Xpert® HIV-1 Viral Load

GXHIV-VL-CE-10

In Vitro Diagnostic Medical Device 301-3068, Rev. C January 2015

Trademark, Patents and Copyright Statements

Xpertise, Cepheid®, the Cepheid logo, GeneXpert®, Xpert®, and Xpertise® are trademarks of Cepheid.
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Armored RNA® is a patented technology jointly developed by Asuragen Inc. and Cenetron Diagnostics, LLC under U.S. Patent
Nos. 5,677,124, 5,919,625, 5,939,262 and other patents pending.

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PRODUCT.

Copyright © Cepheid 2015. All rights reserved.

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Xpert® HIV-1 Viral Load

For In Vitro Diagnostic Use Only.

1 Proprietary Name
Xpert® HIV-1 Viral Load
2 Common or Usual Name
HIV-1 VL
3 Intended Use
The HIV-1 VL Assay, performed on the GeneXpert® Instrument Systems, is an in vitro diagnostic test designed for the rapid
quantitation of Human Immunodeficiency Virus type 1 (HIV-1) in human plasma from HIV-1 infected individuals over the range
of 40 to 10,000,000 copies/mL, and is validated for specimens across Group M subtypes A, B, C, D, AE, F, G, H, AB, AG, J, K
and Group N and Group O.
The HIV-1 VL Assay is intended for use in conjunction with clinical presentation and other laboratory markers for disease
prognosis and for use as an aid in assessing viral response to antiretroviral treatment as measured by changes in plasma HIV-1
RNA levels.
The HIV-1 VL Assay is not intended to be used as a donor screening test for HIV-1 or as a diagnostic test to confirm the
presence of HIV-1 infection.
4 Summary and Explanation
Human Immunodeficiency Virus (HIV) is the etiologic agent of Acquired Immunodeficiency Syndrome (AIDS).1,2,3 It can be
transmitted through sexual contact, exposure to infected blood or blood products, prenatal infection of a fetus, or perinatal or
postnatal infection of a newborn.4,5,6
HIV diagnostics have evolved significantly in the past two decades and continue to be significantly important in saving lives of
millions of HIV infected patients. Today, measurement of blood plasma HIV-1 RNA concentration known as viral load using
nucleic acid-based molecular diagnostic assays has been established as standard of care in assessing HIV-positive patient
prognosis and response to antiretroviral therapy.
Untreated HIV-1 infection is characterized by high-level viral production and CD4 T-cell destruction, despite an often lengthy
clinical latency, to significant net loss of CD4 T cells and AIDS.7,8,9
Assessment of viral load levels is a strong predictor of the rate of disease progression and, by itself or in combination with CD4
T-cell counts, has great prognostic value.10,11,12,13,14,15
The HIV-1 VL Assay uses reverse transcriptase polymerase chain reaction (RT-PCR) technology to achieve high sensitivity for
the quantitative detection of HIV-1 RNA in human plasma from HIV-1 infected individuals.
5 Principle of the Procedure
GeneXpert Instrument Systems automate and integrate sample preparation, nucleic acid extraction and amplification, and
detection of the target sequence in simple or complex samples using real-time reverse transcriptase PCR (RT-PCR). The systems
consist of an instrument, personal computer, and preloaded software for running tests and viewing the results. The systems
require the use of single-use disposable GeneXpert cartridges that hold the RT-PCR reagents and host the RT-PCR processes.
Because the cartridges are self-contained, cross-contamination between samples is minimized. For a full description of the
systems, refer to the appropriate GeneXpert Dx Operator Manual or GeneXpert Infinity Operator Manual.
The HIV-1 VL Assay includes reagents for the detection of HIV-1 RNA in specimens and two internal controls used for
quantitation of HIV-1 RNA. The internal controls are also used to monitor the presence of inhibitor(s) in the RT and PCR
reactions. The Probe Check Control (PCC) verifies reagent rehydration, PCR tube filling in the cartridge, probe integrity, and
dye stability.

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6 Reagents and Instruments

6.1 Materials Provided
The HIV-1 VL Assay kit contains sufficient reagents to process 10 specimens or quality control samples. The kit contains the
following:

HIV-1 VL Assay Cartridges with Integrated Reaction Tubes 10

• Bead 1, Bead 2, and Bead 3 (freeze-dried) 1 of each per cartridge
• Lysis Reagent (Guanidinium Thiocyanate) 2.0 mL per cartridge
• Rinse Reagent 0.5 mL per cartridge
• Elution Reagent 1.5 mL per cartridge
• Binding Reagent 2.4 mL per cartridge
• Proteinase K Reagent 0.48 mL per cartridge
Disposable 1 mL Transfer Pipettes 10 per kit
CD 1 per kit
• Assay Definition File (ADF)
• Instructions to import ADF into GeneXpert software
• Package Insert

Note Safety Data Sheets (SDS) are available at www.cepheidinternational.com under the SUPPORT tab.

The bovine serum albumin (BSA) in the beads within this product was produced and manufactured exclusively from bovine plasma
Note sourced in the United States. No ruminant protein or other animal protein was fed to the animals; the animals passed ante- and post-
mortem testing. During processing, there was no commingling of the material with other animal materials.

