Originally posted by GenomeWeb. May 26, 2020 | Kelsy Ketchum, Editor, GenomeWeb
NEW YORK – Ensuring adequate access to testing has been a key hurdle during the COVID-19 pandemic, with test and supply shortages causing roadblocks and capacity not being met.
But a new test in the works from Missoula, Montana-based FYR Diagnostics could be part of the solution.
The ALRT SARS-CoV-2 molecular assay uses the company’s “adaptive low-resource testing” technology, based on isothermal amplification of RNA with a special reaction condition and primer design that requires only a single temperature to amplify the viral target gene, said Chris Booth, the company’s CEO and director of R&D.
“We can utilize just a simple water bath or a heat block, or you can use a thermocycler,” Booth said. “There’s all sorts of off-the-shelf, really simple, cheap heating devices that you can use to maintain the single temperature that’s required for the reaction.”
This technique removes the need for thermocycling, eliminating potential equipment bottlenecks and allowing the technology to be utilized in a variety of laboratory settings, Booth added.
This includes “settings that have different levels of infrastructure, anywhere from high-complexity labs … in a hospital to remote areas or very low-resource settings, in particular outside of the country and [in] less-developed countries that do not have the testing infrastructure that the United States does,” Booth noted.
The minimal equipment requirements are particularly compelling aspects of the technology, said Seth Strattan, a venture partner at Two Bear Capital, a venture capital firm that has invested in FYR Diagnostics. “It is suitable for these low-resource environments, which is what we have to be able to do if we are going to roll out testing at the scale that we know we’re going to have to in order to manage the epidemic before a vaccine is widely available,” Strattan said.
The technology, which works with respiratory or saliva samples, also uses a colorimetric binary readout visible by eye, eliminating the need for a detection device. With FYR’s ALRT test, users can take the reaction tubes off the heat block or water bath and see whether the color has changed, determining the test result. That color change is visible within 30 to 40 minutes, and that quick turnaround time is one of the biggest benefits of the test, Booth said. Strattan added that the turnaround time will also facilitate contact tracing for the virus and allows the test to be deployed where people are, rather than asking them to come to a central location to be tested. “It moves the front line of testing forward by a quantum leap, instead of trying to increase the testing capacity of centralized labs or clinical labs,” he said.
Expanding testing outside of clinical laboratories is a major plus, Strattan said. “It makes it possible without tremendous investment to do a distributed testing approach where the testing becomes a ubiquitous tool as opposed to a centralized tool,” he noted.
The company is also “trying to minimize the amount of work to the end user” by providing reaction tubes with everything preloaded except the sample, Booth said. Having it ready to go “will be great in a low-resource environment where you may not have as many tubes and pipettes and all of these things that you might have in a hospital or private testing lab,” he continued. There’s minimal training required to perform the test as well, with Booth noting “as long as you can learn to use a pipette, this is something that anyone could do.”
FYR Diagnostics was originally developed around isothermal amplification technologies for small non-coding microRNAs which could then be applied to biomarker development and detection for a variety of diseases, mainly neurological ones such as epilepsy and Alzheimer’s disease. Avery Sonnenberg, a principal at Two Bear Capital, called this original technology “a more forward-looking diagnostic technology,” because it is looking at biomarkers that aren’t commonly used today. It can “give you a better window into the gene regulation pathways,” by looking at what is actively happening within a person’s cells, Sonnenberg added.
When Booth joined the company last year, they expanded the technology to cancer and opioid-related disorders, and began considering potential agricultural applications. Last October, the firm received a $618,000 grant from the National Institutes of Health to develop a test to detect acquired epilepsy.
Further expansion came when the firm decided to work on isothermal amplification for DNA and long RNA, such as a virus. That planned expansion came in handy once the COVID-19 pandemic began, although as is the case for many firms it also threw a wrench into the works. Originally FYR was working on adapting its technology to the detection of bacteria and tuberculosis, among other diseases, but everything got put on pause while they tried to adapt ALRT for SARS-CoV-2, Booth said.
“Obviously we know that this isn’t something permanent,” Booth said. “We do intend to go back to working on everything else that we were working on in the meantime.”
Right now, company has been focused on developing and optimizing primer sets and designs for the ALRT technology, as well as collecting data for the analytical studies and clinical validation needed to submit the test for Emergency Use Authorization to the US Food and Drug Administration. Booth said he hopes the analytical studies and validation will be done within the next two months, allowing for submission to the FDA.
One concern for many test manufacturers is that isothermal amplification is generally less accurate than qPCR testing. Abbott’s ID Now test, for example, has faced pushback from users doubting its claims about accuracy, including one notable study from New York University that found Abbott’s test missed one-third of positive samples. As a result, Abbott agreed to conduct further clinical studies for the test, and the FDA is investigating the accuracy issues. Abbott announced last week an interim analysis of its multi-site clinical study showing the ID Now test demonstrates 95 percent sensitivity and 99 percent specificity when compared to lab-based PCR tests.
“Isothermal amplification technologies can work extremely well and it ultimately comes down to the underlying technology and how well optimized the test is,” David Booth, FYR Diagnostics co-founder, said in an email when asked about potential accuracy issues. “RT-PCR can also be really inaccurate if the primers/probes and reaction conditions are not optimized correctly.”
“Our isothermal amplification technology that we are using has a unique primer design that prevents amplification in the absence of the target that is being detected,” he continued. “In our testing with our optimized primers, we do not get any amplification in the absence of the target during the reaction time.”
Last week, Color received EUA to provide SARS-CoV-2 testing using isothermal amplification technology. Other manufacturers using isothermal amplification include Atila BioSystems and Rendu Biotechnology.
FYR has already established relationships for manufacturing and distributing the reagents and consumables for the kits, so once the primer set and reaction conditions are optimized everything will be ready for launch, Booth said.
Ultimately, Booth said he hopes the ALRT technology will be applicable to detection of new pathogens or viruses, where FYR just has to tweak the primer design or create new primers but can leave the underlying reaction conditions the same.
Booth specifically noted the company is targeting military utilization outside of the US for the ALRT test but said it would also have utility in a hospital setting, as long as the hospital is capable of doing high-throughput processing of clinical specimens. For hospitals that don’t perform purification onsite, FYR’s test has little value to them — but for hospitals with the infrastructure, the test will be cheaper, faster, and easier to use. The company is also, for the time being, focusing on expanding testing capabilities in its home state of Montana before expanding elsewhere.
One potential hiccup when expanding to countries outside the US, Sonnenberg noted, is that FYR won’t be lyophilizing its components in the short-term. If the test was shipped to other regions, it would need a longer shelf life, which Sonnenberg said would require “a lot more testing and development” to complete the lyophilization process and stabilize the components. But that process isn’t a priority for FYR right now, Sonnenberg said, because the company is trying to make the test available as soon as possible. “I don’t think shelf life is going to be a concern,” he added. “I think these tests are going to be used as fast as they’re made.”