GeneXpert Frequently Asked Questions (FQAs)

May 06, 2020

During the Webinar on "Leveraging GeneXpert for Coronavirus and Tuberculosis testing" held on 21 April 2020, we received an overwhelming amount of questions and comments.

Cepheid has kindly compiled a set of Frequently Asked Questions (FQAs) for your use. We realize there are many other questions that are related diagnostics, testing and the use of GeneXpert at country-level. The FQAs below do not answer all questions, and we would encourage you to take up any pending questions and post them in the COVID19 and TB Forum  for discussion with colleagues. 


Frequently asked questions regarding the Xpert® Xpress SARS-CoV-2 test relevant to countries served by the Global Access Team/ Emerging Markets


  • The science and clinical information on Coronavirus Disease- 2019 (COVID-19) and SARS-CoV-2 are rapidly changing and the material in this document is subject to change based on emerging data on COVID-19.
  • Cepheid is not a regulatory body or agency. Readers should consult their local regulatory body/ agency for most the recent recommendations.
  • Customers are advised to refer to Cepheid’s website for the Xpert Xpress SARS-CoV-2 test for updated information (

1. What is the limit of detection for this test and what is the sensitivity and specificity?

  • The LoD is 250 copies/mL and 0.01 plaque forming units (PFU)/mL.
  • The performance studies were performed on contrived specimens to determine accuracy. The test performed with 100% accuracy with contrived positive specimens at 2x LoD and higher and at 100% accuracy with negative specimens.
  • This is a qualitative test.

2. Presumptive positive results: What is the meaning of a “presumptive positive” result and what should I do if I get this result?

  • A “presumptive positive” result means that the SARS-CoV-2 nucleic acids may be present.
  • In areas known to have high rates of circulating SARS-CoV-2, a “presumptive positive” is likely to be a true positive.
  • A “presumptive positive” may also be positive for SARS-CoV-1 (virus responsible for SARS outbreak in 2003) or other Sarbecovirus currently unknown to infect humans.
  • The sample should be retested according to the Retest Procedure in Section 17.2 of the package insert. For samples with a repeated presumptive positive result, additional confirmatory testing may be conducted, if it is necessary to differentiate between SARS-CoV-2, SARS-CoV-1, or other Sarbecovirus for epidemiological purposes or clinical management.

3. Presumptive positive results: If I repeat the sample that was presumptive positive and the repeat result is negative, then what do I do?

  • If the sample is repeated and the repeat result is negative for SARS-CoV-2, consider the clinical picture of the patient, other laboratory data obtained, and the known rates of SARS-CoV-2 in your territory or region for decision making.
  • The person tested may be a true positive for SARS-CoV-2 and the negative result may be due to low viral load in the sample (as a result of specimen collection technique, or the patient is very early or very late in the disease course).
  • If needed and other platforms are available, consider testing using another platform.

4. Will the test be positive in asymptomatic patients or patients who have recovered from COVID-19?

  • The PCR test will only detect samples with SARS-CoV-2 present in levels above the limit of detection. Samples obtained during the asymptomatic period, early incubation or active phase may be positive for the virus and may be detected by this test. Peak viral loads are expected about 5 days after exposure but samples may be positive earlier than this period.
  • The test is not currently intended to be used for test of cure. Viral RNA may be detected even after completing therapy. Detection of viral RNA does not equal detection of infectious virus. However, some regulations require documentation of absence of virus over a certain period to remove patients from isolation or discharge from the hospital and this test would be able to provide information on lack of detection in samples. However, use of the test for this purpose is outside of its stated intended use.

5. What biosafety precautions do I need to use this test?

  • Cepheid agrees that biosafety level 2 (BSL-2) or a Class II Biological Safety Cabinet (BSC) should be used when available and when testing is conducted in a laboratory setting, as is currently recommended by several regulatory bodies.
  • Aligned with the current recommendations from the Centers for Disease Control and Prevention (CDC) in the United States and other regulatory agencies, Cepheid supports the use of this test outside of the BSL-2 laboratory and in point of care settings. These may be widely applicable in several low- and middle-income country (LMIC) settings.
  • Testing is likely to be performed safely in the absence of a BSC provided an appropriate risk assessment is made. Anyone collecting specimens from patients for testing should wear adequate personal protective equipment (PPE), and standard precautions should be used to provide a barrier between the specimen and personnel during specimen handling. Additionally, if procedures are likely to generate aerosols or droplets, additional precautions such as a surgical mask or face shield, or other physical barriers may also be needed.
  • Please consult with your local agency/ regulatory body for detailed recommendations. Recommendations may also be available from World Health Organization (WHO).