7 Storage and Handling

• Store the HIV-1 VL Assay cartridges at 2–28 °C.
• Do not open the cartridge lid until you are ready to perform the test.
• Use cartridge within four hours after opening the cartridge lid.
• Do not use a cartridge that has leaked.
8 Materials Required but Not Provided
• GeneXpert Dx System or GeneXpert Infinity System (catalog number varies by configuration): GeneXpert instrument,
computer with proprietary GeneXpert Software Version 4.6a, Xpertise 6.2a or higher, barcode scanner, and operator manual
• Printer: If a printer is needed, contact Cepheid Technical Support to arrange for the purchase of a recommended printer.
• Bleach

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9 Warnings and Precautions

• Treat all biological specimens, including used cartridges, as if capable of transmitting infectious agents. Because it is often
impossible to know which might be infectious, all biological specimens should be treated with standard precautions.
Guidelines for specimen handling are available from the U.S. Centers for Disease Control and Prevention16 and the Clinical
and Laboratory Standards Institute.17
• Follow your institution's safety procedures for working with chemicals and handling biological samples.
• Consult your institution’s environmental waste personnel on proper disposal of used cartridges and unused reagents. Check
state, territorial, or local regulations as they may differ from national disposal regulations. This material may exhibit
characteristics of hazardous waste requiring specific disposal requirements. Institutions should check their country
hazardous waste disposal requirements.
• Do not substitute HIV-1 VL Assay reagents with other reagents.
• Do not open the HIV-1 VL Assay cartridge lid until you are ready to add the plasma specimen.
• Do not use a cartridge that has been dropped after removing it from the packaging.
• Do not shake the cartridge. Shaking or dropping the cartridge after opening the lid may yield invalid results.
• Do not place the sample ID label on the cartridge lid or on the barcode label.
• Each single-use HIV-1 VL Assay cartridge is used to process one specimen. Do not reuse spent cartridges.
• Do not use a cartridge that has a damaged reaction tube.
• Single-use disposable pipette is used to transfer one specimen. Do not reuse disposable pipettes.
• Wear clean lab coats and gloves. Change gloves between processing each sample.
• In the event of contamination of the work area or equipment with samples or controls, thoroughly clean the contaminated
area with a solution of 1:10 dilution of household chlorine bleach and then 70% ethanol. Wipe work surfaces dry completely
before proceeding.
• Store the Xpert® HIV-1 Viral Load kit at 2–28 °C.
• Lysis Reagent contains guanidinium thiocyanate, which is toxic if swallowed (H302), irritating to eyes and skin (H316,
H320), may cause damage to organs through prolonged or repeated exposures (H373), and is harmful to aquatic life (H402).
See Regulation EC 1272/2008 (EU CLP).
10 Specimen Collection, Transport, and Storage
Whole blood should be collected in EDTA, EDTA-PPT, or ACD collection tubes and centrifuged to separate the plasma and red
blood cells per the manufacturer's instructions.
• A minimum of 1 mL plasma is required for the HIV-1 VL Assay. If using the transfer pipette included in the kit, a minimum
of 1.2 mL plasma is required. Alternatively, if using a precision pipette, a minimum of 1 mL plasma is required.

+15
+30 • Whole blood may be held at 15–30 °C for up to 8 hours or at 2–8 °C for up to 72 hours, prior to preparing and testing the
°C
specimen.
+8
+2
°C
• After centrifugation, plasma may be held at 15–30 °C for up to 24 hours or at 2–8 °C for up to 6 days, prior to testing.
-70
-18
• Plasma specimens are stable frozen (≤ -18 °C and ≤ -70 °C) for six weeks.
°C
• Plasma specimens are stable up to three freeze/thaw cycles.
• Plasma specimens must be thawed and equilibrated to room temperature prior to transfer to cartridge.
11 Procedure
11.1 Preparing the Specimen
+20
+35
°C
1. If using frozen specimens, place the specimens at room temperature 20–35 °C until completely thawed and equibrate to
room temperature before use.
+2
+8
°C
2. Plasma samples stored in 2–8 °C should be removed from the refrigerator and equilibrated to room temperature before use.
3. Vortex plasma for 15 seconds before use. If the specimen is cloudy, clarify by a quick spin.

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11.2 Preparing the Cartridge

Important Start the test within four hours of adding the sample to the cartridge.

Loading less than 1 mL plasma into the cartridge will trigger an insufficient volume error (ERROR 2097), preventing the instrument
from running the sample.
Note
Allow samples to come to room temperature prior to loading plasma into the cartridge.

1. Wear protective disposable gloves.

2. Inspect the test cartridge for damage. If damaged, do not use it.
3. Open the lid of the test cartridge.

Note There is a thin plastic film that covers the inner ring of 13 ports of the test cartridge. This film should not be removed.

• Option 1: If using the transfer pipette included in the kit (Figure 1), fill to just below the bulb but above the line to
transfer at least 1 mL plasma from the collection tube into the sample chamber of the test cartridge (Figure 2). Do
NOT pour the specimen into the chamber!
• Option 2: If using an automatic pipette, transfer at least 1 mL of plasma into the sample chamber of the test cartridge
(Figure 2). Do NOT pour the specimen into the chamber!

Bulb

Fill specimen to just below

the bulb and above the
mark on the pipette

Figure 1. HIV-1 VL Assay Transfer Pipette

Sample Chamber
(Large Opening)

Figure 2. Xpert HIV-1 VL Cartridge (Top View)

4. Close the cartridge lid.
5. Load the cartridge into the GeneXpert Dx instrument or Infinity system.

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11.3 Starting the Test

Important Before starting the test, make sure the HIV-1 VL Assay Definition File (ADF) is imported into the software.

