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SARS-CoV-2 Pandemic May Promote Progress in Paper MDx

NEW YORK – The Emergency Use Authorization pathway for COVID-19 testing is providing a boost to a number of novel diagnostic technologies, including paper-based ones. Using methods such as isothermal nucleic acid amplification and CRISPR, research groups and start-up companies are advancing paper-based SARS-CoV-2 tests in the hopes of driving this technology to a commercial product.

Jackie Linnes, a biomedical engineer at Purdue University, is deeply enmeshed in the paper-based diagnostics space and to her knowledge there are not yet any rapid, point-of-care paper-based molecular diagnostic tests that have been fully commercialized.

But the COVID-19 EUA process might soon change all that.

"The EUA is the most efficient that the FDA has ever been for diagnostics," Linnes said in an interview. "Everybody wants to get their devices through before that door closes."

Linnes has noticed some new entrants to the paper-based testing field of late, as well as a few companies with paper technologies that have become more public now that the pandemic has drawn attention to the importance of diagnostics.

Paper-based tests offer certain unique advantages over traditional molecular technologies, including those that rely on plastic microfluidics. Paper tests are typically somewhat more inexpensive to manufacture and easier to make in large volumes. Like the oft-cited pregnancy test, they can also be developed to run without any instrumentation.

"Paper includes a lot of things that in a regular microfluidic chip you have to do off-chip," Linnes explained. "It's got the wicking capabilities to ensure that you don't need a separate pump and electronics that could fail, and instead you have all of the fluidics integrated, so that, in theory, paper just flows similarly every time." Thus, paper provides consistency, with one less component.

Originally focused on extreme portability for use in low-resource settings, the COVID-19 pandemic is now leading paper MDx developers to expand their horizons.

"Any place can be a low-resource setting when the system is overwhelmed," Linnes said.

Still, true to their roots, most paper-based diagnostics companies remain focused on getting molecular tests to low- and middle-income countries as well, where there may not be many reliable alternatives.

From bench to bedside

Bridging the gap between diagnostics research and commercialization is critical. "All of us know that the things sitting on our lab benches don't do much good," Linnes said.

Linnes has developed a number of different diagnostic methods over the years, and helped launch Purdue spinout OmniVis, a firm working to commercialize a cholera surveillance using paper-based techniques paired with smartphone detection. She is currently working with a company called CASPR on a CRISPR-based paper diagnostic for COVID-19.

In general, paper test developers have many choices for amplifying nucleic acids, such as loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), helicase-dependent amplification (HAD), or isothermal strand displacement amplification (iDSA). Linnes noted that some of these methods are more robust but prone to false positives, while others are less robust but can yield falsely negative results.

In addition, sample prep is generally a hurdle for paper tests, and can be more challenging depending on the sample type. Unprocessed samples are the easiest to obtain, and skipping the processing step makes the test faster. "The problem with raw samples is that you are not concentrating and not getting rid of inhibitors," Linnes said, so the risk of lower sensitivity needs to be calibrated to the abundance of the target.

Paul Yager, a bioengineer at the University of Washington, is also working to spin his research into a SARS-CoV-2 diagnostic test through a startup company called UbiDx.

"Ironically, COVID-19 has presented paper-based diagnostics developers with a unique opportunity to commercialize their tests in [both] the developed and developing worlds," Yager said in an email.

UbiDx is using technology based on molecular pathogen detection methods originally developed with support from DARPA between 2011 and 2017, Yager said, namely methods for at-home, instrument-free, disposable testing. The company has now received gift funding from two sources to develop a paper-based SARS-CoV-2 diagnostic test, he said.

The SARS-CoV-2 test uses isothermal strand displacement amplification (iDSA) and swab samples. It is processed on a device that can transmit real-time fluorescence curves to a user's smartphone, with the additional capability to transmit data to physicians and public health authorities, if needed.

UbiDx is currently working with the FDA on its EUA submission and plans to be ready to produce millions of tests by the beginning of next year. It also has recently demonstrated a paper-based diagnostic system for detection of chlamydia and gonorrhea in urine, Yager said, as well as a swab-based test for the respiratory syncytial virus, and will be completing a full respiratory panel soon. 

