COVID-19 Diagnostic Tests Webinar Series...‒ E primers and probes are not specific for SARS-CoV-2...
Transcript of COVID-19 Diagnostic Tests Webinar Series...‒ E primers and probes are not specific for SARS-CoV-2...
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GeneXpert® Platform
COVID-19 Diagnostic Tests Webinar Series
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GeneXpert® System*
• Thermal and optical module(s)
• Computer System and GeneXpert Dx Software
• ADF (Assay Definition File)
• Barcode scanner
The GeneXpert® system package
US-IVD, CE-IVD In vitro diagnostic medical device
Cartridge
• Self-Contained
• Disposable
Recommended Accessories
• UPS/ Power generator (Backup)
• Surge protector
Optional Accessories
• Printer
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MTB/XDR
Xpress CT/NG#
Xpress GBS#
Xpress Multiplex Vaginal Panel
HIV-1 Qualitative XC#
HIV-1 Viral Load XC #
BCR-ABL Minor (p190)
AML
MRSA NxGSA Nasal CompleteMRSA/SA BCMRSA/SA SSTIC. difficile BT vanA/vanB for VRE Carba-RNorovirus
Xpress Strep AXpress Flu/RSVSARS-CoV-2^*MTB/RIF Ultra EVEbola^
CT/NG CTTrichomonasHPVGBSResistancePlus MG**
HBV Viral LoadHCV Viral LoadHCV VL FingerstickHIV-1 Qualitative HIV-1 Viral Load
Bladder CA DetectionBladder CA Monitor Breast CA STRAT4BCR-ABL Ultra FII & FV
Critical Infectious Diseases
Virology
Women’s & Sexual Health
Targeted Test Menu subject to revision, particularly in the 2022 section.
*CE-IVD pending submission and approval by regulatory body.
# Tests are updates/upgrades, and not included in the test count.
** FleXible Cartridge program in partnership with selected Trusted Reagent Manufacturers and not included in product count.
^EUA (Emergency Use Authorization)
HealthcareAssociated
Infections
Oncology & Genetics
Expanding on the Best-in-Class MDx Menu – CE-IVDAvailable Now
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2020–21* 2022+*
Carba-R NextGen#
GI Panel
Candida auris
Respiratory Panel
TB Host Response
MTB/RIF/INH Ultra
Tropical Fever
Breast cancer
Prostate cancer
Lung cancer
AML
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The Cepheid Solution – Xpert® Xpress SARS-CoV-2*
• Detection of SARS-CoV-2 RNA
‒ E and N2 targets
• On-board internal controls for each sample
‒ Probe Check Control (PCC)
‒ Sample Processing Control (SPC)
• Closed cartridge system minimizes risk of contamination
‒ The test is complete in approximately 45
minutes
• On-demand results
• Random access
*EUA: Emergency Use Authorization from U.S. FDA
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GeneXpert® Systems
• GeneXpert® Dx software version 4.7b or higher
• Xpertise software version 6.4b or higher
Test Kits
• US-EUA^: XPRSARS-COV2-10
Materials Required but not Provided
• Nasopharyngeal (NP), nasal, or mid-turbinate swabs collected by a healthcare provider and/or nasal wash/aspirate specimens in 3mL of UTM/VTM
• Personal Protective Equipment (PPE)
• 1:10 Bleach
• 70% ethanol or denatured ethanol
Optional
• Uninterruptible Power Supply /Surge Protector
• Printer
Xpert® Xpress SARS-CoV-2 Requirements
^For Emergency Use Authorization Only
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Xpert® Xpress SARS-CoV-2 Kit Contents
Cartridges contain chemically hazardous substances-please see Instructions For Use and Safety Data Sheet for more detailed information.
Kit of 10 cartridges
Kit of 50 cartridges
Xpert® Xpress SARS-CoV-2
Catalog Number US-EUA^: XPRSARS-COV2-10
Tests Per Kit 10
Kit CD
Assay Definition File (ADF)
Assay Import Instructions
Flyer- instructions to access on-line reference
materials including Instructions For Use
Disposable Transfer
Pipettes12
Storage 2- 28 °C
^For Emergency Use Authorization Only
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Specimen Collection
Specimen Types*:
Nasopharyngeal (NP), nasal, or mid-turbinate swabs
and/or nasal wash/aspirate specimens
Place into a VTM/UTM tube containing 3mL transport medium
to preserve and transport respiratory virus specimens
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Nasopharyngeal swab
Refer to the CDC Interim Guidelines for Collecting, Handling, and Testing Clinical Specimens from Persons Under Investigation (PUIs) for
Coronavirus Disease 2019 (COVID-19)
https://www.cdc.gov/coronavirus/2019-nCoV/lab/guidelines-clinical-specimens.html
*See package insert for details; specimen types may vary by system
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1. Transfer 600 μL of the sample into the 3 mL Viral Transport Medium tube.
