intended Use / Indications for Use" section explicitly states that the assay is "intended for the in vitro qualitative detection and differentiation of influenza B and 2009 H1N1 influenza viral RNA." The term "in vitro" is a key indicator of an IVD, meaning it is used to test samples outside of the living body.
• Device Description: The "Device Description" also refers to the device as a "rapid, automated in vitro diagnostic test".
• Purpose: The assay is used to analyze biological specimens (nasal aspirates/washes and nasopharyngeal swabs) to provide information that aids in the diagnosis of influenza. This is the fundamental purpose of an IVD.

PCCP (Predetermined Change Control Plan) Authorized

N/A

Overview

Intended Use / Indications for Use

The Cepheid® Xpert Flu Assay is an automated, multiplex real-time RT-PCR assay intended for the in vitro qualitative detection and differentiation of influenza B and 2009 H1N1 influenza viral RNA. The Xpert Flu Assay uses nasal aspirates/washes and nasopharyngeal swab specimens collected from patients with signs and symptoms of respiratory infection in conjunction with clinical and epidemiological risk factors. The Xpert Flu Assay is intended as an aid in the diagnosis of influenza.

Negative results do not preclude influenza virus infection and should not be used as the sole basis for treatment or other patient management decisions.

Performance characteristics for influenza A were established during the 2009-2010 influenza season when 2009 H1N1 influenza was the predominant influenza A virus in circulation. When other influenza A viruses are emerging, performance characteristics may vary.

If infection with a novel influenza A virus is suspected based on current clinical and epidemiological screening criteria recommended by public health authorities, specimens should be collected with appropriate infection control precautions for novel virulent influenza viruses and sent to state or local health department for testing. Viral culture should not be attempted in these cases unless a BSL 3+ facility is available to receive and culture specimens.

Product codes

OQW, OCC, OOI

Device Description

The Xpert Flu Assay is a rapid, automated in vitro diagnostic test for qualitative detection and differentiation of influenza A, influenza B and influenza A, subtype 2009 HINI. The assay is performed on the Cepheid GeneXpert Instrument Systems. The GeneXpert Instrument Systems automate and integrate sample purification, nucleic acid amplification, and detection of the target sequence in simple or complex samples using real-time PCR and RT-PCR assays. The systems require the use of single-use disposable cartridges that hold the PCR reagents and host the PCR process. Because the cartridges are self-contained and specimens never come into contact with working parts of the instrument modules, cross-contamination between samples is eliminated.

The Xpert Flu Assay includes reagents for the detection and differentiation of influenza A, influenza B and influenza A, subtype 2009 H1N1 directly from nasal aspirates/washes (NA/W) and nasopharyngeal (NP) swab specimens from patients with signs and symptoms of respiratory infection. A Sample Processing Control (SPC) and a Probe Check Control (PCC) are also included. The SPC is present to control for adequate processing of the target viruses and to monitor the presence of inhibitors in the PCR reaction. The Probe Check Control (PCC) verifies reagent rehydration, PCR tube filling in the cartridge, probe integrity and dye stability.

The liquid specimen (NA/W) or swab specimen (NP) is collected according to the institution's standard procedures and placed into Universal Transport Medium (3mL UTM tubes). Following a brief mixing by inverting the UTM tube five times, the eluted material and one single-use reagent (Reagent 1), that is provided with the assay, are transferred to different, uniquely-labeled chambers of the disposable fluidic cartridge (the Xpert Flu cartridge). The user initiates a test from the system user interface and places the cartridge into the GeneXpert instrument platform, which performs hands-off reverse transcription and real-time, multiplex polymerase chain reaction (PCR) for detection of DNA. In this platform, additional sample preparation, amplification, and real-time detection are all fully-automated and completely integrated.

The single-use, multi-chambered fluidic cartridges are designed to complete sample preparation and real-time RT-PCR for detection and differentiation of influenza A, influenza B and influenza A, subtype 2009 H1N1 in 75 minutes. The GeneXpert Instrument Systems have 1 to 48 randomly accessible modules that are each capable of performing separate sample preparation and real-time PCR tests. Each module contains a syringe drive for dispensing fluids (i.e., the syringe drive activates the plunger that works in concert with the rotary valve in the cartridge to move fluids between chambers), an ultrasonic horn for lysing cells or spores, and a proprietary I-CORE® thermocycler for performing real-time PCR and detection.

Mentions image processing

Not Found

Mentions AI, DNN, or ML

Not Found

Input Imaging Modality

Not Found

Anatomical Site

nasal aspirates/washes (NA/W), nasopharyngeal (NP) swab specimens

Indicated Patient Age Range

Not Found

Intended User / Care Setting

CLIA Moderate to High Complexity laboratory users.

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

Not Found

Summary of Performance Studies (study type, sample size, AUC, MRMC, standalone performance, key results)

Non-Clinical Studies:

• Analytical Sensitivity (Inclusivity): Evaluated 39 strains of influenza A (H1N1, H3N2, H5N2, H5N1, H7N3 subtypes), influenza A 2009 H1N1, and influenza B. Three replicates of each viral strain were tested at 5 - 500 TCID50/mL (or PFU/mL, pg/µL).
• Limit of Detection (LoD): Determined the analytical LoD for two seasonal influenza A (H1N1), two seasonal influenza A (H3N2), five influenza A 2009 H1N1, and two influenza B strains diluted into a surrogate nasopharyngeal matrix. Each strain was tested in replicates of 20 per concentration of virus. LoD defined as the lowest concentration reproducibly distinguished from negative samples with 95% confidence (19/20 or 20/20 positive replicates).
• Analytical Specificity (Exclusivity): Evaluated a panel of 40 cultures (18 viral, 21 bacterial, 1 yeast) representing common respiratory pathogens. Three replicates of bacterial and yeast strains were tested at ≥10^6 CFU/mL. Three replicates of each virus were tested at ≥10 TCID50/mL. Purified nucleic acids were tested for Cytomegalovirus, Bordetella pertussis, and Haemophilus influenzae. The analytical specificity was 100%.
• Interfering Substances: Evaluated potentially interfering substances (blood, mucin, nasal sprays, antibiotics, throat lozenges). Highly viscous samples with 1.5% and 2.5% (w/v) mucin yielded false negative results. 1% (w/v) mucin caused delayed detection of influenza A, influenza A subtype 2009 H1N1, and influenza B.
• Carry-Over Contamination Study: Demonstrated that single-use, self-contained GeneXpert cartridges prevent carry-over contamination. A negative sample was processed immediately after a very high positive sample (approx. 10^0 TCID50/test) for influenza A 2009 H1N1 or influenza B. This was repeated 20 times on 4 GeneXpert modules (total 88 runs: 40 positive, 48 negative). All 40 positive and 48 negative samples were correctly reported.
• Linearity: Evaluated the linear relationship between target input and assay output using two seasonal influenza A H1N1, two seasonal influenza A H3N2, two influenza A 2009 H1N1, and two influenza B strains diluted over four to five logs. Replicates of 4 were tested. The assay showed linearity over six logs for seasonal influenza A H1N1, seasonal influenza A H3N2, and influenza A 2009 H1N1, and over 5 logs for influenza B strains.
• Reproducibility: A panel of 10 specimens with varying concentrations of influenza A, influenza B, and influenza A subtype 2009 H1N1 were tested in duplicate on 10 different days at each of three sites (10 specimens x 2 times/day x 10 days x 3 sites = 60 runs per sample, 600 total). One lot of assay was used per site.
  • Overall total agreement: 97.0% (578/596)
• Instrument System Reproducibility: In-house study comparing GeneXpert Dx and Infinity instrument systems. 10 specimens with varying concentrations of influenza A, influenza B, and influenza A subtype 2009 H1N1 were tested in duplicate on 12 different days by two operators. Each operator conducted four runs of each panel specimen per day on each system (11 specimens x 2 times/day x 12 days x 2 operators x 2 instrument systems). One lot of assay was used.
  • Overall total agreement: 96.1% (1845/1919)

