SystemOne Advisory: Many but Not All GeneXperts Ready for Immediate COVID-19 Testing
April 30, 2020
The GeneXpert, a technology that revolutionized TB molecular diagnostic testing, can now be utilized for COVID-19 testing through the recent release of the new Xpert® Xpress SARS-CoV-2 cartridge (1). In a time when testing is an integral component to COVID-19 preparedness and response, the new assay comes as a welcome addition to the market, especially by countries who already utilize the GeneXpert platform. GeneXpert has a massive footprint worldwide, which allows countries to leverage this existing technology to rapidly increase their testing capacity for COVID-19.
GeneXperts are capable of running tests for multiple diseases. In many low- and middle-income countries, where the GeneXpert is primarily used for TB response, plans are underway to repurpose or maximize some of these instruments for COVID-19 testing. However, an important factor to bear in mind when transitioning a testing fleet to accommodate COVID-19 testing, is that the new cartridge only operates on GeneXpert software version 4.7b or later. For countries operating on lower versions of the software, upgrades will be required before testing can commence. This process will need careful planning as it may take time and have cost implications due to the need for additional human resource capacity. Coordination may also be required with the manufacturer (Cepheid) or Authorised Service Providers (ASP) to ensure the process runs smoothly (2).
To gain a better understanding of what software versions countries are currently using, an analysis of 18 countries connected to the GxAlert software platform (SystemOne, LLC) was performed. The analysis included 594 GeneXpert TB testing sites, which we categorized into two groups, 1) those that require a software upgrade (i.e operating on version 4.7a or lower) or 2) those that are COVID-19 ready (i.e those operating on version 4.7b or higher).
Figure 1 below summarizes our findings. The main takeaway from this analysis is that the majority of sites in our sample are ready to begin COVID-19 testing immediately. Only 75 of the 594 sites (12.6%) would require a software upgrade before commencing testing, and these sites were predominantly located across only nine of the 18 countries we looked at. Of the sites requiring upgrade, most are operating on version 4.4a and thus would be able to upgrade to 4.7b or higher directly i.e without the need for an intermediate upgrade to 4.4 before upgrading to 4.7b or higher (2).
Whilst we acknowledge that maximizing existing capacity will require careful attention to laboratory workflow to ensure TB testing is not put on the back burner, the fact that most instruments are operationally ready to begin COVID-19 testing is still good news for countries. Previous research by SystemOne demonstrates that many GeneXpert instruments used in low- and middle income countries for TB testing have spare capacity for COVID-19 testing (View Article), meaning that TB testing will not necessarily be negatively impacted by the demand for COVID-19 testing. We suggest countries assess their testing sites on a case-by-case basis, ideally before procurement and implementation, in order to ascertain if they are ready to test using this new cartridge.
SystemOne data experts are ready to assist countries in planning their COVID-19 response with readily available local GeneXpert data.