Uncertainty and fear about coronavirus’ spread and the course of the illness is causing shockwaves in our daily lives. A simple paper test could provide answers to basic questions and shape a sensible course forward.
In the media, within local communities, and even among our elected leaders, there’s reasonable debate about whether the threat of coronavirus has been over-exaggerated or understated. But the lack of consistent guidance on what we should do collectively and individually has caused uncertainty and fear. The markets have tumbled, employees are asked to work from home, and major events are postponed indefinitely.
All of this uncertainty and fear stems from a lack of data about the spread and severity of the SARS-CoV-2 virus in our communities. Where is this virus concentrated, and how does it spread from person to person? What’s the exact range of symptoms, and how does the COVID-19 illness progress? We are unable to answer these basic questions, which in turn leads us to fear and prepare for the worst. To answer these questions, we need to test massive populations of people for SARS-CoV-2 quickly, cheaply, and scalably.
CRISPR to the rescue
One potential solution to this diagnostic problem may have presented itself in the form of the gene editing molecular tool called CRISPR. If you haven’t heard about CRISPR, it’s a genetic engineering tool that allows us to find-and-replace DNA with extremely high precision. Combined with high-scale advances in automation and computation, CRISPR promises to be a real game-changer in the field of synthetic biology, impacting everything from chemicals and materials to food and health.
Jennifer Doudna, Professor at UC Berkeley, is one of the discoverers of the CRISPR tool that enables researchers around the world to precisely find and replace DNA sequences in a cell. She’s a co-founder of Mammoth Biosciences, which is using the technology as the basis for developing a rapid, cheap test for coronavirus and much more. UC BERKELEY
CRISPR’s precision has an uncanny ability to find a specific sequence within a sample, and one startup has a way to test for coronavirus in 30 minutes (the whole process including sample preparation will take about 4 hours).
The startup is Mammoth Biosciences, and it was spun out of the laboratory of Jennifer Doudna, one of the inventors of CRISPR. Mammoth has been working on its diagnostic system called DETECTR to be a robust platform to test for diseases. In collaboration with professor of laboratory medicine Charles Chiu at UCSF—the epicenter of the brain trust for the coronavirus especially in the Bay Area—Mammoth has prototyped a rapid detection diagnosis kit using CRISPR to detect the SARS-COV-2 in human samples.
“On the clinical side, the main area of need right now for us is the ability to ramp up capacity for diagnostic testing for this virus,” said Chiu during a coronavirus town hall I hosted earlier this week. “It’s absolutely imperative for us to be able to diagnose infection both rapidly and accurately as a way to prevent further spread.”
Mammoth and Chiu’s lab co-published a white paper on their method two weeks ago, along with actual findings and results from human samples in a pre-print paper this past Tuesday. They released the data before peer review as part of the rapid response to the pandemic. For use in diagnostic testing outside the research lab, the FDA would first need to approve the diagnostic test.
“We are breaking land speed records here in prototyping and development,” said Trevor Martin, co-founder and CEO of Mammoth, about SARS-COV-2 DETECTR and the team’s ability to develop a system so quickly. he said. He told me how DETECTR works compared to current tests.
Trevor Martin, Ph.D. co-founder and CEO of Mammoth Biosciences, says his company’s CRISPR technology can act as a “Google search” of coronavirus or any other disease, and be deployed on paper test strips, much like a home pregnancy test. MAMMOTH BIOSCIENCES
How we test for coronavirus today: slow and sloppy
Many current diagnostic methods and resources are slow, have limited distribution, and costly. The US CDC6 58 created an Emergency Use Authorization (EUA) assay to test the components of patients samples for SARS-CoV-2 . The assays’ analysis methods take up to 4-6 hours to complete for each patient.
On top of that, the necessary turnaround time needed to screen and diagnose patients takes more than 24 hours, as these samples need to be shipped to laboratories that have the proper machinery to perform tests. All in all, this process could potentially take 2 days to a week for a single patient’s sample.