Clinical Performance Study:

• Study Type: Prospective and Archived Specimen evaluation.
• Study Site: Six institutions in the U.S. and Australia.
• Comparator: Viral culture followed by direct fluorescent assay (DFA). For archived specimens where viral culture was not performed, an FDA cleared molecular assay was used. Sequencing was performed for all influenza A positive specimens.
• Sample Size:
  • Prospective NA/W specimens: 342
  • Prospective NP swab specimens: 297
  • Archived NA/W specimens: 425
  • Archived NP swab specimens: 150 (viral culture/DFA comparator); 177 (FDA cleared molecular comparator)
• Key Results for Prospective Specimens:
  • NA/W:
    • Influenza A: Sensitivity 85.7% (95% CI: 42.1-99.6), Specificity 99.1% (95% CI: 97.4-99.8)
    • Influenza A, 2009 H1N1: Sensitivity 100% (95% CI: 39.8-100), Specificity 98.8% (95% CI: 97.0-99.7)
    • Influenza B: Sensitivity 100% (95% CI: 65.2-100), Specificity 99.4% (95% CI: 98.1-99.9)
  • NP Swab:
    • Influenza A: Sensitivity 100% (95% CI: 59.0-100), Specificity 98.3% (95% CI: 96.0-99.4)
    • Influenza A, 2009 H1N1: Sensitivity 100% (95% CI: 47.8-100), Specificity 99.0% (95% CI: 97.0-99.8)
    • Influenza B: Sensitivity 87.5% (95% CI: 47.3-99.7), Specificity 99.7% (95% CI: 98.1-100)
• Key Results for Archived Specimens:
  • NA/W (vs. FDA Cleared Molecular Comparator):
    • Influenza A: Positive Agreement 99.4% (95% CI: 96.6-100), Negative Agreement 100% (95% CI: 98.6-100)
    • Influenza A, 2009 H1N1: Positive Agreement 98.4% (95% CI: 94.4-99.8), Negative Agreement 99.7% (95% CI: 98.1-100)
    • Influenza B: Positive Agreement 100% (95% CI: 91.2-100), Negative Agreement 100% (95% CI: 99.0-100)
  • NP Swab (vs. Culture/DFA):
    • Influenza A: Positive Agreement 97.5% (95% CI: 92.7-99.5), Negative Agreement 100% (95% CI: 89.1-100)
    • 2009 H1N1: Positive Agreement 100% (95% CI: 95.7-100), Negative Agreement 100% (95% CI: 94.5-100)
    • Influenza B: Positive Agreement 93.8% (95% CI: 79.2-99.2), Negative Agreement 99.2% (95% CI: 95.4-100)
  • NP Swab (vs. FDA Cleared Molecular Comparator):
    • Influenza A: Positive Agreement 98.1% (95% CI: 89.7-100), Negative Agreement 99.2% (95% CI: 95.5-100)
    • 2009 H1N1: Positive Agreement 100% (95% CI: 88.1-100), Negative Agreement 99.3% (95% CI: 96.2-100)
    • Influenza B: Positive Agreement 93.8% (95% CI: 69.8-99.8), Negative Agreement 100% (95% CI: 97.7-100)
• Overall success rate: 97.1% (1351/1391) of runs were successful on the first attempt.
• Assay success rate: Archived specimens [96.8% (727/751)] and fresh specimens [97.5% (624/640)] were equivalent.

Key Metrics (Sensitivity, Specificity, PPV, NPV, etc.)

See "Summary of Performance Studies" for detailed metrics. Key metrics presented include Analytical Reactivity, Limit of Detection, Analytical Specificity (100%), Reproducibility (overall total agreement 97.0% for site evaluation, 96.1% for instrument system comparison), Sensitivity, Specificity, Positive Agreement, and Negative Agreement.

Predicate Device(s)

K073029: ProFLU+™ Assay, Gen-Probe Prodesse, Inc., K100148: Simplexa™ Influenza A H1N1(2009), Focus Diagnostics, Inc.

Reference Device(s)

Not Found

Predetermined Change Control Plan (PCCP) - All Relevant Information

Not Found

Regulation Number and Section

§ 866.3332 Reagents for detection of specific novel influenza A viruses.

(a)
Identification. Reagents for detection of specific novel influenza A viruses are devices that are intended for use in a nucleic acid amplification test to directly detect specific virus RNA in human respiratory specimens or viral cultures. Detection of specific virus RNA aids in the diagnosis of influenza caused by specific novel influenza A viruses in patients with clinical risk of infection with these viruses, and also aids in the presumptive laboratory identification of specific novel influenza A viruses to provide epidemiological information on influenza. These reagents include primers, probes, and specific influenza A virus controls.(b)
Classification. Class II (special controls). The special controls are:(1) FDA's guidance document entitled “Class II Special Controls Guidance Document: Reagents for Detection of Specific Novel Influenza A Viruses.” See § 866.1(e) for information on obtaining this document.
(2) The distribution of these devices is limited to laboratories with experienced personnel who have training in standardized molecular testing procedures and expertise in viral diagnosis, and appropriate biosafety equipment and containment.

Summary

0

K103766

510(k) Summary

As required by 21 CFR Section 807.92(c).

