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David Beebe
April 22, 2020

Researchers aim to develop alternative COVID-19 testing method

Written By: Staff


As COVID-19 continues to impact just about every aspect of everyday life, health researchers across the country are engaging in projects to better understand—and treat—this rapidly spreading public health threat.

Researchers at the University of Wisconsin-Madison and the UW Carbone Cancer Center are among those eager to help. Recently, the National Cancer Institute announced it would be offering one-time grant supplements of up to $250,000 for projects targeting COVID-19, and the virus that causes it, known as SARS-CoV-2.

In a matter of days, UW Carbone members and colleagues from across campus submitted nearly 25 proposals.

Each cancer center was able to nominate two projects for funding consideration from the NCI. Research projects did not need to be limited to cancer patients, and applicants didn’t need to be limited to cancer researchers. David Beebe, a professor of pathology and laboratory medicine and biomedical engineering at UW-Madison, is leading one of the two projects selected to move forward.

The availability of COVID-19 tests in recent weeks has been limited, and demand is only expected to increase going forward. Many researchers, including Beebe, are working on developing a viable alternative.

Beebe is an expert in microfluidics, with experience developing low-cost assays for infectious disease. A couple of weeks ago, David O’Connor, a professor at the UW School of Medicine and Public Health, and Thomas Friedrich, a professor in the UW School of Veterinary Medicine, who have been studying various aspects of COVID-19, contacted him with a problem.

They had an idea for a different approach to COVID-19 testing, and they had already made progress, but they realized they would likely need a way to concentrate the sample to be successful—an area Beebe specializes in.

“We very much are taking an alternative and complementary approach to the current testing,” Beebe says. “If it works, it will not put additional pressure on the supply chain and would expand the number of tests that can be run.”

Both O’Connor and Friedrich had been trying an alternative method of COVID-19 testing using an isothermal amplification method to detect viral RNA in swab samples. Typical COVID-19 tests have relied upon what’s known as polymerase chain reaction, or PCR, which is standard for this kind of testing. However, demand for the necessary lab equipment and supplies is high.

Using isothermal amplification, which doesn’t require cycling a sample through numerous hot and cold cycles, offers an alternative, but in early testing of this method by O’Connor and Friedrich for COVID-19, the sensitivity of the test wasn’t as high as it needed to be.

That’s where Beebe’s lab at UW-Madison comes in. By using a combination approach of exclusion-based sample preparation (ESP) and exclusive liquid repellency (ELR), his team should be able to better concentrate viral RNA from a complex mixture found in a swab sample.

“By adding that sample prep step, which will only take a minute, we can increase the sensitivity of the test,” Beebe says.

Beebe is also exploring a different sample prep approach through work at his private company, Salus Discovery, to give the collaborative group the best chance of success.

Both approaches combine extraction and detection into an integrated workflow. The result is a high-throughput, low-cost test that can be quickly and broadly implemented, using instruments that are available in nearly all clinical labs. Beebe estimates that about 100 samples could be tested in an hour using this process.

Implementation of this test will begin alongside the current COVID-19 testing method to ensure accuracy. The next step would be to start to use the new test in a research capacity to understand how the virus is spreading in the community.

“We need to ideally be testing everybody a lot more, but until diagnostic testing is more universal there is a need to understand how many people are being missed with current guidelines,” Beebe says.

This story was first published by UW Health.