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From Genome Engineering to COVID-19 Diagnostic Testing at IGI

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The COVID-19 pandemic has caused unprecedented changes across the globe, changes in day-to-day life, healthcare systems and scientific research. How do we best respond to change? We adapt, and, in the context of a global pandemic, we adapt fast. The Innovative Genomics Institute (IGI), comprising researchers at the University of California, Berkeley and the University of California, San Francisco, has done just that by launching an impressive COVID-19 diagnostic testing laboratory at UC Berkeley.

Under normal circumstances, the institute focuses on genome engineering research aimed to treat human diseases and to end hunger. Now, they are testing over 1000 patient samples per day to diagnose COVID-19, incorporating robotics into their pipeline to make the process as efficient and safe as possible.

Technology Networks spoke with Professor Jennifer Doudna, Executive Director at IGI and Professor of Molecular and Cell Biology and Chemistry at the University of California, Berkeley, to learn exactly how this ambitious effort has been achieved.

Molly Campbell (MC): For our readers that are unfamiliar with IGI, please can you discuss the “typical” focus of research, and the decision to set up a COVID-19 testing laboratory?

Jennifer Doudna (JD):
During normal times, research at the IGI is focused on using genome engineering to treat human disease and end hunger. We’re also always working to further advance the tools we use including CRISPR, which makes genome engineering possible. On March 13, we realized we weren’t in normal times anymore. The shelter-in-place order was forcing the UC Berkeley campus to shut down all non-essential work, so we faced a decision as an institute.

I called an IGI meeting to gather ideas on how we could best serve the community during this time. We have an institute filled with deeply knowledgeable people with a drive to help, and public impact is deeply woven into IGI’s culture, so it wasn’t a question of whether we wanted to do something, but we had to figure out how we could have an immediate impact. Our solution was to launch a COVID-19 diagnostic testing lab right away, and then build on that with research that could help lead to better diagnostics and treatments.

Can you talk us through the logistics of creating the testing laboratory? What were the greatest challenges you encountered?

If only we had known all of the things we didn’t know when we started down this road! There were many challenges, many very long days, but we learned quickly because we had to. COVID-19 testing was extremely hard to come by in the East Bay — and the whole country — but it was also clearly critical to getting the outbreak under control, so we didn’t have the luxury of time. UC Berkeley is many things, but it is not a medical school, so one of the biggest challenges was navigating all of the regulatory hurdles required to run a clinical laboratory. Our volunteers staff had to be trained to work with patient samples and privacy protocols, something we don’t normally have to consider in our day-to-day research. All of this would normally take many months of work, but we were able to do it in just three weeks.

Other challenges were technological. We had to quickly develop a laboratory information management system (LIMS) to track patient-linked information and communicate securely with physicians, which we managed through the help of partners including Salesforce and Third Wave Analytics. We also had to find a way to quickly scale up our testing capacity, and protect our volunteers, which meant automating as much of the process as possible using robots.

What resources did you have to outsource, and what resources were already available to IGI?

We started with a few key advantages, but also some major hurdles. We had a willing team with the technical knowhow to perform COVID-19 diagnostic tests, labs willing to donate supplies and time and we were lucky to have a space in the IGI building that we could convert to use for the testing lab. But the lab also needed a LIMS, and one that was HIPAA compliant. Like everyone else around the country, we had to find a consistent source of test kits and PPE. The robots for the automated pipeline had to be acquired and set up for our specific use. And none of this was free or supported by our existing grants, so we had to find donors to support our efforts and technology partners willing to volunteer their time and expertise.

MC: Can you talk us through the testing procedure at IGI?

Probably the most challenging step in the process is sample collection itself, and we’re lucky to have a network of healthcare providers that are on the frontlines collecting the samples in the first place. When samples come to us, they have already been inactivated so no live virus is ever present in our facility. A sample has to be requisitioned by a physician, so every sample that comes in is tied to a unique identifier in our LIMS that follows it through the test. The first robot in the pipeline, a liquid-handling robot, scans and loads samples into 96-well plates. A second robot extracts the RNA from the sample. And then we use a thermocycler to detect the presence or absence of specific viral genetic material. The results get fed back into the LIMS, and then clinicians can communicate the results with patients.

A comic outlining IGI's COVID-19 testing process. Credit: Rachel Lew. 

MC: What populations are IGI currently conducting tests for, and do you have any expectations to expand this?

We’re currently working with partners in the East Bay to test first responders, high-risk groups, and underserved communities. We’re also partnering with public utilities across California to test essential workers who quite literally keep the lights on and the water running. The biggest expansion that we’re currently working on is a new saliva-based test for asymptomatic staff, faculty and students on the UC Berkeley campus as part of the plan to help campus reopen in Fall.

Typically, how many tests are being conducted per day?

Our pipeline can accommodate over 1000 tests per day. The exact number of tests depends on how much we’re receiving from our testing partners in the East Bay and around California, and we’re constantly balancing our capacity and the demand for tests. Now that we’ve launched asymptomatic saliva testing on the UC Campus, we’re anticipating that demand will grow, so we’re planning to add additional robots to expand the testing capacity.

How have members of staff found the experience of transitioning from research to COVID-19 testing?

When you’re told to put down your research and walk away, no scientist is thrilled to hear that. But everyone has been so enthusiastic to be part of the testing lab work. There’s a real sense of joint purpose, and an understanding that what we’re doing really matters right now to people in our community. At some point, we’ll all be back doing our core research, but I don’t think we’ll approach it quite the same way after this experience. We can do so much when we’re all behind a common goal.

What impact has COVID-19 had on the IGI’s research strategy?

In the short term, it has become our singular focus. We’ve now awarded over $2 million to fund rapid COVID-19 research projects designed to produce results in just 6–12 months. These cover next-gen diagnostics, genome sequencing and tracking, structural biology to identify therapeutic targets, and some really creative approaches like using wastewater testing to track outbreaks. In the long term, we now have a clinical laboratory — something that has never existed on the UC Berkeley campus — and that has a lot of us thinking about how we can apply that to our future work.

MC: The lab recently transitioned to using a robotic pipeline to increase the capacity of testing in the lab. Can you please tell us more about this and the impact it has had on the efficiency of conducting tests?

In short, switching to robotics has increased our capacity roughly ten-fold, and it allows us to continue to scale from there. We were able to jump from just over 100 tests per day to over 1000, and the tests are all integrated into our laboratory information management system from start to finish. Automation is not just about increasing capacity it is also about taking care of our volunteers. Manual testing takes a lot of effort and focus from our team. Automation allows fewer people to do more with less effort and reduces the number of people in the laboratory at any given time. Automation isn’t the end of what we can do. We’re doing the best we can with an accurate but inherently slow test. What we’re really excited about is what comes next. We’re working hard on developing next-generation CRISPR diagnostics that will be cheaper, faster and at least as sensitive as the current qPCR tests, and a big advantage is that they can be performed wherever you are. Tests like these could remove the need for robotics in the first place.

MC: Do you have any expectations with regards to timelines for how long the pop-up testing lab will be in operation?

Everything is changing so quickly, it’s hard to predict even what the next week will bring. Our goal isn’t to be in the testing lab business long-term, but as long as we can serve our campus and our local community, we’ll keep at it.

Jennifer Doudna was speaking to Molly Campbell, Science Writer for Technology Networks.