Rebecca Richards-Kortum, another prominent diagnostics researcher, is also reportedly developing a SARS-CoV-2 assay. Her lab at Rice University had previously pioneered a body heat activated isothermal molecular testing method and a quantitative RPA-based method for HIV testing.

The lab recently won funding in collaboration with researchers at the University of Texas MD Anderson Cancer Center to develop a 30-minute SARS-CoV-2 test. It would likely not be an at-home test, since the $2 assay requires a simple-to-use instrument that costs less than $5,000, according to a recent press release. But the team is currently working with the US Agency for International Development, or USAID, as well as industry partners to scale the test for use in five countries in Africa.

Commercial push

At Purdue, Linnes is helping to develop some of the fluidics methodologies for CASPR's test, which will target markets in the US and Latin America.

Franco Goytia is CEO of CASPR, a San Francisco, California- and Buenos Aires, Argentina-based startup. To his mind, the way the US regulatory process has adapted to the pandemic has been beneficial across the industry.

"The EUA has helped a lot of emerging technologies become ready to be quickly deployed, while still striving for good clinical sensitivity and specificity," he said in an interview.

And, he noted that for the increasing SARS-CoV-2 diagnostic and screening needs in the US and globally, "paper diagnostics are very compatible."

CASPR's technology relies on isothermal amplification as well as newly discovered CRISPR-CAS enzymes that enable molecular diagnostics with enhanced precision. Other SARS-CoV-2 diagnostic tests that rely on CRISPR technology include ones from Sherlock Bioscience and Mammoth Biosciences.

CASPR has already submitted an EUA for a CRISPR-based fluorescence assay that can potentially be used in decentralized settings, but its collaboration with the Linnes lab extends that work, integrating the technology into a point-of-care solution potentially using paper fluidics and wax valves.

Goytia said CASPR is aiming to submit an EUA for the paper-based test later this year. It is also collaborating with labs and health ministries in Latin America and hopes to make products available there this year as well.

Another company working on paper-based MDx for SARS-CoV-2 is GoDx, based in Madison, Wisconsin.

The firm's CEO, Chang Hee Kim, concurred that although the overall field of point-of-care diagnostics had previously been focused on the developing world and global health needs, the COVID-19 pandemic has made rapid, on-site detection more urgent everywhere, in order to hopefully achieve better outbreak control.

For GoDx, "The big value that we are trying to bring is that the test is instrument free," Kim said. The test in development is targeted toward at-home use or assessment of employees in a workplace. 

GoDx's SARS-CoV-2 diagnostic test uses real-time LAMP, and is able to clear the sample prep hurdle with its own a proprietary, rapid, and low-cost method, Kim said. The firm is developing the paper-based test for saliva samples, in part to obviate the need for swabs. It is working with a contract research organization to support the clinical evaluations required for EUA submission.

GoDx is also developing a multiplexed paper-based test for gastrointestinal disease in children. The test detects seven bacterial, viral, and parasitic pathogens. Diarrheal disease is the second leading cause of death in children under age five worldwide, Kim said, and knowing which bug is causing a child's illness could have treatment implications and be useful for surveillance efforts in low-resource settings.

GoDx is funded through a small business innovation research (SBIR) grant from the National Center for Advancing Translational Sciences for its GI test. It applied for supplemental funding when the COVID-19 outbreak began, and in April it was awarded $192,999 in Phase II SBIR funding from NCATS, which will support development of the COVID-19 test. Separately, GoDx has Phase I SBIR funding from the National Institute of Allergy and Infectious Disease for a rapid paper-based neonatal sepsis biomarker test that can test directly from whole blood, Kim said.

At the moment, it seems likely that at least one nascent paper-based diagnostic will make it through the US emergency regulatory process.

Linnes said that authorization would allow developers to be able to prove that paper is an effective technology. "Even if it is just one or two companies that manage to get [a product] out, I would be excited for the field," she said.

The pandemic has also had the collateral effect of providing a crash course in diagnostics for the lay public. A growing level of education among patients may help them someday effectively lobby for more point-of-care testing. Coupled with an overall excitement about diagnostics among investors, paper-based technology could be poised to actually thrive.