A Major Opportunity to Utilize Current Diagnostic Investment in Cepheid's GeneXpert and SystemOne's GxAlert and Aspect Software to Rapidly Detect, Track, and Control COVID-19 Without Reducing TB Efforts
April 30, 2020
By Natasha Gous, PhD
No one really knows the true extent of spread of the novel coronavirus that has killed over 229,220 people worldwide and decimated healthcare systems since it was first reported in China December 2019. Available reports indicate that there are 3,245,791 confirmed cases (as of 30 April 2020), 62% of which still have active COVID-19 disease (1). These numbers are likely the tip of the iceberg. It is uncertain how many people with mild or asymptomatic disease have not been tested, making accurate tracking of COVID-19 impossible.
As the world grapples with how to interrupt transmission and contain the virus, the WHO Director General had one simple message for all countries during his media briefing on the 16th March 2020, ‘You cannot fight a fire blindfolded. Test, test, test’ (2). Countries such as South Korea, have been widely praised for implementing an aggressive and expansive testing approach facilitating early identification of positive cases for quarantine. Based on this strategy, they have essentially managed to slow down transmission rates and are seeing a sharp drop in reported cases (3). Whilst this approach clearly works, adequate testing capacity is severely lacking worldwide.
As countries with already fragile health systems brace for the impact of COVID-19, many are ramping up their available testing capacity. The WHO African region has launched a massive upscaling of their testing capacity; there are currently 47 countries with laboratory facilities available to test for coronavirus, at the start of the outbreak, there were only two. However, there are many challenges ahead. Not only will laboratories face critical shortages in test kits, but many fear they will not have enough capacity to perform the testing on available diagnostic instruments. Laboratories are already being inundated with samples and this will only increase in the coming weeks.
But, amidst all the uncertainty, a glimmer of hope emerges.
The FDA have endorsed various new diagnostic tests at unprecedented speeds in an effort to reduce testing backlog. One such diagnostic test is Cepheid’s Xpert® Xpress SARS-CoV-2 assay (4), which will be released in the US first and then globally. The Xpert test can provide rapid detection of the coronavirus in just 45 minutes, in stark contrast to current testing protocols which can take hours to obtain a result. By accelerating the speed at which coronavirus can be diagnosed, healthcare providers can make more informed and timely decisions regarding isolation of patients. It will also assist government and stakeholders to obtain more real-time case numbers to inform intervention needs.
The biggest draw with Cepheid’s new test however, is that the platform that it is run on, GeneXpert, is already widely available. GeneXpert has a footprint of 23,000 (4) instruments globally and presence in 130 low- and middle-income countries where it is used primarily for Tuberculosis testing (5). This current landscape represents an opportunity to rapidly scale and move forward with coronavirus testing.
However, many are wondering how will they utilize this existing capacity for coronavirus testing when the burden of TB is so great?
A quick analysis of test numbers from 618 GeneXpert instruments across 8 countries reporting TB tests to GxAlert, was completed. Assuming that a laboratory can run three TB tests per module, per day and there are 21 working days in a month, we calculated each instrument’s yearly utilization as the number of tests actually run per year, divided by the theoretical maximum number of tests an instrument could achieve in a year. We then categorized the instruments into distinct buckets showing their yearly utilization (figure 1). Note that the Xpert® MTB/RIF and Xpert® Ultra assays take approximately 2 hours to complete on the GeneXpert platform.
What we found was encouraging.
Of the 618 instruments looked at, only 10% (64/618) are reaching utilization rates of above 80%. The vast majority of instruments, 75% (466/618), are performing at below 50% utilization currently for TB testing.
Essentially, what this means is, if 466 instruments still have 50% testing capacity available, an approximate 700,000 additional TB tests could be run on these instruments in a year. The Xpert Xpress SARS-CoV-2 test takes approximately 45 minutes to complete. As such, in the existing network evaluated, there would exist capacity for an approximate additional 2,100,000 COVID-19 diagnostic tests. This represents a significant opportunity to use current diagnostic investment to absorb testing for coronavirus without the need for additional investment in any new diagnostic systems.
But increased testing alone is not enough to effectively combat COVID-19. Countries need to be able to communicate results quickly to all stakeholders. Countries will also be able to leverage existing companion information systems, such as SystemOne’s GxAlert, to quickly enable real-time reporting and notification of COVID-19 diagnostic data. SystemOne has already connected more than 3,000 GeneXperts across 40 countries. For countries with these existing GxAlert networks, a remote COVID-19 module and support model can be quickly deployed without travel into countries. Our Aspect Reporter app is also available on the Google Play store to allow COVID-19 results to be delivered directly to healthcare workers on the frontline in real-time, thus improving timeliness of response.
Whilst we prepare to ramp up systems to meet the “Test, test, test” call-to-arms provided by Dr. Tedros, it is comforting to know much of the capacity needed to rapidly scale up testing is already available on the GeneXpert platforms in many countries. Leveraging these technologies in the fight against COVID-19 will be a political battle, not a technical one.
Natasha Gous, PhD is the Medical Science Liaison for SystemOne. She holds a PhD in Molecular Medicine, specializing in point of care technologies and has over ten years of technical and operational experience in molecular diagnostic systems for infectious diseases. Dr Gous is based in Johannesburg, South Africa.
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