This section lists the basic steps for running the test. For detailed instructions, see the GeneXpert Dx System Operator Manual or
the GeneXpert Infinity System Operator Manual, depending on the model of instrument that is being used.
1. Turn on the GeneXpert instrument:
• If using the GeneXpert Dx instrument, first turn on the instrument and then turn on the computer. The GeneXpert
software will launch automatically. If it doesn't, double-click the GeneXpert Dx software shortcut icon on the
Windows® desktop.
or
• If using the GeneXpert Infinity instrument, power up the instrument. The GeneXpert software will launch
automatically. If it doesn't, double-click the Xpertise software shortcut icon on the Windows® desktop.
2. Log on to the GeneXpert Instrument System software using your user name and password.
3. In the GeneXpert System window, click Create Test (GeneXpert Dx) or Orders and Order Test (Infinity).
4. Scan in the Patient ID (optional). If typing the Patient ID, make sure the Patient ID is typed correctly. The Patient ID is
associated with the test results and is shown in the View Results window.
5. Scan or type in the Sample ID. If typing the Sample ID, make sure the Sample ID is typed correctly. The Sample ID is
associated with the test results and is shown in the View Results window and all reports. The Scan Cartridge dialog box
appears.
6. Scan the barcode on the Xpert® HIV-1 Viral Load cartridge. The Create Test window appears. Using the barcode
information, the software automatically fills the boxes for the following fields: Select Assay, Reagent Lot ID, Cartridge SN,
and Expiration Date.
7. Click Start Test (GeneXpert Dx) or Submit (Infinity). Enter your password, if requested.
8. For the GeneXpert Infinity System, place the cartridge on the conveyor belt. The cartridge will be automatically loaded, the
test will run, and the used cartridge will be placed into the waste container.
or
For the GeneXpert Dx Instrument:
A. Open the instrument module door with the blinking green light and load the cartridge.
B. Close the door. The test starts and the green light stops blinking. When the test is finished, the light turns off.
C. Wait until the system releases the door lock before opening the module door and removing the cartridge.
D. The used cartridges should be disposed in the appropriate specimen waste containers according to your institution’s
standard practices.
12 Viewing and Printing Results
This section lists the basic steps for viewing and printing results. For more detailed instructions on how to view and print the
results, see the GeneXpert Dx System Operator Manual or the GeneXpert Infinity System Operator Manual, depending on the
instrument used.
1. Click the View Results icon to view results.
2. Upon completion of the test, click the Report button of the View Results window to view and/or generate a PDF report file.
13 Quality Control
Each test includes a Sample Volume Adequacy (SVA) control, Internal Quantitative Standard High and Low (IQS-H and IQS-L),
which is also a Sample Processing Control (SPC), and a Probe Check Control (PCC).
• Sample Volume Adequacy (SVA): Ensures that the sample was correctly added to the cartridge. The SVA verifies that the
correct in-volume of sample has been added in the sample chamber. The SVA passes if it meets the validated acceptance
criteria. If the SVA does not pass, an ERROR 2096 will display if there is no sample or an ERROR 2097 if there is not
enough sample. The system will prevent the user from resuming the test.

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• Internal Quantitative Standard High and Low (IQS-H and IQS-L): IQS-H and IQS-L are two Armored RNAs® non-
specific to HIV in the form of a dry bead that goes through the whole GX process. The IQS-H and IQS-L are standards
calibrated against the WHO 3rd International Standard. They are used for quantification by using lot specific parameters for
the calculation of HIV-1 RNA concentration in the sample. Additionally, IQS-H and IQS-L detect specimen-associated
inhibition of the RT-PCR reaction. The IQS-H and IQS-L pass if they meet the validated acceptance criteria.
• Probe Check Control (PCC): Before the start of the PCR reaction, the GeneXpert Instrument System measures the
fluorescence signal from the probes to monitor bead rehydration, reaction tube filling, probe integrity, and dye stability. The
PCC passes if it meets the assigned acceptance criteria.
• External Controls: External controls, not available in the kit, should be used in accordance with local and state accrediting
organizations’ requirements as applicable.
14 Interpretation of Results
The results are interpreted automatically by the GeneXpert Instrument System from measured fluorescent signals and embedded
calculation algorithms and are clearly shown in the View Results window (Figure 3 and Figure 4). Possible results are shown in
Table 1.

Table 1. Xpert® HIV-1 Viral Load Results and Interpretation

Result Interpretation
HIV-1 DETECTED HIV-1 RNA is detected at XX copies/mL.
XX copies/mL • HIV-1 RNA has quantitative value within the analytical measurement range.
See Figure 3. • IQS-H and IQS-L: PASS.
• Probe Check: PASS; all probe check results pass.
HIV-1 DETECTED HIV-1 RNA is detected above the analytical measurement range.
7 • IQS-H and IQS-L: PASS.
> 1 × 10 copies/mL
• Probe Check: PASS; all probe check results pass.
HIV-1 DETECTED HIV-1 RNA is detected below the analytical measurement range.
< 40 copies/mL • IQS-H and IQS-L: PASS.
• Probe Check: PASS; all probe check results pass.
HIV-1 NOT DETECTED HIV-1 RNA is not detected.
See Figure 4. • IQS-H and IQS-L: PASS.
• Probe Check: PASS; all probe check results pass.
INVALID Presence or absence of HIV-1 RNA cannot be determined. Repeat test according to the
instructions in Section 15.2, Retest Procedure.
• IQS-H and/or IQS-L: FAIL; Cycle thresholds (Cts) are not within valid range.
• Probe Check: PASS; all probe check results pass.
ERROR Presence or absence of HIV-1 RNA cannot be determined. Repeat test according to the
instructions in Section 15.2, Retest Procedure.
• Probe Check: FAIL*; all or one of the probe check results fail.
NO RESULT Presence or absence of HIV-1 RNA cannot be determined. Repeat test according to the
instructions in Section 15.2, Retest Procedure. A NO RESULT indicates that insufficient data
were collected. For example, the operator stopped a test that was in progress.