6. What sample reagent is included in the kit and does it inactivate the virus?

  • The SARS-CoV-2 test does NOT include sample reagent. The specimen must be obtained from the patient, placed into viral transport medium (VTM), and the VTM pipetted into the cartridge. Please see the package insert for details of this procedure. VTM does not inactivate virus. We do not specify which VTM is needed.

7. I perform Xpert TB testing at my location. Can I also test for SARS-CoV-2 with your cartridge?

  • The GeneXpert® instrument can also be used with the Xpress SARS-CoV-2 test with the relevant ADF. No software upgrade is required. Within the same instrument, different modules can run different tests at the same time (e.g. one module may be running Xpert MTB/RIF while another is running the Xpert Xpress SARS-CoV-2 test).

8. Since I need sputum samples to test for TB, can I use this for SARS-CoV-2 testing?

  • The acceptable samples types for SARS-CoV-2 testing are from the upper respiratory tract and are listed in the package insert. Sputum is not an acceptable sample type currently.
  • If you intended to test a patient for both TB and SARS-CoV-2, you will need to collect two separate specimens (sputum for TB testing and a sample from the upper respiratory tract for SARS-CoV-2 testing) and process each separately according to the respective package inserts.
  • There is currently no combined SARS-CoV-2+MTB test but Cepheid will take this development request under advisement.

9. How do I dispose of the SARS-CoV-2 cartridge?

  • Biological specimens, transfer devices, and used cartridges should be considered capable of transmitting infectious agents requiring standard precautions.
  • Follow your institution’s environmental waste procedures for proper disposal of used cartridges and unused reagents. These materials may exhibit characteristics of chemical hazardous waste requiring specific national or regional disposal procedures.
  • If national or regional regulations do not provide clear direction on proper disposal, biological specimens and used cartridges should be disposed per WHO medical waste handling and disposal guidelines

10. When will the Xpert Xpress SARS-CoV-2 test be available for procurement by HBDC countries?

  • The test has received the US FDA Emergency Use Authorization and is in the process for receiving CE-IVD and WHO Emergency Use Listing, which should take a few more weeks. Cepheid has begun manufacturing tests for the rest of the world and will be ramping up the production in the coming weeks and months to meet the global demand as much as possible.

11. What is the HBDC price for the Xpert Xpress SARS-CoV-2 test? $

  • 19.80 USD per test pre-paid ex-works

12. What’s the expiry dating on the Xpert Xpress SARS-CoV-2 test?

  • Shelf life details will be provided with the order/quote.

13. Would Cepheid consider a price reduction from the $19.80 USD per test for HBDC?

  • We are still in the early days of manufacturing and will develop a better understanding of what is feasible.

14. Will Cepheid be able to scale up the production of Xpert Xpress SARS-CoV-2 to provide enough tests for countries others than the US?

  • Cepheid has started the manufacturing of the cartridges in both the US and Sweden plants to meet demand. We expect a ramp up to happen gradually in the coming weeks to serve both the demand from the US, Europe and the rest of the world as much as possible.

15. Will Cepheid be able to maintain sufficient capacity for the production of TB or other tests given the demand of the Xpert Xpress SARS-CoV-2 test?

  • We are planning to meet the TB and virology tests forecasted demand in the coming months. We just ask for programs’ cooperation not to stockpile inventory during this period and accept staggered shipments if required. Cepheid encourages programs to follow the WHO recommendations for ensuring the continuity of TB services during the COVID-19 pandemic as much as possible.

16. Will Cepheid be accepting orders for new instruments in HBDC?

  • Cepheid will also be accepting orders for new GeneXpert instruments, but delivery times may also be longer than usual. Countries deciding to acquire more GeneXpert instruments may consider procuring instruments with 10-color optic modules, as these instruments will allow for rapid second-line drug susceptibility testing with the Xpert MTB/XDR cartridge planned for release in 2020.

17. Will the launch of Xpert MTB/XDR be delayed because of the Cepheid COVID test?

  • No, we still expect to launch Xpert MTB/XDR by the end of Q2 2020.


Contact Medical and Scientific Affairs at for more information.

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