APR 2 1 2011

| Submitted by: | Cepheid®
904 Caribbean Drive
Sunnyvale, CA 90489
Phone number: [phone].
Fax number: [phone] |
|--------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| Contact: | Russel K. Enns, Ph.D. |
| Date of Preparation: | April 22, 2011 |
| Device: | |
| Trade name: | Xpert® Flu |
| Common name: | Xpert Flu Assay |
| Type of Test: | Automated, multiplex real-time reverse transcription-
polymerase chain reaction (rRT-PCR) assay intended for the
in vitro qualitative detection and differentiation of influenza
A, influenza B and 2009 H1N1 influenza viral RNA. |
| Regulation number/
Classification name: | 866.3980/Respiratory viral panel multiplex nucleic acid assay |
| Product code: | OQW, OCC, OOI |
| Classification
Advisory Panel | Microbiology (83) |
| Predicate Devices: | K073029: ProFLU+™ Assay,
Gen-Probe Prodesse, Inc.
K100148: Simplexa™ Influenza A H1N1(2009),
Focus Diagnostics, Inc. |

Device Description:

The Xpert Flu Assay is a rapid, automated in vitro diagnostic test for qualitative detection and differentiation of influenza A, influenza B and influenza A, subtype 2009 HINI. The assay is performed on the Cepheid GeneXpert Instrument Systems. The GeneXpert Instrument Systems automate and integrate sample purification, nucleic acid amplification, and detection of the target sequence in simple or complex samples using real-time PCR and RT-PCR assays. The systems require the use of single-use disposable cartridges that hold the PCR reagents and host the PCR process. Because the cartridges are self-contained and specimens never come into contact with working parts of the instrument modules, cross-contamination between samples is eliminated.

1

The Xpert Flu Assay includes reagents for the detection and differentiation of influenza A, influenza B and influenza A, subtype 2009 H1N1 directly from nasal aspirates/washes (NA/W) and nasopharyngeal (NP) swab specimens from patients with signs and symptoms of respiratory infection. A Sample Processing Control (SPC) and a Probe Check Control (PCC) are also included. The SPC is present to control for adequate processing of the target viruses and to monitor the presence of inhibitors in the PCR reaction. The Probe Check Control (PCC) verifies reagent rehydration, PCR tube filling in the cartridge, probe integrity and dye stability.

The liquid specimen (NA/W) or swab specimen (NP) is collected according to the institution's standard procedures and placed into Universal Transport Medium (3mL UTM tubes). Following a brief mixing by inverting the UTM tube five times, the eluted material and one single-use reagent (Reagent 1), that is provided with the assay, are transferred to different, uniquely-labeled chambers of the disposable fluidic cartridge (the Xpert Flu cartridge). The user initiates a test from the system user interface and places the cartridge into the GeneXpert instrument platform, which performs hands-off reverse transcription and real-time, multiplex polymerase chain reaction (PCR) for detection of DNA. In this platform, additional sample preparation, amplification, and real-time detection are all fully-automated and completely integrated.

The single-use, multi-chambered fluidic cartridges are designed to complete sample preparation and real-time RT-PCR for detection and differentiation of influenza A, influenza B and influenza A, subtype 2009 H1N1 in 75 minutes. The GeneXpert Instrument Systems have 1 to 48 randomly accessible modules that are each capable of performing separate sample preparation and real-time PCR tests. Each module contains a syringe drive for dispensing fluids (i.e., the syringe drive activates the plunger that works in concert with the rotary valve in the cartridge to move fluids between chambers), an ultrasonic horn for lysing cells or spores, and a proprietary I-CORE® thermocycler for performing real-time PCR and detection.

Device Intended Use:

The Cepheid® Xpert Flu Assay is an automated, multiplex real-time RT-PCR assay intended for the in vitro qualitative detection and differentiation of influenza B and 2009 H1N1 influenza viral RNA. The Xpert Flu Assay uses nasal aspirates/washes and nasopharyngeal swab specimens collected from patients with signs and symptoms of respiratory infection in conjunction with clinical and epidemiological risk factors. The Xpert Flu Assay is intended as an aid in the diagnosis of influenza.

Negative results do not preclude influenza virus infection and should not be used as the sole basis for treatment or other patient management decisions.

Performance characteristics for influenza A were established during the 2009-2010 influenza season when 2009 H1N1 influenza was the predominant influenza A virus in circulation. When other influenza A viruses are emerging, performance characteristics may vary.

2

If infection with a novel influenza A virus is suspected based on current clinical and epidemiological screening criteria recommended by public health authorities, specimens should be collected with appropriate infection control precautions for novel virulent influenza viruses and sent to state or local health department for testing. Viral culture should not be attempted in these cases unless a BSL 3+ facility is available to receive and culture specimens.

Substantial Equivalence:

The Xpert Flu Assay is substantially equivalent to the following predicate assays:

• K073029: ProFLU+TM Assay, Gen-Probe Prodesse, Inc. .
• K100148: Simplexa™ Influenza A H1N1(2009), Focus Diagnostics, Inc. .

Similarities and differences between the Cepheid Xpert Flu Assay and the predicate devices are shown in Table 5.1.

A clinical study at six sites was conducted to compare Xpert Flu Assay performance to the standard of care, viral culture followed by direct fluorescent assay (DFA). Sequencing for all influenza A positive specimens. For archived specimens, where viral culture was not performed prior to freezing, a FDA cleared molecular assay was performed as the comparator assay followed by sequencing of all influenza A positive specimens.

Table 5.1: Comparison of Similarities and Differences of the Xpert Flu Assay with
the Predicate Devices