Results can be converted from copies/mL to IU/mL within the software. Please see the GeneXpert Dx System Operator Manual or
Note the GeneXpert Infinity System Operator Manual for instructions on how to change this setting.
The conversion factor for the HIV-1 VL Assay is 1 copy= 1.72 IU.

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Figure 3. HIV-1 Detected

Figure 4. HIV-1 Not Detected

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15 Retests
15.1 Reasons to Repeat the Assay
If any of the test results mentioned below occur, repeat the test according to the instructions in Section 15.2, Retest Procedure.
• An INVALID result indicates one or more of the following:
• The IQS-H and/or IQS-L Cts are not within valid range.
• The sample was not properly processed or PCR was inhibited.
• An ERROR result indicates that the assay was aborted. Possible causes include: insufficient volume of sample was added, the
reaction tube was filled improperly, a reagent probe integrity problem was detected, or the maximum pressure limit was
exceeded.
• A NO RESULT indicates that insufficient data were collected. For example, the operator stopped a test that was in progress,
or a power failure occurred.
15.2 Retest Procedure
For retest of an INVALID, ERROR, or NO RESULT result, use a new cartridge (do not re-use the cartridge).
1. Remove a new cartridge from the kit.
2. See Section 11, Procedure, including Section 11.2, Preparing the Cartridge, and Section 11.3, Starting the Test.
16 Limitations
• Good laboratory practices and changing gloves between handling specimens are recommended to avoid contamination of
specimens or reagents.

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17 Performance Characteristics
17.1 Limit of Detection
The limit of detection (LOD) of the HIV-1 VL Assay was determined by testing five different dilutions prepared from two
different HIV-1 subtype B reference standards, one cell culture stock, and two clinical specimens diluted in HIV-1 negative
EDTA plasma. The HIV-1 subtype B materials used in the LOD study included Viral Quality Assurance Laboratory (VQA)
reference material of the AIDS Clinical Trial Group, WHO 3rd International standard NIBSC code 10/152, cell culture stock
isolate BK132 and two clinical specimens. The assignment of the nominal concentration of the cell culture stock material and
clinical specimens was performed by the Abbott RealTime HIV-1 Assay. The limit of detection was determined for three reagent
lots and a total of 72 replicates per level. The evaluation was performed according to CLSI guideline E17-A2.18 The HIV-1
RNA concentration that can be detected with a positivity rate of greater than 95% was determined by Probit regression analysis.
The results for the individual lots and specimens are shown in Table 2. The maximum/highest observed LOD with Probit
analysis for HIV-1 subtype B in EDTA plasma was 32.0 cp/mL (95% CI 24.7-39.3). The LOD for the VQA reference material
was confirmed in ACD plasma using one reagent lot. The LOD estimate for the HIV-1 subtype B VQA specimen in ACD
plasma was 15.8 cp/mL (95% CI 12.1-19.5).

Table 2. HIV-1 VL Assay LOD Estimates with Probit Regression and 95% Upper and Lower Confidence
Intervals for HIV-1 Subtype B Specimens in EDTA Plasma

LoD
Specimen Lot (cp/mL) 95% CI
Lot 1 21.1 16.1–26.0
WHO Lot 2 14.3 11.2–17.5
Lot 3 19.0 14.3–23.7
Lot 1 15.5 12.5–18.6
VQA Lot 2 14.0 11.2–16.7
Lot 3 16.3 13.0–19.5
Lot 1 24.0 18.1–29.9
Clinical
Lot 2 25.5 19.5–31.5
Specimen 1
Lot 3 23.1 17.5–28.7
Lot 1 20.3 15.8–24.7
Clinical
Lot 2 15.4 12.0–18.7
Specimen 2
Lot 3 28.5 21.3–35.7
Lot 1 18.8 14.6–23.1
Cell Culture
Lot 2 20.0 15.6–24.4
Specimen
Lot 3 32.0 24.7–39.3

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Hit rate analysis shows a positivity rate of >95% at 40 cp/mL for all for HIV-1 subtype B materials tested as shown in Table 3.
The LOD for the HIV-1 VL Assay is determined to be 40 cp/mL for HIV-1 subtype B in EDTA and ACD plasma.