CAS12: The “Google search” for coronavirus
Enter DETECTR and CAS12, a CRISPR protein. All that is needed are reagents, a heat block, pipette, and lateral flow strips. No expensive equipment needed, and no need to send a product to a lab far away. Instead, DETECTR is a simple system that requires only what materials in a hospital or lab often already have. As Martin explained it, it’s “as much off the shelf as possible.” Local test centers could get the supplies sent to them relatively easily as it requires no clunky machinery to set-up. “We thought about the supply and manufacturing chain at every step,” Martin told me. This is specifically so that the system could potentially be used in a pandemic situation, even in developing countries with little infrastructure.
The DETECTR method is unique in that it is simple. Patients provide a sample in the form of a nasal or oral swab, the RNA is converted to DNA via a reaction combined with an initial isothermal amplification and then CAS12 is mixed with pre-defined SARS-COV-2 guide sequences with the reaction read out on Mammoth’s lateral flow strips. The CAS12 protein searches across the DNA sample to look for the presence of the programmed SARS-COV-2 sequence. If there is a match, CAS12 binds to the DNA and gives off a signal by cleaving reporter molecules, causing the strip to change color.
“If you need a rapid result quickly without complicated machinery, then we have demonstrated the assay concept”, Martin told me.
Mammoth may have done more than show that CRISPR can diagnose SARS-COV-2 cheaper and faster. They proved that they can create a platform that can undergo quick development cycles (less than two weeks for SARS) to address emerging diseases.
Where DETECTR could take us in the future
Dr. Chiu discussed how they could improve the current platform. He described the next step is to build out the “ability to develop multiplex tests that would test not only for coronaviruses, but other respiratory viruses and other respiratory pathogens simultaneously.” Instead of testing for one virus, patients can check if they have SARS-CoV-2 or another flu strand.
Charles Chiu, M.D., Ph.D. of UCSF’s Department of Laboratory Medicine, has been saying what many are just now realizing: Testing is absolutely imperative for us to be able to diagnose infection and prevent further spread of coronavirus. UCSF
James Currier, Managing Partner of NFX and investor in the company, described the platform’s potential in a blog post: “Imagine one of those quick pregnancy tests you buy at the pharmacy, but instead of just pregnancy you could test for nearly anything. Applied to healthcare, you could detect the presence of flu, STDs, cancers, TB, strep, etc.”
You can zoom out even further, says Currier. “Applied to industry, you could test for biomaterial in oil, chemicals, and plastics. In agriculture you would be able to screen meat, fish, and every silo of grain both before and after shipping, or before pricing. You’d be able to do all this at room temperature, on site, in under an hour, with no special equipment.”
This level of testing can be abstracted even further to measure real-time movements of viruses, chemicals, and materials. Currier imagines that a day when consumers can order a strip for the specific genetic sequence they are testing for, and within a short time have a colorized response whether the sequence is present. Then they could upload their results via a mobile app to the cloud, which in turn would provide “real time insights as specific strains spread through different geographies, and better predict which strains should go into future flu shots. Timely warning systems could be developed to impact the spread of infectious diseases.”
What Mammoth is creating is a “high quality molecular tests that you can deploy anywhere”, Martin says. Current decentralized diagnostic methods just don’t exist right now and clearly we are seeing the effects of it now with this pandemic.
Accelerating the manufacturing pipeline
In the coronavirus town hall meeting, Martin and Chiu made it clear that SARS-COV-2 DETECTR was a proof of concept that is not yet ready for manufacturing. What’s the bottleneck? What’s standing in the way of making these tests available to consumers in weeks or months?
“There’s a desire for partners that have demonstrated manufacturing capability for each of the components,” said Martin, “ from lateral flow strips to the reagent chemistry itself.” That’s the short-term need. In the medium to long term, it will take cartridge manufacturers, disposable chemistry systems, and companies that have experience manufacturing on the scale of hundreds of thousand to millions of units.
Basically, scientists are going to have to learn how to make their technology manufacturable, and manufacturers are going to have to learn how to innovate at the speed of Silicon Valley. It is a huge, coordinated effort, but one that is needed for us to respond effectively to this pandemic—and the next.
Thank you to Vinit Parekh and Kevin Costa for additional research and reporting in this article. I’m the founder of SynBioBeta, and some of the companies that I write about—including Mammoth Biosciences and NfX—are sponsors of the SynBioBeta conference and weekly digest — here’s the full list of SynBioBeta sponsors.0