| Item | Device
Cepheid Xpert Flu | Gen-Probe Prodesse,
Inc. ProFLU+ | Predicates
Focus Simplexa
Influenza A H1N1 |
|-----------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 510(k) No. | K103766 | K073029 | K100148 |
| Regulation | 866.3332 and 866.3980 | 866.3980 | 866.3332 |
| Product Code | OQW, OCC, OOI | OCC | OQW |
| Device Class | II | II | II |
| Technology/
Detection | Multiplex real time RT/PCR | Multiplex real time
RT/PCR | Multiplex real time
RT/PCR |
| Intended Use | An automated, multiplex
real-time RT-PCR assay
intended for the in vitro
qualitative detection and
differentiation of influenza
A, influenza B and 2009
H1N1 influenza viral RNA.
The Xpert Flu Assay uses
nasal aspirates/washes and
nasopharyngeal swab | A multiplex Real Time
RT-PCR in vitro
diagnostic test for the
rapid and qualitative
detection and
discrimination of
Influenza A Virus,
Influenza B Virus, and
Respiratory Syncytial
Virus (RSV) nucleic | For use on the 3M
Integrated Cycler as part of
the Microfluidic Molecular
System for the in vitro
qualitative detection and
differentiation of influenza
A and 2009 H1N1
influenza viral RNA in
nasopharyngeal swabs
(NPS), nasal swabs (NS), |
| | Device | | Predicates |
| Item | Cepheid Xpert Flu | Gen-Probe Prodesse,
Inc. ProFLU+\ | Focus Simplexa
Influenza A H1N1 |
| | specimens collected from
patients with signs and
symptoms of respiratory
infection in conjunction
with clinical and
epidemiological risk factors.
The Xpert Flu Assay is
intended as an aid in the
diagnosis of influenza.
Negative results do not
preclude influenza virus
infection and should not be
used as the sole basis for
treatment or other patient
management decisions.
Performance characteristics
for influenza A were
established during the 2009-
2010 influenza season when
2009 H1N1 influenza was
the predominant influenza
A virus in circulation. When
other influenza A viruses
are emerging, performance
characteristics may vary.
If infection with a novel
influenza A virus is
suspected based on current
clinical and epidemiological
screening criteria
recommended by public
health authorities,
specimens should be
collected with appropriate
infection control
precautions for novel
virulent influenza viruses
and sent to state or local
health department for
testing. Viral culture should
not be attempted in these
cases unless a BSL 3+
facility is available to
receive and culture
specimens. | acids isolated and
purified from
nasopharyngeal (NP)
swab specimens
obtained from
symptomatic patients.
This test is intended for
use to aid in the
differential diagnosis of
Influenza A, Influenza
B and RSV2 viral
infections in humans
and is not intended to
detect Influenza C.
A negative test is
presumptive and it is
recommended these
results be confirmed by
cell culture. Negative
results do not preclude
influenza or RSV virus
infection and should
not be used as the sole
basis for treatment or
other management
decisions. | and nasopharyngeal
aspirates (NPA) from
human patients with signs
and symptoms of
respiratory infection in
conjunction with clinical
and epidemiological risk
factors.
Negative results do not
preclude influenza virus
infection and should not be
used as the sole basis for
treatment or other patient
management decisions.
Performance characteristics
for influenza A were
established during the
2009-2010 influenza season
when 2009 H1N1 influenza
was the predominant
influenza A virus in
circulation. When other
Influenza A viruses are
emerging, performance
characteristics may vary.
If infection with a novel
Influenza A virus is
suspected based on current
clinical and
epidemiological screening
criteria recommended by
public health authorities,
specimens should be
collected with appropriate
infection control
precautions for novel
virulent Influenza viruses
and sent to state or local
health department for
testing. Viral culture should
not be attempted in these
cases unless a BSL 3+
facility is available to
receive and culture
specimens |
| | Device | Predicates | |
| Item | Cepheid Xpert Flu | Gen-Probe Prodesse,
Inc. ProFLU+\ | Focus Simplexa
Influenza A H1N1 |
| Indication for Use | Patients with signs and
symptoms of respiratory
infection in conjunction
with clinical and
epidemiological risk factors. | Symptomatic patients | Patients with signs and
symptoms of respiratory
infection in conjunction
with clinical and
epidemiological risk factors |
| Assay Targets | Influenza A,
influenza B, and influenza
A, subtype 2009 H1N1 | Influenza A, influenza
B. Respiratory
Syncytial Virus Type A
and Type B | Influenza A/
2009 H1N1 influenza |
| Specimen Types | Nasal aspirates/washes
(NA/W) and
Nasopharyngeal (NP) swabs | NP swab | NP swab, Nasal Swab (NS)
and nasopharyngeal
aspirates (NA/W) |
| Technological
Principles | RT/PCR | RT/PCR | RT/PCR |
| Nucleic Acid
Extraction | Yes | Yes | Yes |
| Extraction
Methods | Sample preparation
integrated in GeneXpert
Cartridge and GeneXpert
Instrumentation System | Roche MagNA Pure
LC Total NA Isolation
Kit | Roche MagNA Pure LC
Total NA Isolation Kit,
QIAGEN QIAamp Viral
RNA mini Kit |
| Assay Results | Qualitative | Qualitative | Qualitative |
| Instrument System | Cepheid GeneXpert
Instrument Systems | Cepheid Smartcycler®
II | 3M Integrated cycler |
| Assay Controls | Encapsulated (armored)
RNA pseudovirus as a
sample processing
control.
Available but not
provided are inactivated
virus controls for Flu A/B
and Flu A H1N1 as
external positive controls
and Coxsackie virus as an
external negative control. | Inf A RNA Control, Inf
B RNA Control, RSV
A RNA Control, RSV
B RNA Control and an
internal | Armored RNA Internal
Control, No Template
Control, and H1N1 Positive
Control provided |
| Test results | Total 75 minutes for sample
preparation and
rRT-PCR | Total 205 minutes
(~45 minutes for
sample preparation
~2.0 hours for
rRT-PCR) | Total 115 minutes
(~45 minutes for sample
preparation
~70 minutes for
rRT-PCR) |
| | Device | Predicates | |
| Item | Cepheid Xpert Flu | Gen-Probe Prodesse,
Inc. ProFLU+\ | Focus Simplexa
Influenza A H1N1 |
| Laboratory Users | CLIA Moderate to High
Complexity | CLIA High Complexity | CLIA High Complexity |

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Non-Clinical Studies:

Analytical Sensitivity

Analytical Reactivity (Inclusivity)

The analytical reactivity of the Xpert Flu Assay was evaluated against thirty-nine (39) strains of influenza A (H1N1, H3N2, H5N2, H5N1, and H7N3 subtypes), influenza A 2009 H1N1 and influenza B. Of these, influenza A subtype H1N1 (12), influenza A subtype H3N2 (7), influenza A subtype 2009 H1N1 (6), influenza A subtype H5N1 (1), influenza A subtype H5N2 (1), influenza A subtype H7N3 (1) and influenza B (11) were included. Three replicates of each viral strain were tested at 5 - 500 TCID50mL unless noted otherwise. Results are shown in Table 5.2.

