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With New NIH Funding, PathogenDx Pivots From Cannabis Screening to Clinical Diagnostics


NEW YORK – In vitro diagnostics maker PathogenDx is positioning its microarray-based testing system to target the clinical lab market. The Scottsdale, Arizona-based firm recently received funding from the National Institutes of Health's Rapid Acceleration of Diagnostics, or RADx, initiative to scale up its COVID-19 testing, and the firm expects to launch a clinical diagnostic test as soon as it receives Emergency Use Authorization from the US Food and Drug Administration.

PathogenDx was founded about six years ago with proprietary open DNA microarray technology and has staked out a sizeable claim in cannabis testing, as previously reported.

But Milan Patel, CEO and cofounder of PathogenDx, said in a recent interview that the firm had always intended to move the technology into the clinical lab testing market.

"We were planning to make the transition next year, but COVID-19 brought it to our doorstep," Patel said. Indeed, although the firm has specialized in supporting cannabis testing labs, its science team has expertise in clinical diagnostics, primarily in tests used to screen patients prior to organ transplantation.

Compared to the cannabis testing space, clinical testing is "a much bigger market, and we want to serve this market primarily; this is where we always wanted to be," Patel said. The firm will also continue to serve its current cannabis testing lab customers as well, he said.  

PathogenDx raised $7.5 million in Series B funding in September 2019, in part to expand from cannabis testing to the food and agricultural testing spaces.

However, the COVID-19 pandemic seems to have already led to many unexpected shifts in the clinical diagnostics space, including revitalized interest in inexpensive and portable technologies like paper-based testing and isothermal diagnostics that had been relegated to the periphery for some time.  

In July, PathogenDx was awarded an undisclosed amount in Phase 1 of the RADx program funding to pivot its microarray-based technology to SARS-CoV-2 testing.

RADx "realized the flexibility of this platform given the challenges that RT-qPCR platforms are having," Patel said. "This test can detect at very low viral load — whether it is asymptomatic positive or presymptomatic positive — which RT-qPCR cannot detect," Patel said. "The good news is that we are now able to deliver that for the clinical diagnostics market, and RADx embraced that," he added.

PathogenDx also announced additional infectious disease-related funding on Monday, noting it has won a one-year, $317,109 award from the NIH's National Institutes of Allergy and Infectious Disease to further develop the SARS-CoV-2 multiplex array.

The firm's core technology had previously incorporated probes printed in a 12-well microarray, but Patel said the RADx funding quickly enabled the firm to scale that up to a 96-well format.

"Then, what we've done in the last month is take that same format and now print 384 wells on that same footprint," Patel said.

Within the array, the firm prints probes for the N1, N2, N3 SARS-CoV-2 genes, as well as influenza A and B, and all the requisite controls. Patel said its microarray also targets a SARS-CoV-2 strain that has a mutation in the spike protein, or S gene, that characterizes a strain originating in Europe rather than Wuhan.

According to Patel, the test's sensitivity and specificity are both 100 percent. This high accuracy is due in part to the fact that the assay is end point PCR rather than the typical RT-qPCR tests for SARS-CoV-2. Patel said that with this method "the primers actually take the reaction all the way to the end point, until there is no more primer left in the reaction, so you are amplifying every single piece of DNA once you find that analyte in your sample."

The limit of detection the firm has calculated for the test overall is 63 copies per milliliter in clinical isolates, which Patel said is more sensitive than any other SARS-CoV-2 detection methods that have received EUA from the US FDA. 

The COVID-19 test, called DetectX-Rv, has a turnaround time of approximately six hours and requires standard lab equipment as well as a proprietary imaging instrument to read the slides. Patel said the instrument reads all the analytes in each well in less than 10 seconds per sample.

The firm uses a magnetic bead-based extraction method from Zymo Research, which is less commonly used by other SARS-CoV-2 diagnostics makers. It has also developed an extraction-free methodology that is incorporated in the firm's core intellectual property. "If labs have a problem getting reagents in the market in three or four months, they can flip the switch and be able to use that" method, Patel said. 

PathogenDx has submitted its EUA package to the FDA, and once it has authorization, it will roll the test out to clinical labs and CLIA labs, Patel said. He noted part of the RADx program also involves liaising with large commercial labs that might take up the technology.

The firm sourced the nasopharyngeal clinical isolates it needed for assay validation from biobanks with the help of the RADx program. It has also identified local sources for saliva samples and plans to amend the EUA with that sample type as well as a mouthwash-based sample type that can be incorporated into a self-administered sample collection protocol. The latter will be validated with a partner, but Patel declined to name the partner at this time.

PathogenDx plans to sell the arrays in 96-well and 384-well kits along with instruments to run the arrays and interpret the results. In terms of cost, Patel said the basic instrument, without additional automation and robotics, is about one-third the price of any other system at around $60,000, and the microarray assays at full manufacturing scale will cost about $20 per patient sample, or $7,680 per 384-well microarray slide.

The firm has already launched the assay for research use and has customers deploying it to identify environmental SARS-CoV-2 viral contamination.

Now, "The RADx program is the springboard and the vehicle for scaling up," Patel said, noting that the program is facilitating the process via a collaboration with the University of Massachusetts.

PathogenDx currently has capacity to make around 200,000 tests per month, but it anticipates that by the end of the year it will scale to 4 million tests per month. "Our test, at 4 million tests per month, will be able to test for not just COVID-19, but also influenza A and B, and potentially" respiratory syncytial virus, Patel said, adding that this multiplexing is done on each patient's nasopharyngeal, saliva, or mouthwash sample.

Ultimately, "getting the FDA stamp of approval means the world to us," Patel said. "It means acceptance at a federal level, that somebody has looked deep and hard into our technology and said, 'This works, this helps improve the public health of the United States.'"

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