Table 3. HIV-1 VL Assay LOD for HIV-1 Subtype B Specimens in EDTA Plasma

Nominal
concentration No. No. Positivity
Specimen (cp/mL) Replicates Positives Rate (%)
1 72 10 14
2.5 72 18 25
5 72 40 56
WHO
10 72 55 76
20 72 65 90
40 72 72 100
1 72 5 7
2.5 72 20 28
5 72 30 42
VQA 7.5 72 50 69
10 72 61 85
20 72 67 93
40 72 72 100
1 72 11 15
2.5 72 20 28
Clinical 5 72 38 53
Specimen
1 10 72 49 68
20 72 69 96
40 72 69 96
1 72 8 11
2.5 72 17 24
Clinical 5 71 27 38
Specimen
2 10 72 47 65
20 72 62 86
40 72 72 100
1 72 4 6
2.5 72 17 24
Cell 5 72 30 42
Culture
Specimen 10 72 46 64
20 72 64 89
40 72 70 97

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In addition, dilutions of cell culture stocks or clinical specimens representing the HIV-1 group M subtypes A, C-D, F-H, J, K,
CRF- A/B, CRF-A/E, CRF-A/G, group O, and group N in negative human EDTA plasma were analyzed with one reagent lot and
24 replicates per concentration level. The assignment of the nominal concentration of the cell culture stocks and clinical
specimens was determined by Abbott® RealTime HIV-1 assay. Hit rate analysis shows a positivity of > 95% for all subtypes and
groups at 40 cp/mL as shown in Table 4.

Table 4. HIV-1 VL Assay LOD Hit Rate Analysis for HIV-1 non- B Subtype Specimens in EDTA Plasma

Lowest Concentration Level

Subtype >95% Hit Rate (cp/mL) Hit Rate (%)
A 20 96
C 40 100
D 20 100
F 40 100
G 40 96
H 20 96
J 20 100
K 40 96
CRF A/B 20 100
CRF A/E 20 96
CRF A/G 40 96
Group N 10 100
Group O 20 100
Group O 20 100
Group O 10 100

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17.2 Limit of Quantitation

The LoQ is defined as the lowest concentration of HIV-1 RNA that is determined with acceptable precision and trueness and
determined using total analytical error (TAE). The total TAE was calculated using estimates determined through analysis of data
from LOD study (WHO and VQA standards) and the Precision/Reproducibility study according to CLSI guideline E17-A2.18
The TAE for the dilutions that had an observed concentration at or near the assay limit of detection 40 cp/mL (1.60 log10) are
presented in Table 5. TAE was estimated by two different methods. The results of the TAE analysis demonstrate that the HIV-1
VL Assay can determine 40 cp/mL(1.60 log10) with an acceptable trueness and precision i.e the LOQ of the HIV-1 VL Assay is
40 cp/mL.

Table 5. HIV-1 VL Total Analytical Error (TAE) Estimates Log cp/mL

Concentration TAEa
(log cp/mL) Absolute TAEb
Specimen DL Total Bias + SQRT (2)
(Study) Lot N Expected Observed Bias SD (2xSD) x (2xSD)

Reference DL6 72 2.00 1.96 0.04 0.19 0.43 0.55

Material DL7 71 2.00 1.91 0.09 0.19 0.46 0.53
(Precision) DL8 72 2.00 1.92 0.08 0.21 0.51 0.60

Reference DL6 70 1.60 1.56 0.04 0.22 0.48 0.62

Material DL7 71 1.60 1.53 0.08 0.28 0.64 0.80
(Precision) DL8 71 1.60 1.54 0.06 0.22 0.50 0.62
DL6 24 1.60 1.53 0.07 0.23 0.52 0.65
WHO (LoD) DL7 24 1.60 1.39 0.21 0.24 0.68 0.67
DL8 24 1.60 1.49 0.11 0.19 0.48 0.52
DL6 24 1.60 1.61 0.00 0.18 0.37 0.51
VQA (LoD) DL7 24 1.60 1.54 0.06 0.26 0.58 0.74
DL8 24 1.60 1.58 0.02 0.26 0.54 0.73
a. TAE calculated according to the Westgard model in CLSI EP17-A2 (Section 6.2).
b. TAE based upon the difference between two measurements approach.

The results of the TAE analysis demonstrate that the HIV-1 VL Assay can determine 40 cp/mL (1.60 log10) with an acceptable
trueness and precision.

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17.3 Precision/Reproducibility
The precision/reproducibility of the HIV-1 VL Assay was determined by analysis of parallel dilutions of HIV-1 reference
material (HIV-1 subtype B) in HIV-1 negative EDTA plasma. The reference material used was calibrated to the WHO
International Standard NIBSC, 3rd HIV-1 International Standard (10/152). The study was a two-site, blinded, comparative study
using a seven-member panel of HIV-1 reference material in HIV-1 negative EDTA plasma with RNA concentrations that span
the HIV-1 VL Assay quantitation range. Two operators at each of the two study sites tested one panel of twenty-one samples
once per day over six testing days. One site used an Infinity-80 instrument and the other site used GeneXpert Dx instruments.
Three lots of HIV-1 VL Assay reagents were used for the study. Precision/Reproducibility was evaluated in accordance with
“Evaluation of Precision Performance of Clinical Chemistry Devices; Approved Guideline” CLSI document EP5-A2.20 The
precision results for each regent lot and three reagent lots combined are shown in Table 6.