| Viral Strain | Concentration
(TCID50/mL) | Influenza
A | Influenza A
2009 H1N1 | Influenza
B |
|----------------------------------------------------|------------------------------|----------------|--------------------------|----------------|
| Influenza A/Denver/1/57 (H1N1) | 500 | + | - | - |
| Influenza A/NewYork/55/2004 (H1N1) | 500 | + | - | - |
| Influenza A/Mal/302/54 (H1N1) | 50 | + | - | - |
| Influenza A/New Jersey/8/76 (H1N1) | 500 | + | - | - |
| Influenza A/NWS/33 (H1N1) | 5 | + | - | - |
| Influenza A/PR/8/34 (H1N1)a | 500 | + | - | - |
| Influenza A/Taiwan/42/06 (H1N1)a | 500 | + | - | - |
| Influenza A/WS/33 (H1N1)a | 5 | + | - | - |
| Influenza A/Swine/1976/31 (Swine
H1N1) | 500 PFU/mLa | + | - | - |
| Influenza A/Swine/Iowa/15/30 (Swine
H1N1) | 500 PFU/mLa | + | - | - |
| Influenza A/Brisbane/59/07 (H1N1)a | 5 | + | - | - |
| Influenza A/NewCalendonia/20/1999
(H1N1)a | 50 | + | - | - |
| Influenza A/Victoria/3/75 (H3N2) | 500 | + | . | |
| Viral Strain | Concentration
(TCID50/mL) | Influenza
A | Influenza A
2009 H1N1 | Influenza
B |
| Influenza A/Aichi2/68 (H3N2) | 500 | + | | |
| Influenza A/Hong Kong/8/68 (H3N2) | 50 | + | - | - |
| Influenza A/Hawaii/15/2001 (H3N2) | 500 | + | - | - |
| Influenza A/Port Chalmers/1/73 (H3N2) | 500 | + | - | - |
| Influenza A/Brisbane/10/07 (H3N2) | 10 | + | - | - |
| Influenza A/Wisconsin/67/05 (H3N2) | 10 | + | - | - |
| Influenza A/SwineNY/01/2009
(2009 H1N1) | 10 | + | + | - |
| Influenza A/SwineNY/02/2009
(2009 H1N1) | 100 | + | + | - |
| Influenza A/SwineNY/03/2009
(2009 H1N1) | 10 | + | + | - |
| Influenza A/California/4/2009
(2009 H1N1) | 5 | + | + | - |
| Influenza A/Canada/6294
(2009 H1N1) | 500 | + | + | - |
| Influenza A/WI/929-S1
(2009 H1N1) | 100 | + | + | - |
| Influenza A/Mallard/WI/34/75 (H5N2) | 3 pg/μLb | + | - | - |
| Influenza A/Anhui/02/2005/PR8-
IBCDC-RG5 (H5N1) | 0.122 pg/µLb | + | - | - |
| Influenza A/chicken/NJ/15086-3/94
(H7N3) | 5 pg/µLb | + | - | - |
| Influenza B/Allen/45 | 500 | - | - | + |
| Influenza B/Florida/02/06 | 10 | - | - | + |
| Influenza B/Florida/04/06 | 500 | - | - | + |
| Influenza B/Florida/07/04 | 50 | - | - | + |
| Influenza B/GL/1739/54 | 500 | - | - | + |
| Influenza B/Hong Kong/5/72 | 500 | - | - | + |
| Influenza B/Lee/40 | 500 | - | - | + |
| Influenza B/Malaysia/2506/04 | 500 | - | - | + |
| Influenza B/Maryland/1/59 | 500 | - | - | + |
| Viral Strain | Concentration
(TCID50/mL) | Influenza
A | Influenza A
2009 H1N1 | Influenza
B |
| Influenza B/Panama/45/90 | 500 | - | - | + |
| Influenza B/Taiwan/2/62 | 50 CEID50/mLc | - | - | + |

Table 5.2: Analytical Reactivity (Inclusivity) of Xpert Flu Assay

6

Xpert Flu Assay 510(k) Summary

7

ªConcentration expressed as PFU/mL

Concentration expressed in picograms/uL Concentration expressed as CEIDsofmL

Analytical Sensitivity

Limit of Detection

Studies were performed to determine the analytical limit of detection (LoD) of two seasonal influenza A (H1N1), two seasonal influenza A (H3N2), five influenza A 2009 HINI and two influenza B strains diluted into a surrogate nasopharyngeal matrix, containing human blood, mucin and sodium chloride. The LoD is defined as the lowest concentration (tissue culture infective dose [TCID]50/mL) per sample that can be reproducibly distinguished from negative samples with 95% confidence or the lowest concentration at which 19 of 20 replicates were positive. Each strain was tested in replicates of 20 per concentration of virus.

The LoD was determined empirically as the first concentration that had 19/20 or 20/20 positive results. The LoD values for each strain tested are summarized in Tables 5.3 -ર .6.

| Strain ID - Influenza A
subtype H1N1 | Confirmed LoD
(TCID50/mL)
(at least 19/20 positive) |
|-----------------------------------------|-----------------------------------------------------------|
| Influenza A/H1/Brisbane/59/07 | 5 (20/20) |
| Influenza A/H1/New
Caledonia/20/1999 | 25 (20/20) |

Table 5.3: Confirmed LoD (TCID50/mL) – Seasonal Influenza A H1N1

Table 5.4: Confirmed LoD (TCID50/mL) - Seasonal Influenza A H3N2

| Strain ID - Influenza A
subtype H3N2 | Confirmed LOD
(TCID50/mL) (at least 19/20 positive) |
|-----------------------------------------|--------------------------------------------------------|
| Influenza A/H3/Brisbane/10/07 | 2.5 (19/20) |
| Influenza
A/H3/Wisconsin/67/05 | 10 (20/20) |

8

| Strain ID -- Influenza A
subtype 2009 H1N1 | Confirmed LOD
(TCID50/mL) (at least 19/20 positive) |
|-----------------------------------------------|--------------------------------------------------------|
| Influenza A/SwineNY/01/2009 | 1 (19/20) |
| Influenza A/SwineNY/02/2009 | 5 (19/20) |
| Influenza A/SwineNY/03/2009 | 3.5 (20/20) |
| Influenza A/Canada/6294 | 100 (20/20) |
| Influenza A/WI/629-S1/2009 | 20 (20/20) |

Table 5.5: Confirmed LoD (TCID50/mL) - Influenza A 2009 H1N1
--------------------------------------------------------------	--	--	--	--

Table 5.6: Confirmed LoD (TCID50/mL) - Influenza B

| Strain ID - Influenza B | Confirmed LOD
(TCID50/mL) (at least 19/20 positive) |
|---------------------------|--------------------------------------------------------|
| Influenza B/Florida/02/06 | 2 (19/19) |
| Influenza B/Florida/07/04 | 75 (20/20) |

Analytical Specificity (Exclusivity)

The analytical specificity of the Xpert Flu Assay was evaluated by testing a panel of 40 cultures consisting of 18 viral, 21 bacterial, and one yeast representing common respiratory pathogens or those potentially encountered in the nasopharynx. Three replicates of each bacterial and yeast strains were tested at concentrations ≥10° CFU/mL. Three replicates of each virus were tested at concentrations ≥10 TCID50/mL. Purified nucleic acids (genome copies/mL) were tested for one virus strain (Cytomegalovirus) and two bacterial strains (Bordetella pertussis and Haemophilus influenzae). Positive and negative controls were included in the study. The analytical specificity was 100%. Results are shown in Table 5.7.

