UC Berkeley lab pivots from editing DNA to processing COVID-19 tests

What happens when you combine a viral pandemic, an empty laboratory and a bunch of biologists who’ve been forced to put their regular work on pause?

Postdoctoral fellows Jenny Hamilton and Enrique Shao with an automated liquid-handling robot (Hamilton STARlet) that will be used to analyze swabs from patients to diagnose COVID-19. Hamilton and Shao volunteered to train to become CLIA certified so as to process patient samples. When analyzing real samples from patients, they would be wearing full personal protective equipment (PPE), including mask, face shield, gown and gloves. Photo: Max & Jules Photography/UC Berkeley

What happens when you combine a viral pandemic, an empty laboratory and a bunch of biologists who’ve been forced to put their regular work on pause?

In a matter of days, a UC Berkeley science building has converted to a COVID-19 test processing center, with researchers hoping to enable up to thousands more coronavirus tests per day in the East Bay.

The Innovative Genomics Institute at Berkeley Way and Oxford Street — founded by Jennifer Doudna, co-developer of gene-editing technology CRISPR — houses robots that will process samples from nearby medical centers and return the results in 12-24 hours instead of the usual several days, scientists say. The initiative is set to begin processing samples from UC Berkeley’s Tang Center by the end of the week, but the researchers hope to expand the effort to other medical clinics in the region too.

“We put in place a robotic pipeline for doing thousands of tests per day, with a pipeline for managing the data and getting it back to clinicians,” said Doudna in a statement from IGI. “Imagine setting that up — a process that would normally take months to years — in a couple of weeks. It’s really extraordinary and not something I’ve ever seen in my career.”

The initiative is launching as reports abound of shortages and delays at every point in the coronavirus testing process across California and the United States. The city of Berkeley does not know how many people in Berkeley have been tested for the virus because, until a recent order, labs were only required to report positive results.

The IGI initiative will use a common technique called RT-PCR, which enables the detection of viral RNA in samples.

After UC Berkeley shuttered its labs and the novel coronavirus began spreading throughout the area, many scientists were hoping to apply their expertise to the local mitigation effort. About 800 faculty, graduate students and community members immediately volunteered to help out with the Berkeley effort, according to IGI.

“My own research is shut down and there’s not very much I can do other than stay in my home,” said doctoral student Holly Gildea, who early in the effort put out a Bay Area-wide call for chemical substances needed to process the samples. “Someone on Twitter compared this to being on a plane and someone asking for doctor — finally I’m useful.”

Hamilton and Shao, both postdocs in the lab of Jennifer Doudna working under a fume hood to test the diagnostic pipeline for analyzing patient samples. When analyzing samples from actual patients, they would be wearing full personal protective equipment (PPE). Photo: Max & Jules Photograph/UC Berkeley

Around 30 people — mostly doctoral students and postdoctoral researchers — are currently being trained to oversee the process and “babysit the robots,” said Jenny Hamilton, postdoctoral researcher.


The volunteers were selected for their experience working with unsafe materials — “people who have the training to do clean practices and people who have the skillset needed,” Hamilton said.

One UC Berkeley doctoral student who asked not to be named, however, said she was concerned that this “front-line work” is being done by volunteers instead of the initiative paying the skilled researchers.

Although IGI will receive samples after they’re collected at the clinic, the initiative will also supply Tang and other medical centers with the tubes and swabs they need to conduct the tests, aiming to significantly increase their testing capacity. The critical items are in short supply these days, so the Berkeley scientists have spent the past week or so seeking out products from non-traditional distributors around the world. They had to ask health care workers whether they’d be willing to use the slightly different products than they’re used to, but they were largely eager to accept any new testing materials, Hamilton said.

“Everything in this process is limiting,” she said. “The major thing we’ve been doing in the past week is to secure a supply chain.”

Revised guidelines from federal health authorities and Gov. Gavin Newsom’s emergency declaration also permitted expedited approval for the initiative, according to the IGI statement.

The Berkeley researchers are working with UC San Francisco and the Chan Zuckerberg Biohub on the sample processing work. The initiative was also inspired by similar work being done at the University of Washington, Hamilton said.

The effort is also getting underway just as the Berkeley Lab (not located in the IGI building) reported its first employee who tested positive for COVID-19. There is no indication that he got the virus while at work, however, and the lab stressed that cases are likely across all workplaces.

Hamilton said there will only be a few people in the IGI lab at a given time, always practicing social distancing.

“I’m much more concerned about someone catching SARS-CoV-2 at Berkeley Bowl than I am about anyone being exposed from one of these samples,” she said.

Natalie Orenstein reports on housing and homelessness for The Oaklandside. She was previously a reporter for Berkeleyside. Email: natalie@oaklandside.org. Twitter: nat_orenstein.