Trevor Martin, PhD, Mammoth Biosciences co-founder and CEO

Mammoth Biosciences—the CRISPR-based diagnostics developer whose co-founders include Nobel laureate and genome editing pioneer Jennifer Doudna, PhD—plans to develop, scale-up, and commercialize its molecular diagnostic assay for COVID-19 through partnerships with MilliporeSigma and Hamilton.

MilliporeSigma will serve as contract manufacturer for Mammoth’s DETECTR BOOST™ SARS-CoV-2 Reagent Kit. Based on Mammoth’s CRISPR-based DETECTR (DNA Endonuclease-Targeted CRISPR Trans Reporter) platform, the high-throughput testing system will be designed to leverage standard, automated liquid handling equipment from Hamilton to allow rapid processing of both nasal swab and saliva samples.

Through the agreements, whose values were not disclosed, Mammoth intends to position its SARS-CoV-2 test as a sample-to-answer turnkey solution enabling commercial laboratories to increase their testing capacity multi-fold.

Mammoth aims to process approximately 1,500 tests per 8-hour shift with less than an hour of hands-on interaction time—a speed the company said will offer central labs regulated through the Clinical Laboratory Improvement Amendments (CLIA) significant improved speed over traditional PCR tests while maintaining comparable accuracy.

“The goal here is to supercharge the thousands of labs around the country that have these kinds of liquid automation setups, so that they can run two or three times the amount of tests that they’re currently running today,” Mammoth CEO Trevor Martin, PhD, told GEN. “What’s exciting is that this is the start of a new platform for molecular diagnostics.”

Also exciting, he added, is the opportunity to tap into the commercial and scale-up expertise of MilliporeSigma, the name through which the Life Science business of Merck KGaA, Darmstadt, Germany, operates in the U.S. and Canada.

“This is something that can scale, and it can really have an impact on dealing with the pandemic. We’re excited to get it into many labs across the country and to make sure that they have supply,” Martin said. “We’re super excited to be working with a world leader in that space.”

He said Mammoth and Hamilton were familiar with each other’s various efforts throughout the COVID-19 pandemic due to their shared connection with University of California, Berkeley (UCB). Doudna’s lab is based at UCB, which houses the Innovative Genomics Institute (IGI), a partnership of UCB and University of California, San Francisco (UCSF) that was founded by Doudna.

Mammoth contacted Hamilton this summer about the DETECTR BOOST system and has been working closely with them ever since.

Tests to Propel CRISPR Growth

CRISPR’s use in diagnostics is expected to propel growth in the broader CRISPR technology market over the next several years. ResearchAndMarkets has projected the overall CRISPR market to grow from $760 million in 2019 to $920 million this year and $1.55 billion in 2023. Grand View Research has forecast that the market size will balloon at a compound annual growth rate of 16.6%, to $4.88 billion by 2027.

Mammoth is among companies working to develop CRISPR-based COVID-19 diagnostics. Mesa Biotech received one of the FDA’s earliest emergency use authorizations (EUAs) for a CRISPR-based COVID-19 diagnostic for its Accula SARS-CoV-2 Test, a palm-sized test designed to deliver qualitative, visual detection of nucleic acid from SARS-CoV-2 in throat swab and nasal swab specimens within 30 minutes.

Last July, Sherlock Biosciences and binx health entered a partnership intended to develop the world’s first point-of-care diagnostic test for leveraging CRISPR technology. Sherlock’s co-founders include Feng Zhang, PhD (Broad), who chairs the company’s advisory board.

Last month, Sherlock reported data from a pilot study of 20 clinical samples showing that results from the Sherlock™ CRISPR SARS-CoV-2 kit were 100% concordant with results from Dartmouth-Hitchcock Health’s lab-based PCR test method. Sherlock’s test received EUA from the FDA in May.

Mammoth emerged from stealth mode in April 2018, disclosing plans to develop an easy-to-use and affordable point-of-care test enabling fast, simultaneous detection of multiple conditions, in real-time, both in the hospital and at home, through a single credit card-sized strip form factor. Mammoth raised $23 million later that year to fund the initial development of the test, later completing a $45 million Series B financing.

Martin, Janice Chen, PhD, and Doudna, of UC Berkeley, co-founded Mammoth with Lucas Harrington, Mammoth’s CSO; and Ashley Tehranchi, PhD, who served as CTO until May 2019.

This year, Mammoth responded to the urgent need for improved and more accessible testing for COVID-19 by rapidly reconfiguring the company’s CRISPR-based diagnostics platform to detect the presence of SARS-CoV-2.

EUA Request by Year’s End

Mammoth Biosciences’ high-throughput testing system will be designed to leverage standard, automated liquid handling equipment from Hamilton to allow rapid processing of both nasal swab and saliva samples. [Mammoth Biosciences]
Mammoth plans to request an EUA from the FDA by year’s end for the SARS-CoV-2 test his company is co-developing with MilliporeSigma.

“This collaboration will allow us to help Mammoth with the development and production of their new SARS-CoV-2 test, which, once approved by the FDA, will increase testing capacity here in the U.S. at the scale needed to combat this pandemic,” said Jean-Charles Wirth, head of Applied Solutions at MilliporeSigma. “MilliporeSigma is helping to advance the future of testing at scale. This is an important step in detecting Covid-19 quickly.”