| Strain | Concentration
(per Cartridge) | Influenza
A | Influenza A
2009 H1N1 | Influenza
B |
|---------------------------------------------------|----------------------------------|----------------|--------------------------|----------------|
| Positive Control 1 - Influenza
A/influenza B | N/A | + | - | + |
| Positive Control 2 – Influenza A
2009 H1N1 | N/A | + | + | - |
| Negative Control | N/A | - | - | - |
| Adenovirus Type 7A | 1x106 TCID50/mL | - | - | - |
| Adenovirus Type 1 | 1x106 TCID50/mL | - | - | - |
| Human Coronavirus 229E | 1x106 TCID50/mL | - | - | - |
| Human Coronavirus OC43 | 1x104 TCID50/mL | - | - | - |
| Cytomegalovirusb | 1x105 Copies /mL | - | - | - |
| Enterovirus Type 71 | 1x106 TCID50/mL | - | - | - |
| Epstein-Barr Virus | 1x105 TCID50/mL | - | - | - |
| Strain | Concentration
(per Cartridge) | Influenza
A | Influenza A
2009 H1N1 | Influenza
B |
| Parainfluenzavirus Type 1 | 1x105 TCID50/mL | - | - | - |
| Parainfluenzavirus Type 2 | 1x106 TCID50/mL | - | - | - |
| Parainfluenzavirus Type 3 | 1x106 TCID50/mL | - | - | - |
| Measles Virus | 1x106 TCID50/mL | - | - | - |
| Human Metapneumovirus | 1x106 TCID50/mL | - | - | - |
| Mumps Virus | 1x106 TCID50/mL | - | - | - |
| Respiratory Syncytial Virus A | 1x106 TCID50/mL | - | - | - |
| Respiratory Syncytial Virus B | 1x106 TCID50/mL | - | - | - |
| Human HSV Type 1 | 1x106 TCID50/mL | - | - | - |
| Human Rhinovirus Type 4 | 1x106 TCID50/mL | - | - | - |
| Echovirus 11 | 1x106 TCID50/mL | - | - | - |
| Bordetella pertussis b | 1x106 Copies/mL | - | - | - |
| Chlamydia pneumoniae | 1x106 CFU/mL | - | - | - |
| Corynebacterium xerosis | 1x106 CFU/mL | - | - | - |
| Escherichia coli | 1x106 CFU/mL | - | - | - |
| Proteus vulgaris | 1x106 CFU/mL | - | - | - |
| Proteus mirabilis | 1x106 CFU/mL | - | - | - |
| Klebsiella pneumoniae | 1x106 CFU/mL | - | - | - |
| Haemophilus influenzae b | 1x106 Copies/mL | - | - | - |
| Lactobacillus crispatus | 1x106 CFU/mL | - | - | - |
| Legionella pneumophila | 1x106 CFU/mL | - | - | - |
| Moraxella catarrhalis | 1x106 CFU/mL | - | - | - |
| Mycobacterium tuberculosis
(BCG strain) | 1x106 CFU/mL | - | - | - |
| Mycoplasma pneumoniae | 1x106 CFU/mL | - | - | - |
| Neisseria meningitides | 1x106 CFU/mL | - | - | - |
| Neisseria Cinneria | 1x106 CFU/mL | - | - | - |
| Pseudomonas aeruginosa | 1x106 CFU/mL | - | - | - |
| Staphylococcus aureus | 1x106 CFU/mL | - | - | - |
| Staphylococcus epidermidis | 1x106 CFU/mL | - | - | - |
| Streptococcus pneumoniae | 1x106 CFU/mL | - | - | - |
| Streptococcus pyogenes | 1x106 CFU/mL | - | - | - |
| Streptococcus salivarius | 1x106 CFU/mL | - | - | - |
| Candida albicans | 1x106 CFU/mL | - | - | - |

Table 5.7: Analytical Specificity of Xpert Flu Assayª

9

·

·

・

.

10

a Cross-reactivity with other swine-origin strains was not evaluated. bNucleic acid was tested for Cytomegalovirus, Bordetella pertussis, and Haemophilus influenzae.

Interfering Substances

In a non-clinical study, potentially interfering substances that may be present in the nasopharynx were evaluated directly relative to the performance of the Xpert Flu Assay. Potentially interfering exogenous substances in the nasopharynx may include, but are not limited to: blood, nasal secretions or mucus, and nasal and throat medications used to relieve congestion, nasal dryness, irritation, or asthma and allergy symptoms. These substances are listed in Table 5.8 with active ingredients and concentrations tested shown. Highly viscous samples, resulting from the addition of 1.5% (w/v) and 2.5% (w/v) mucin yielded false negative test results from the Xpert Flu Assay. Inhibition of the Xpert Flu Assay was also observed from the addition of 1% (w/v) mucin, resulting in delayed detection of influenza A, influenza A subtype 2009 H1N1 and influenza B.

Substance	Description/Active Ingredient	Concentration Tested
Blood (human)	N/A	2% (v/v)
Mucin	Purified mucin protein (Bovine or porcine submaxillary gland)	2.5%, 1.5%, 1% and 0.5% (w/v)
Neo-Synephrine® Nasal Drops	Phenylephrine HCl	15% (v/v)
Anefrin Nasal Spray	Oxymetazoline Hydrochloride	15% (v/v)
Zicam® Nasal Gel	Luffa opperculata, Galphimia glauca, Histaminum hydrochloricum Sulfur	5% (v/v)
Saline Nasal Spray	Sodium Chloride with preservatives	15% (v/v)
Antibiotic, nasal ointment	Mupirocin	10 mg/mL
Antibacterial, systemic	Tobramycin	4.0 µg/mL
Throat lozenges, oral anesthetic and analgesic	Menthol	1.7 mg/mL menthol

Table 5.8: Potentially Interfering Substances in Xpert Flu Assay.

11

Carry-Over Contamination Study

A study was conducted to demonstrate that single-use, self-contained GeneXpert cartridges prevent carry-over contamination in negative samples run following very high positive samples in the same GeneXpert module. The study consisted of a negative sample processed in the same GeneXpert module immediately following a very high influenza A subtype 2009 H1N1 sample (approximately 10° TCID50/test) or influenza B sample (approximately 10° TCID50/test). This testing scheme was repeated 20 times on four GeneXpert modules for a total of 88 runs resulting in 40 positive and 48 negative specimens. All 40 positive samples were correctly reported as influenza A 2009 H1N1 positive or influenza B positive. All 48 negative samples were correctly reported as Flu A negative, 2009 H1N1 not detected and Flu B negative.