Table 6. HIV-1 VL Assay Precision per Lot and Total of Three Lots

Total Precision
Total Precision per Lot 3 Lots
Expected HIV-1 RNA
Concentration Lot 1 Lot 2 Lot 3 Total
a b a b a b a
(log10 cp/mL) SD CV SD CV SD CV SD CVb
1.60 0.24 58.6% 0.29 73.6% 0.23 57.6% 0.25 62.5%
2.00 0.20 48.8% 0.20 47.3% 0.22 53.1% 0.20 49.1%
3.00 0.10 22.6% 0.08 18.2% 0.10 22.6% 0.09 20.5%
4.00 0.06 13.7% 0.07 17.3% 0.09 19.8% 0.07 17.1%
5.00 0.06 13.8% 0.07 16.3% 0.08 17.7% 0.08 17.8%
6.00 0.05 12.4% 0.07 15.3% 0.07 16.2% 0.08 19.3%
7.00 0.06 14.3% 0.07 15.5% 0.09 21.5% 0.10 22.6%
a. Total SD in log10.
b. "CV" is lognormal CV, as obtained using the formula:

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The reproducibility of the HIV-1 VL Assay was evaluated by using nested ANOVA with terms for Site/Instrument, Lot, Day,
Operator/Run, and Within-Run. The standard deviation and the percentage of variability due to each component of the log10
HIV-1 transformed concentrations were calculated (see Table 7).

Table 7. HIV-1 VL Assay Contribution to Total Variance and Total Precision

HIV-1 RNA Concentration Total

(log10 cp/mL) Contribution to Total Variance SD (CV%) Precision
Site Lot Day Operator/Run Within-Run Total
Actual
a
Expected (Average) N SD (%) SD (%) SD (%) SD (%) SD (%) SD CVb
1.60 1.54 212 0.00 0.0% 0.00 0.0% 0.00 0.0% 0.09 11.7% 0.23 88.3% 0.25 62.5%
2.00 1.93 215 0.00 0.0% 0.00 0.0% 0.00 0.0% 0.04 4.8% 0.20 95.2% 0.20 49.1%
3.00 2.98 215 0.01 0.9% 0.01 1.2% 0.00 0.0% 0.01 2.6% 0.09 95.3% 0.09 20.5%
4.00 3.98 214 0.00 0.0% 0.01 3.5% 0.01 1.7% 0.02 9.1% 0.07 85.7% 0.07 17.1%
5.00 4.99 213 0.00 0.0% 0.04 21.8% 0.00 0.0% 0.03 15.0% 0.06 63.2% 0.08 17.8%
6.00 5.96 215 0.00 0.0% 0.05 42.1% 0.02 4.4% 0.02 6.9% 0.06 46.7% 0.08 19.3%
7.00 6.94 213 0.00 0.0% 0.07 45.3% 0.01 0.9% 0.02 5.3% 0.07 48.5% 0.10 22.6%

a. Number of valid replicates within assay range

b. "CV" is lognormal CV, as obtained using the formula:

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17.4 Linear Range

The linear range of the HIV-1 VL Assay was determined by analysis of a nine member panel from 30 (1.48 log10) to
1 x 107 (7 log10) cp/mL prepared by parallel dilutions of HIV-1 reference material (HIV-1 subtype B) in HIV-1 negative EDTA
plasma. The reference material used was calibrated to the WHO International Standard NIBSC, 3rd HIV-1 International
Standard (10/152). Two operators tested the panel in replicates of three on three testing days using one kit lot. In addition, the
same panel was tested in replicates of three on one day of testing using two additional kit lots resulting in a total 30 replicates
per panel member. The linearity analysis was performed according to CLSI guideline EP06-A.19 The combined results for all
three lots are shown in Figure 5. The HIV-1 VL Assay is linear within a range 30-1 x 107cp/mL with a R2 value of 0,994.

Figure 5. Linearity for the HIV-1 VL Assay

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17.5 Analytical Reactivity (Inclusivity)

The analytical reactivity of the HIV-1 VL Assay was evaluated by testing cell culture supernatant representative of the HIV-1
Group M subtypes A-D, F-H, CRF A/G, and A/E; Group N; and Group O. The assignment of nominal concentrations to the cell
culture supernatants was performed by Abbott HIV-1 RealTime assay. Each cell culture supernatants was diluted to
concentrations of 1 x 102, 1 x 104 and 1 x 106 cp/mL in HIV-1 negative EDTA plasma. Each concentration was tested in
replicates of six on one day using one HIV-1 VL Assay kit lot. The mean log10 concentrations obtained with HIV-1 VL Assay
for all subtypes and groups were compared to nominal log10 concentrations. The results presented in Figure 6 shows equivalent
performance for all tested representatives of HIV-1 Group M subtypes and Group O. Mean log10 results for all tested subtypes
and group O were within +/-0.5 log10 of the assigned input concentration.

Figure 6. Inclusivity for the HIV-1 VL Assay

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17.6 Analytical Specificity (Exclusivity)

The analytical specificity of the HIV-1 VL Assay was evaluated by adding cultured organism at 5 x 104 particles or cp/mL input
concentration into HIV-1 negative EDTA plasma and in plasma that contained 1000 cp/mL HIV-1 reference material (HIV-1
subtype B). Tested organisms are listed in Table 8.

Table 8. Analytical Specificity Organisms

Human Immunodeficiency virus 2

Human T-cell lymphotropic virus 1
Human T-cell lymphotropic virus 2
Candida albicans
Cytomegalovirus
Epstein-Barr virus
Hepatitis A virus
Hepatitis B virus
Hepatitis C virus
Herpes simplex virus 1
Herpes simplex virus 2
Human herpes virus 6
Influenza A
Staphylococcus aureus

None of the organisms tested showed cross reactivity and all HIV-1 positive replicates resulted in a titer within ± 0.5 log of the
HIV-1 positive control when tested using the HIV-1 VL Assay.