While MilliporeSigma’s expertise extends into CRISPR, Mammoth isn’t discussing what if any of its partner’s intellectual property will be used in the co-developed SARS-CoV-2 test.

In May, MilliporeSigma was granted its third and fourth U.S. patents—the company’s 25th and 26th CRISPR patents worldwide—for MilliporeSigma’s CRISPR-Cas9 cleavage and integration technology, which is designed to allow researchers to “knock in” or replace a disease-associated mutation with a beneficial or functional sequence, or to “knock out” or delete such a mutation. Both methods are used in creating disease models.

Mammoth won funding for its development of a scalable COVID-19 test in July, when the company was awarded $23.1 million of $248.7 million in contracts to the first seven lab-based and point-of-care tests diagnostics developers funded through the NIH’s Rapid Acceleration of Diagnostics (RADx) initiative.

The testing system can be adapted to detect for other viruses, though Mammoth has not made public which ones. Martin says, “as things continue, you can imagine multiplexing with other respiratory viruses.”

On July 9, the FDA granted an EUA to UCSF Health Clinical Laboratories for the SARS-CoV-2 RNA DETECTR Assay, a 45-minute test using the CRISPR-Cas12 enzyme, which targets double-stranded DNA. Mammoth co-developed the test through its partnership with UCSF professor Charles Chiu, MD, PhD, who is also director of the UCSF-Abbott Viral Diagnostics and Discovery Center, and a member of the company’s Scientific Advisory Board.

In “CRISPR–Cas12-based detection of SARS-CoV-2,” a study published last April as a letter in Nature Biotechnology, Chiu, Mammoth CTO Janice Chen, PhD, and colleagues validated the SARS-CoV-2 RNA DETECTR Assay as a faster alternative to the U.S. Centers for Disease Control and Prevention (CDC)’s RT–PCR assay, capable of detecting SARS-CoV-2 from respiratory swab RNA extracts in under 45 minutes.

“The positive predictive agreement and negative predictive agreement of SARS-CoV-2 DETECTR relative to the CDC qRT–PCR assay were 95% and 100%, respectively, for detection of the coronavirus in 83 total respiratory swab samples,” the researchers reported.

They added: “The future development of portable microfluidic-based cartridges and lyophilized reagents to run the assay could enable point-of-care testing outside of the clinical diagnostic laboratory, such as airports, local emergency departments and clinics and other locations.”

Speaking with GEN earlier this year, Chiu articulated the need for rapid diagnostics to detect COVID-19: “It’s absolutely critical that we have very rapid diagnostics that can be moved from the clinical labs to point-of-care settings,” Chiu said. After noting that one of the few tools available to stop the spread of the virus is self-quarantine, he added: “Having the ability to test at home is going to be critical.”

Proteins Disclosed

In addition to Cas12, Mammoth has disclosed the use of its platform with two other unique CRISPR proteins: Cas13, which targets and recognizes single-stranded RNA; and Cas14, a protein which targets single-stranded DNA, and was discovered by Doudna’s laboratory. Used together, the proteins enable the diagnostic to sense virtually any type of nucleic acid. All three are programmable by a guide RNA that aligns with the sequence users want to detect. Then the Cas nuclease cleaves reporter molecules to signal that a match has been found.

The company is also exploring a new Cas protein family, CasΦ, which is encoded exclusively in the genomes of huge bacteriophages. CasΦ was also discovered and characterized by Doudna’s laboratory, and was detailed in “CRISPR-CasΦ from huge phages is a hypercompact genome editor,” a study published July 17 in Science.

“We hope Cas14 and CasΦ will enable more efficient genome editing in diverse organisms and tissues,” Tyler J. Ford PhD, wrote in an October 19 post on Mammoth’s blog. “Neither Cas14 nor CasΦ comes from a human pathogen. Thus, they may be less likely than SpCas9 to trigger immune responses when used in humans.”

Ford added that Cas14 nor CasΦ have the advantages of having less restrictive PAM requirements than SpCas9, and being smaller than SpCas19, making it easier for proteins from both families to deliver to target tissues.

Last August, Mammoth was granted an EUA from the FDA for its SARS-CoV-2 DETECTR Reagent Kit, designed to detect nucleic acid from SARS-CoV-2 in upper respiratory specimens. The test extracts, isolates, and purifies SARS-CoV-2 nucleic acid for simultaneous reverse transcription into cDNA, followed by amplification using loop-mediated amplification (RT-LAMP).

Last year, Mammoth exclusively licensed two U.S. patents  granted to the regents of the University of California that cover CRISPR collateral cleavage diagnostic systems.

The scalable assay for central labs isn’t the only test Mammoth is developing against COVID-19.

In May, the company announced a collaboration with GlaxoSmithKline’s GSK Consumer Healthcare to develop a handheld test designed to apply the DETECTR platform at “point of need,” allowing for use wherever patients are, versus traditional “point of care” diagnostics used in healthcare facilities, but which require centralized processing of samples. By developing a point-of-need test, Mammoth said, it can better stop COVID-19 spreading from pre-symptomatic and asymptomatic patients through a test that is accurate, easy-to-use, fully disposable, and rapid.

That handheld test is still in the works, Martin said, without offering new details.

“We’re continuing to be very excited about that partnership, and we’re making a lot of progress,” Martin said. “We’ll have more announcements about that in the future.”

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