Linearity

A study was conducted to define the reportable range of the Xpert Flu Assay and demonstrate a linear relationship between target input and assay output. Linearity was evaluated using two seasonal influenza A H1N1, two seasonal influenza A H3N2, two influenza A 2009 H1N1, and two influenza B strains diluted over four to five logs and processed using the Xpert Flu Assay. Replicates of 4 were tested.

Under the conditions of the study, the Xpert Flu Assay responds linearly over six logs for seasonal influenza A H1N1, seasonal influenza A H3N2 and influenza A 2009 H1N1; and over 5 logs for influenza B strains tested.

Reproducibility

A panel of 10 specimens with varying concentrations of influenza A, influenza B, and influenza A subtype 2009 H1N1 were tested in duplicate on 10 different days at each of three sites (10 specimens x 2 times/ day x 10 days x 3 sites). One lot of Xpert Flu Assay was used at each of the 3 testing sites. Xpert Flu Assays were performed according to the Xpert Flu Assay procedure. Results are summarized in Table 5.9.

| Sample ID | Site 1 | Site 2 | Site 3 | % Total Agreement
by Sample |
|--------------------------------|-----------------|------------------|------------------|--------------------------------|
| Negative | 100%
(20/20) | 100%
(20/20) | 100%
(20/20) | 100%
(60/60) |
| Flu A
moderate positive | 100%
(20/20) | 100%
(19/19)a | 100%
(20/20) | 100%
(59/59) |
| Flu A
low positive | 100%
(20/20) | 100%
(20/20) | 100%
(20/20) | 100%
(60/60) |
| Flu A
high negative | 100%
(20/20) | 95.0%
(19/20) | 90.0%
(18/20) | 95.0%
(57/60) |
| 2009 H1N1
moderate positive | 100%
(20/20) | 100%
(20/20) | 100%
(20/20) | 100%
(60/60) |
| 2009 H1N1
low positive | 100%
(20/20) | 100%
(19/19)b | 100%
(20/20) | 100%
(59/59) |

Table 5.9: Summary of Reproducibility Results

12

| Sample ID | Site 1 | Site 2 | Site 3 | % Total Agreement
by Sample |
|----------------------------|--------------------|--------------------|--------------------|--------------------------------|
| 2009 H1N1
high negative | 94.7%
(18/19)a | 100%
(20/20) | 89.5%
(17/19)a | 94.8%
(55/58)c |
| Flu B
moderate positive | 100%
(20/20) | 100%
(20/20) | 100%
(20/20) | 100%
(60/60) |
| Flu B
low positive | 100%
(20/20) | 100%
(20/20) | 100%
(20/20) | 100%
(60/60) |
| Flu B
high negative | 90.0%
(18/20) | 95.0%
(19/20) | 55.0%
(11/20) | 80.0%
(48/60) |
| % Total Agreement | 98.5%
(196/199) | 99.0%
(196/198) | 93.5%
(186/199) | 97.0%
(578/596) |

*n=19 because repeat yielded indeterminate result.

be = 19 because one sample was indeterminate and not retested.

59/55 samples negative for 2009 HINI resulted in a valid Flu A positive call, as the Flu A signal was detected. A valid 2009 HINI positive call requires detection of both the Flu A and 2009 HINI signals.

Instrument System Reproducibility

An in-house reproducibility study was conducted to compare the performance of the GeneXpert Dx and the Infinity instrument systems. A panel of 10 specimens with varying concentrations of influenza A, influenza B, and influenza A subtype 2009 H1N1 were tested in duplicate on 12 different days by two operators. Each operator conducted four runs of each panel specimen per day on each of the two instrument systems (11 specimens x 2 times/ day x 12 days x 2 operators x 2 instrument systems). One lot of Xpert Flu Assay was used for the study. Xpert Flu Assays were performed according to the Xpert Flu Assay procedure. Results are summarized in Table 5.10.

| Sample ID | GeneXpert Dx | Infinity | % Total Agreement
by Sample |
|--------------------------------|-------------------|-------------------|--------------------------------|
| Negative | 100.0%
(96/96) | 100.0%
(96/96) | 100.0%
(192/192) |
| Flu A
moderate positive | 100.0%
(96/96) | 100.0%
(96/96) | 100.0%
(192/192) |
| Flu A
low positive | 100.0%
(96/96) | 100.0%
(96/96) | 100.0%
(192/192) |
| Flu A
high negative | 89.6%
(86/96) | 86.5%
(83/96) | 88.0%
(169/192) |
| 2009 H1N1
moderate positive | 100.0%
(96/96) | 100.0%
(96/96) | 100.0%
(192/192) |
| 2009 H1N1
low positive | 100.0%
(96/96) | 100.0%
(96/96) | 100.0%
(192/192) |
| 2009 H1N1
high negative | 84.4%
(81/96) | 92.6%
(88/95)a | 88.5%
(169/191) |
| Flu B
moderate positive | 100.0%
(96/96) | 100.0%
(96/96) | 100.0%
(192/192) |

Table 5.10: Summary of Instrument System Reproducibility Results

13

| Sample ID | GeneXpert Dx | Infinity | % Total Agreement
by Sample |
|------------------------|--------------------|--------------------|--------------------------------|
| Flu B
low positive | 100.0%
(96/96) | 100.0%
(96/96) | 100.0%
(192/192) |
| Flu B
high negative | 87.5%
(84/96) | 82.3%
(79/96) | 84.9%
(163/192) |
| % Total Agreement | 96.1%
(923/960) | 96.1%
(922/959) | 96.1%
(1845/1919) |

ªn=95 because repeat yielded indeterminate result.

Clinical Performance Characteristics

Clinical Performance Study

Performance characteristics of the Xpert Flu Assay on prospective and archived specimens were evaluated at six institutions in the U.S. and Australia. Due to the low prevalence of influenza viruses and the difficulty in obtaining fresh influenza-positive specimens, the specimen population for this study was supplemented with frozen archived specimens.

Subjects included individuals whose routine care called for collection of NA/W or NP swab specimens for influenza testing. For eligible subjects, aliquots of leftover sample were obtained for testing with the Xpert Flu Assay and reference testing, and patient management continued at the site per the standard practice.

The Xpert Flu Assay performance was compared to viral culture followed by direct fluorescent assay (DFA). Sequencing was performed for all influenza A positive specimens. For archived specimens, where viral culture was not performed prior to freezing, a FDA cleared molecular assay was performed as the comparator assay. Samples included nasal NA/W and NP swab specimens collected for routine testing from patients suspected of influenza infection.