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17.7 Potentially Interfering Substances

The susceptibility of the HIV-1 VL Assay to interference by elevated levels of endogenous substances, by drugs prescribed to
HIV-1 infected patients, and autoimmune disease markers was evaluated. HIV-1 negative EDTA plasma and plasma that
contained 1000 cp/mL HIV-1 reference material (HIV-1 subtype B) were tested.
Elevated levels of the endogenous substances listed in Table 9 were shown to not interfere with the quantification of the HIV-1
VL Assay or impact the assay specificity.

Table 9. Endogenous Substances and Concentration Tested

Substance Tested Concentration

Albumin 9 g/dL
Bilirubin 20 mg/dL
Hemoglobin 500 mg/dL
Human DNA 0.4 mg/dL
Triglycerides 3000 mg/dL

The drug components as presented in Table 10 were shown not to interfere with the quantification of the HIV-1 VL Assay or
impact the assay specificity when tested at three times peak level concentration in five drug pools.

Table 10. Drug Pools Tested

Pool Drugs
Control n/a
1 Zidovudine, Saquinavir, Ritonavir, Clarithromycin
2 Abacavir sulfate, Peginterferon 2b, Ribavirin
3 Tenofovir disoproxil fumarate, Lamivudine, (3TC), Indinavir sulfate, Ganciclovir,
Valganciclovir HCl, Acyclovir, Raltegravir
4 Stavudine ( d4T), Efavirenz, Lopinavir/Ritonavir, Enfuvirtide (T-20), Ciprofloxacin
5 Nevirapine, Nelfinavir mesylate, Azithromycin, Valacyclovir HCl
6 Fosamprenavir Calcium, Interferon alfa-2b

Testing of specimens from five individuals of each autoimmune disease marker; systemic lupus erythematous (SLE), anti-
nuclear (ANA) or rheumatoid factor (RF) showed no interference using the HIV-1 VL Assay.

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17.8 Anti-coagulant Equivalence (EDTA, PPT-EDTA, and ACD)

For each anti-coagulant EDTA, PPT-EDTA, and ACD, specimens from 25 matched HIV-1 positive individuals and 25 matched
HIV-1 negative specimens were collected and tested using one kit lot of the HIV-1 VL Assay.
As shown in Figure 7 and Figure 8 equivalent performance of the HIV-1 VL Assay was shown for EDTA versus ACD anti-
coagulant and EDTA versus PPT-EDTA anti-coagulant. All HIV-1 positive specimens collected in ACD or PPT-EDTA media
produced concentrations of HIV-1 RNA within ±0.5 log10 cp/mL of the HIV-1 positive specimen collected in EDTA media
when tested using the HIV-1 VL Assay. All 25 matched HIV-1 negative specimens were not detected by the assay.

Figure 7. Scatterplot of Log cp/mL PPT-EDTA versus Log cp/mL EDTA

Figure 8. Scatterplot of Log cp/mL PPT-EDTA versus Log cp/mL EDTA

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18 Performance Characteristics – Clinical Performance

18.1 Specificity
The specificity of the HIV-1 VL Assay was evaluated using 109 EDTA plasma specimens from HIV-1 negative blood donors.
None of the 109 specimens tested were detected by the HIV-1 VL Assay equating to 100% specificity (95% CI = 96.7–100.0).
18.2 Method Correlation
A multi-site study was conducted to evaluate the performance of the HIV-1 VL Assay relative to a comparator method using
fresh and frozen human plasma specimens collected from HIV-1 infected individuals. Of the 724 eligible specimens, each from
unique individuals, 519 (71.8%) were collected from male subjects. The average age was 44.5 ± 11.3 years with an age range of
18 to 83 years.
Of the 724 specimens, 390 were within the quantitation range of both assays including 47 HIV-1 Group M non-B subtypes
including A-like, C and C-like, D, F, G, H, J, AE, AG and various other circulating recombinant forms (CRFs). The Deming
regression shows very good correlation between the HIV-1 VL Assay and the comparator method with a slope of 1.0589 and
intercept of 0.1771. The R2 was 0.9696.

* HIV-1 Group M Non-B subtypes are represented as triangles.

