Rapid detection of SARS-CoV-2: Diagnosis of COVID-19

Cepheid, one of the leading molecular diagnostic companies, which is also the manufacturer of  GeneXpert System, has received emergency use authorization (EUA) from FDA for its rapid SARS-CoV-2 test kit. This automated molecular test for the qualitative detection of severe acute respiratory syndrome coronavirus 2  (SARS-CoV-2), virus that causes COVID-19, is named as Xpert Xpress SARS-CoV-2.

SARS-CoV-2 test is a rapid, real-time RT-PCR test intended for the qualitative detection of nucleic acid from the SARS-CoV-2 in either nasopharyngeal swab and/or nasal wash/ aspirate specimens collected from individuals suspected of COVID-19.

According to the manufacturer, this test kit leverages the design principles of Xpert Xpress Flu/RSV cartridge technology and multiple regions of viral genomes are targeted. HospitalS/laboratories who are using Cepheid’s GeneXpert Systems will be able to use the same system with SARS-CoV-2 cartridge. Healthcare professionals at those facilities will decide who meets the eligibility criteria for the testing based on signs/symptoms.

Detection of SARS-CoV-2 for COVID-19
Rapid detection of SARS-CoV-2, virus that causes COVID-19

With less than a minute of hands-on time to prepare the sample and detection of current pandemic coronavirus SARS-CoV-2 within 45 minutes, Xpert Xpress SARS-CoV-2 has the potential to be the preferred test system to combat 2019 pandemic.

When hospitals are relying on reference laboratories for the test results of SARS-CoV-2 where the turnaround time 2-5 days, depending on the test capacity and loads, delivering accurate, point-of-care results in about 45 minutes will expedite diagnostic testing and play a crucial role to manage and contain COVID-19 pandemic.

Choice of Sample: Nasopharyngeal swabs (NPS) in UTM/VTM, nasal aspirates, and nasal washes.

Sample preparation:

Sample is placed into a viral transport tube containing 3 mL transport medium. The specimen is briefly mixed by rapidly inverting the collection tube 5 times. Using the supplied transfer pipette, the sample is transferred to the sample chamber of the Xpert Xpress SARS-CoV-2 cartridge. The GeneXpert cartridge is loaded onto the GeneXpert Instrument System platform, which performs hands-off, automated sample processing, and real-time RT-PCR for the detection of viral RNA.


SARS-CoV-2 cartridge is a complete solution containing all the necessary reagents needed to detect genomic information unique to the SARS-CoV-2 virus. A patient sample is loaded into the cartridge and run through a GeneXpert System. GeneXpert II, IV, XVI, Infinity 48, Infinity 80, and Xpress Systems support SARS-CoV-2.

The GeneXpert Instrument Systems automate and integrate sample preparation, nucleic acid extraction and amplification, and detection of the target sequences in simple or complex samples using real-time PCR assays. The systems consist of an instrument, computer, and preloaded
for running tests and viewing the results. The systems require the use of single-use disposable cartridges that hold the RT-PCR reagents and host the RT-PCR process.

A Sample Processing Control (SPC) and a Probe Check Control (PCC) are also included in the cartridge utilized by the GeneXpert instrument. The SPC is present to control for adequate processing of the sample and to monitor for the presence of potential inhibitor(s) in the RT-PCR reaction. The SPC also ensures that the RT-PCR reaction conditions (temperature and time) are appropriate for the amplification reaction and that the RTPCR reagents are functional.

The probe check control verifies reagent rehydration, PCR tube filling, and
confirms that all reaction components are present in the cartridge including monitoring for probe integrity and dye stability.

Test results will be available within an hour of obtaining a patient sample. Hospitals and labs currently using a GeneXpert system will be able to run the tests. It’s up to the healthcare professionals at those facilities to determine who meets the criteria for being tested.


Preparing the cartridge: Start the test within 30 minutes of adding the sample to the cartridge.

  1. Remove a cartridge from the package.
  2. Check the specimen transport tube is closed.
  3. Mix specimen by rapidly inverting the specimen transport tube 5 times. Open cap on the specimen transport tube.
  4. Open the cartridge lid.
  5. Remove the transfer pipette from the wrapper.
  6. Squeeze the top bulb of the transfer pipette com Squeeze the top bulb of the transfer pipette completely and then place the pipette tip in the specimen transport tube (see Figure 2). Transfer Pipette
  7. Release the top bulb of the pipette to fill the pipette before removing from the tube. After filling pipette, excess sample will be seen in the overflow reservoir bulb of the pipette (see Figure 2). Check that the pipette does not contain bubbles.Xpert Xpress SARS-CoV-2 Cartridge
  8. To transfer the sample to the cartridge, squeeze the top bulb of the transfer pipette completely again to empty the contents of the pipette into the large opening (Sample Chamber) in the cartridge (shown in figure 3). Dispose of the used pipette.
  9. Close the cartridge lid.

Take care to dispense the entire volume of liquid into the Sample Chamber. False-negative results may occur if insufficient sample is added to the cartridge.

Starting the test

  1. Turn on the GeneXpert InstrumentSystem.
  2. Log on to the System software. The login screen appears. Type your username and password.
  3. In the GeneXpert System window, click Create Test (GeneXpert Dx) or Orders followed by Order Test (Infinity).
  4. Scan or type in the Patient ID (optional). If typing the Patient ID, make sure the Patient ID is typed correctly. The Patient ID is shown on the left side of the ViewResults window and is associated with the test result.
  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 shown on the left side of the View Results window and is associated with the test result.
  6. Scan the barcode on the Xpert Xpress SARS-CoV-2 cartridge. Using the barcode information, the software automatically fills the boxes for the following fields: Reagent Lot ID, Cartridge SN, Expiration Date, and Selected Assay.
    Note If the barcode on the Xpert Xpress SARS-CoV-2 cartridge does not scan, then repeat the test with a new cartridge.
  7. Click Start Test

Interpretation of the results

The results are interpreted automatically by the GeneXpert System and are clearly shown in the View Results window. The Xpert Xpress SARS-CoV-2 test provides test results based on the detection of two gene targets according to the algorithms shown below.

Result Text N2 E SPC
SARS-CoV-2 Positive + + +/-
SARS-CoV-2 Positive + +/-
SARS-Cov-2 Presumptive Positive + +/-
SARS-CoV-2 Negative +

For more information, please refer to user manual published by cepheid.

References and further reading

Acharya Tankeshwar

Hello, thank you for visiting my blog. I am Tankeshwar Acharya. Blogging is my passion. As an asst. professor, I am teaching microbiology and immunology to medical and nursing students at PAHS, Nepal. I have been working as a microbiologist at Patan hospital for more than 10 years.

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