Overall Results

Prospective Specimens

A total of 342 prospective NA/W specimens were tested for influenza A, influenza A subtype 2009 H1N1 and influenza B by the Xpert Flu Assay and viral culture plus DFA. A total of 297 prospectively collected NP swab specimens were tested for influenza A, influenza A subtype 2009 H1N1 and influenza B by the Xpert Flu Assay and viral culture plus DFA. All influenza A positive specimens, identified by viral culture/DFA, were sequenced to differentiate influenza A subtype 2009 H1N1 from other influenza A subtypes

On fresh, prospective NA/W specimens, the Xpert Flu Assay demonstrated a sensitivity and specificity for detection of influenza A of 85.7% and 99.1%, respectively, relative to viral culture plus DFA, with sequence confirmation of all influenza A positive viral isolates, or specimens in transport medium if isolates were not available (Table 5.11).

14

The Xpert Flu Assay sensitivity and specificity for influenza A subtype 2009 H1N1 with NA/W specimens were 100% and 98.8%, respectively (Table 5.12). The Xpert Flu Assay sensitivity and specificity for influenza B with NA/W specimens were 100% and 99.4%, respectively (Table 5.13).

	Culture/DFA
pert Flu Assa		Pos	Neg	Total
	Pos	6	3 สิ	ರ
	Neg	l b	332	333
	Total	7	335	342
	85.7% (95% CI: 42.1-99.6)
Sensitivity:
99.1% (95% CI: 97.4-99.8)
Specificity:

Table 5.11: Xpert Flu Assay Performance on Prospective NA/W Specimens: Influenza A

4Testing results by sequencing: 3 of 3 were H1N1.

bTesting results by sequencing: Flu A

Table 5.12: Xpert Flu Assay Performance on Prospective NA/W Specimens: Influenza A, 2009 H1N1

	Culture/DFA & Sequencing
	Pos	Neg	Total
Xpert Flu Assay	Pos	4	4a	8
	Neg	0	334	334
	Total	4	338	342
Sensitivity: 100% (95% CI: 39.8-100)
Specificity: 98.8% (95% CI: 97.0-99.7)

Testing results by sequencing: 3 of 4 were HINI; 1 of 4 was Flu A.

15

	Culture/DFA
Xpert Flu Assay	Pos	Neg	Total
Pos	7	2a	9
Neg	0	333	333
Total	7	335	342
		Sensitivity: 100% (95% CI: 65.2-100)
		Specificity: 99.4% (95% CI: 98.1-99.9)

Table 5.13: Xpert Flu Assay Performance on Prospective NA/W Specimens: Influenza B

ªTesting results by sequencing: 2 of 2 were Flu B.

On prospectively collected NP swabs, the Xpert Flu Assay demonstrated a sensitivity and specificity for detection of influenza A of 100% and 98.3%, respectively, relative to viral culture plus DFA, with sequence confirmation of all influenza A positive viral isolates, or specimens in transport medium if isolates were not available (Table 5.14). The Xpert Flu Assay sensitivity and specificity for influenza A subtype 2009 HIN1 with NP swabs were 100% and 99.0%, respectively (Table 5.15). The Xpert Flu Assay sensitivity and specificity for influenza B with NP swabs were 87.5% and 99.7%, respectively (Table 5.16).

Table 5.14: Xpert Flu Assay Performance on Prospective NP Swab Specimens: Influenza A

	Culture/DFA
Xpert Flu Assay		Pos	Neg	Total
	Pos	7	5a	12
	Neg	0	285	285
Total		7	290	297
	Sensitivity: 100% (95% CI: 59.0-100)
Specificity: 98.3% (95% CI: 96.0-99.4)

4Testing results by sequencing: 3 of 5 were H1N1; 2 of 5 were Flu A.

16

	Culture/DFA & Sequencing
Xpert Flu Assay	Pos	Neg	Total
Pos	5	3a	8
Neg	0	289	289
Total	5	292	297
	Sensitivity:
Specificity:		100% (95% CI: 47.8-100)
99.0% (95% CI: 97.0-99.8)

Table 5.15: Xpert Flu Assay Performance on Prospective NP Swab Specimens: Influenza A, 2009 H1N1

ªTesting results by sequencing: 2 of 3 were H1N1; 1 of 3 was Flu A.

Table 5.16: Xpert Flu Assay Performance on Prospective NP Swab Specimens: Influenza B

	Culture/DFA
Xpert Flu Assay		Pos	Neg	Total
	Pos	7	1a	8
	Neg	1b	288	289
	Total	8	289	297
	Sensitivity: 87.5% (95% CI: 47.3-99.7)
Specificity: 99.7% (95% CI: 98.1-100)

a Testing results by sequencing: Flu B. bTesting results by sequencing: Flu A.

Archived Specimens

A total of 425 archived NA/W specimens were tested for influenza A, influenza A subtype 2009 H1N1 and influenza B by the Xpert Flu Assay and a FDA cleared molecular comparator device. A total of 150 archived NP swab specimens were tested for influenza A. influenza A subtype 2009 H1N1 and influenza B by the Xpert Flu Assay and viral culture plus DFA: 177 archived NP swab specimens did not have viral culture results available and were tested by the FDA cleared molecular comparator device. All influenza A positive specimens indentified by viral culture/DFA or cleared molecular comparator device were sequenced to differentiate influenza A subtype 2009 HINI from other influenza A subtypes.

On archived NA/W specimens, the Xpert Flu Assay demonstrated a positive and negative agreement for detection of influenza A of 99.4% and 100%, respectively, relative to viral culture plus DFA, with sequence confirmation of all influenza A positive viral isolates, or

17

specimens in transport medium if isolates were not available (Table 5.17). The Xpert Flu Assay positive and negative agreement for influenza A subtype 2009 H1N1 with NA/W specimens were 98.4% and 99.7% (Table 5.18). The Xpert Flu Assay positive and negative agreement for influenza B with NA/W specimens were 100% and 100%, respectively (Table 5.19)

	FDA Cleared Molecular Comparator
Xpert Flu Assay		Pos	Neg	Total
	Pos	159	0	159
	Neg	1*	265	266
	Total	160	265	425
	Positive Agreement:
Negative Agreement:		99.4% (95% CI: 96.6-100)
100% (95% CI: 98.6-100)

Table 5.17: Xpert Flu Assay Performance on Archived NA/W Specimens: Influenza A

1Testing by sequencing: no sequence match for Flu A, HIN1 or Flu B

Table 5.18: Xpert Flu Assay Performance on Archived NA/W Specimens: Influenza A, 2009 H1N1

	FDA Cleared Molecular Comparator & Sequencing
Xpert Flu Assay	Pos	Neg	Total
Pos	124	1a	125
Neg	2b	295	297
Total	126	296	422c
	Positive Agreement:
Negative Agreement:		98.4% (95% CI: 94.4-99.8)
99.7% (95% CI: 98.1-100)

aTesting results by sequencing: Flu A, not HINI.

6Testing results by sequencing: 2 of 2 HIN1.

63 samples excluded due to PHRED score