Figure 9. Performance of the HIV-1 VL Assay Relative to a Comparator Method

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19 References
1. Barre-Sinoussi F, Chermann JC, Rey F, et al. Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired
immune deficiency syndrome (AIDS). Science 1983;220:868–871.
2. Popovic M, Sarngadharan MG, Read E, et al. Detection, isolation and continuous production of cytopathic retroviruses
(HTLV-I) from patients with AIDS and pre-AIDS. Science 1984;224:497–500.
3. Gallo RC, Salahuddin SZ, Popovic M, et al. Frequent detection and isolation of cytopathic retroviruses (HTLV-I) from
patients with AIDS and at risk for AIDS. Science 1984;224:500–503.
4. Curran JW, Jaffe HW, Hardy AM, et al. Epidemiology of HIV infection and AIDS in the United States. Science
1988;239:610–616.
5. Schochetman G, George JR, editors. AIDS testing: a comprehensive guide to technical, medical, social, legal, and
management issues. 2nd ed. New York: NY Springer-Verlag; 1994.
6. Nduati R, John G, Mbori-Ngacha D, et al. Effect of breastfeeding and formula feeding on transmission of HIV-1: a
randomized clinical trial. Journal of the American Medical Association 2000;283:1167–1174.
7. Perelson AS, Neumann AU, Markowitz M, Leonard JM, Ho DD. HIV-1 dynamics in vivo: virion clearance rate, infected cell
life-span, and viral generation time. Science 1996; 271:1582–1586.
8. Wei X, Ghosh SK, Taylor ME, Johnson VA, Emini EA, Deutsch P, Lifson JD, Bonhoeffer S, Nowak MA, Hahn BH, et al.
Viral dynamics in human immunodeficiency virus type 1 infection. Nature 1995; 373:117–122.
9. Ho DD, Neumann AU, Perelson AS, Chen W, Leonard JM, Markowitz M. Rapid turnover of plasma virions and CD4
lymphocytes in HIV-1 infection. Nature 1995; 373:123–126.
10. Katzenstein DA, Hammer SM, Hughes MD, Gundacker H, Jackson JB, Fiscus S, Rasheed S, Elbeik T, Reichman R, Japour
A, Merigan TC, Hirsch MS. The relation of virologic and immunologic markers to clinical outcomes after nucleoside
therapy in HIV-infected adults with 200 to 500 CD4 cells per cubic millimeter. AIDS Clinical Trials Group Study 175
Virology Study Team. N Engl J Med 1996; 335:1091–1098.
11. Mellors JW, Munoz A, Giorgi JV, Margolick JB, Tassoni CJ, Gupta P, Kingsley LA, Todd JA, Saah AJ, Detels R, Phair JP,
Rinaldo CR, Jr. Plasma viral load and CD4+ lymphocytes as prognostic markers of HIV-1 infection. Ann Intern Med 1997;
126:946–954.
12. Mellors JW, Rinaldo CR, Jr., Gupta P, White RM, Todd JA, Kingsley LA. Prognosis in HIV-1 infection predicted by the
quantity of virus in plasma. Science 1996; 272:1167–1170.
13. O'Brien WA, Hartigan PM, Martin D, Esinhart J, Hill A, Benoit S, Rubin M, Simberkoff MS, Hamilton JD. Changes in
plasma HIV-1 RNA and CD4+ lymphocyte counts and the risk of progression to AIDS. Veterans Affairs Cooperative Study
Group on AIDS. N Engl J Med 1996; 334:426–431.
14. Ruiz L, Romeu J, Clotet B, Balague M, Cabrera C, Sirera G, Ibanez A, Martinez-Picado J, Raventos A, Tural C, Segura A,
Foz M. Quantitative HIV-1 RNA as a marker of clinical stability and survival in a cohort of 302 patients with a mean CD4
cell count of 300 x 10(6)/l. Aids 1996; 10:F39–44.
15. Saag MS, Holodniy M, Kuritzkes DR, O'Brien WA, Coombs R, Poscher ME, Jacobsen DM, Shaw GM, Richman DD,
Volberding PA. HIV viral load markers in clinical practice. Nat Med 1996; 2:625–629.
16. Centers for Disease Control and Prevention. Biosafety in Microbiological and Biomedical Laboratories. Richmond JY and
McKinney RW (eds) (1993). HHS Publication number (CDC) 93-8395.
17. Clinical and Laboratory Standards Institute. Protection of Laboratory Workers from Occupationally Acquired Infections;
Approved Guideline. Document M29 (refer to latest edition).
18. Clinical and Laboratory Standards Institute. Evaluation of Detection Capability for Clinical Laboratory Measurement
Procedures; Approved Guideline. Document EP17-A2 (Second Edition). Wayne, PA: Clinical Laboratory Standards
Institute; 2012.
19. Clinical and Laboratory Standards Institute. Evaluation of the Linearity of Quantitative Measurement Procedures: A
Statistical Approach; Approved Guideline. NCCLS document EP06-A [ISBN 1-56238-498-8]. NCCLS, 940 West Valley
Road, Suite 1400, Wayne, PA 19087-1898 USA, 2003.
20. Clinical and Laboratory Standards Institute. Evaluation of Precision Performance of Clinical Chemistry Devices; Approved
Guideline. Document EP5-A2.

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20 Cepheid Headquarters Locations

Corporate Headquarters European Headquarters

Cepheid Cepheid Europe SAS
904 Caribbean Drive Vira Solelh
Sunnyvale, CA 94089 81470 Maurens-Scopont
USA France
Telephone: +1 408.541.4191 Telephone: +33 563 825 300
Fax: +1 408.541.4192 Fax: +33 563 825 301
www.cepheid.com www.cepheidinternational.com

21 Technical Assistance
Before contacting Cepheid Technical Support, collect the following information:
• Product name
• Lot number
• Serial number of the instrument
• Error messages (if any)
• Software version and, if applicable, Computer Service Tag number

Region Telephone Email

US +1 888.838.3222 [email protected]
France +33 563 825 319 [email protected]
Germany +49 69 710 480 480 [email protected]
United Kingdom +44 3303 332 533 [email protected]
South Africa +27 861 22 76 35 [email protected]
Other European, Middle East and +33 563 825 319
[email protected]
African countries +971 4 253 3218
Australia, New Zealand +61 1800 107 884 [email protected]
Other countries not listed above +1 408.400.8495 [email protected]

Contact information for other Cepheid offices is available on our website at www.cepheidinternational.com under the SUPPORT
tab. Select the Contact Us option.

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22 Table of Symbols

Symbol Meaning

Catalog number

CE marking - European conformity

IVD In vitro diagnostic medical device

Do not reuse

Batch code

Consult instructions for use

Caution

Manufacturer

Contains sufficient for <n> tests

Control

Expiration date

°C Temperature limitation

Biological risks

Cepheid AB
Röntegenvägen 5
SE-171 54 Solna
Sweden

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