2. Cap the tube.
Specimen Collection - Nasal Wash/Aspirate
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Specimen Collection - Nasopharyngeal Swab
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Specimen Collection - Nasal Swab
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Specimen Collection – Mid-Turbinate Swab
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Cartridge Preparation
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SARS-CoV-2 POSITIVE
The 2019 novel coronavirus (SARS-CoV-2) target
nucleic acids are detected.
• The SARS-CoV-2 signal for the N2 nucleic acid
target or signals for both nucleic acid targets (N2
and E) have a Ct within the valid range and
endpoint above the minimum setting
• SPC: NA; SPC is ignored because coronavirus
target amplification occurred
• Probe Check: PASS; all probe check results pass
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SARS-CoV-2 NEGATIVE
The 2019 novel coronavirus (SARS-CoV-2) target
nucleic acids are not detected.
• The SARS-CoV-2 signals for two nucleic acid
targets (N2 and E) do not have a Ct within the valid
range and endpoint above the minimum setting
• SPC: PASS; SPC has a Ct within the valid range
and endpoint above the minimum setting
• Probe Check: PASS; all probe check results pass
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SARS-CoV-2 PRESUMPTIVE POS
The 2019 novel coronavirus (SARS-CoV-2) nucleic
acids may be present.
Sample should be retested. For samples with a
repeated Presumptive Positive result, additional
confirmatory testing may be conducted, if it is
necessary to differentiate between SARS-CoV-2 and
SARS-CoV-1 or other Sarbecovirus currently unknown
to infect humans, for epidemiological purposes or
clinical management.
• The SARS-CoV-2 signal for only the E nucleic acid
target has a Ct within the valid range and endpoint
above the minimum setting
• SPC: NA; SPC is ignored because a target
amplification has occurred.
• Probe Check: PASS; all probe check results pass
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Analytical Sensitivity
For detailed information, refer to 302-3562 rev B Package Insert EUA GX SARS-COV2
Sensitivity
‒ The analytical sensitivity (LoD) was was performed using AccuPlex
SARS-CoV-2 Reference Material with testing performed on one reagent
lot in replicates of 35 prepared in pooled NP swab clinical matrix. The
claimed LoD for the assay is 250 copies/mL
‒ The analytical sensitivity (LoD) was was performed using Live SARS-
CoV-2 Virus with testing performed on one reagent lot in replicates of 22
prepared in pooled NP swab clinical matrix. The claimed LoD for the
assay is 0.0100 PFU/mL
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Analytical Specificity
Specificity
‒ 7 Microorganisms from the same genetic family and 32 high priority
organisms were tested: Three replicates of each isolate were spiked
into buffer and tested at a concentration of ≥107 CFU/mL
‒ No potential unintended cross reactivity with other organisms is
expected based on the in silico analysis.
‒ E primers and probes are not specific for SARS-CoV-2 and will detect Human and Bat
SARS-coronavirus.
For detailed information, refer to 302-3562 rev B Package Insert EUA GX SARS-COV2
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Biosafety, PPE and Disposal guidance
• Biological specimens, transfer devices, and used cartridges should be
considered capable of transmitting infectious agents requiring standard
precautions
• The biological specimens and used cartridges
should be disposed of per WHO [World Health Organization] guidelines
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- Many other vendors for quality control material are also available in addition to the one outlined above.
- External controls should be used in accordance with local, state accrediting organizations, as applicable
Vendor Description Configuration Storage
SeraCareAccuPlex™ SARS-CoV-2 Reference Material Kit
Catalog # 0505-0126
Positive Control 1.5mL 2-8°C or -20°C
Negative Control 1.5mL 2-8°C or -20°C
1. Open the cartridge lid.
2. Rapidly invert the external control tube 5 times.
3. Using a clean transfer pipette, transfer one draw of the external control sample into the large opening (Sample
Chamber) in the cartridge.
4. Close cartridge lid.
To minimize degradation of the control material, return any unused sample to the recommended storage conditions immediately after use.
Commercially Available External Controls
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Training and online resources
• Training materials
‒ Videos
‒ Cartridge preparation card
‒ Sample collection guidance
‒ Technical training presentation
• Online resources
‒ https://www.cepheid.com/coronavirus
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