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Clinical Laboratories and Pathology Groups

Hosted by Robert Michel
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UC Berkeley Creates COVID-19 Robotic Testing Laboratory in Record Time by Reallocating Equipment and Training Researchers to Do Clinical Analysis

Medical laboratory leaders may be inspired by this rapid start-up and its outreach to students and the Bay area

In what could take a typical clinical laboratory months or even years to launch, the Innovative Genomics Institute (IGI) at the University of California, Berkeley managed to make a COVID-19 diagnostic testing laboratory operational in just a few weeks. 

Even more impressive is that the automated testing lab can reportedly process (with results in four hours) up to 3,000 patient samples daily for SARS-CoV-2, the coronavirus that causes the COVID-19 illness.

The IGI COVID-19 testing laboratory has high-throughput polymerase chain reaction (PCR) machines—some reallocated from idle university research labs—which can process the CDC 2019-novel coronavirus Real-Time (RT) PCR diagnostic panel, according to a Berkeley news release.

“All of our laboratories do PCR every day. But for this test we need to go above and beyond to ensure accurate detection,” said Jennifer Doudna, PhD, IGI Executive Director and UC Berkeley Professor of Molecular and Cell Biology, in an IGA news release.

“We put in place a robotic pipeline for doing thousands of tests per day,” she continued, “with a pipeline for managing the data and getting it back to clinicians. Imagine setting that up in a couple of weeks. It’s really extraordinary and something I’ve never seen in my career.”

In operation since April 6, the Berkeley COVID-19 testing lab’s main source for referrals is the University Health Services Tang Center. Testing services also are offered to medical centers across the East Bay area, San Francisco Business Times reported.

Robert Sanders, UC Berkeley’s Manager Science Communications, told Dark Daily the COVID-19 lab performs about 180 tests per day and has tested 1,000 people so far—80% of the samples came from the campus community. About 1.5% to 4% of the tests were found to be positive for the SARS-CoV-2 coronavirus among the groups tested.

“We hope other academic institutions will set up testing labs too,” he said.

How Did Berkeley Set Up a COVID-19 Diagnostic Lab So Fast?

To get up and running quickly, university officials drew from the campus and surrounding business community to equip and operate the laboratory, as well as, train researchers to do clinical analysis of patient samples.

Though the methodology to test for the coronavirus—isolating RNA from a biological sample and amplifying it with PCR—is standard fare in most research labs worldwide, including at UC Berkeley, the campus’ research labs were shuttered due to the spread of the coronavirus.

IGI reached out to the idle labs for their high-throughput PCR systems to start-up the lab. Through its partnership with University Health Services and local and national companies, IGI created an automated sample intake and processing workflow.

Additionally, several research scientists who were under government-mandated stay-at-home orders made themselves available. “My own research is shut down—and there’s not very much I can do other than stay in my home … finally I’m useful,” said PhD candidate Holly Gildea in a Berkeleyside article which noted that about 30 people—mostly doctoral students and postdoctoral researchers—are being trained to oversee the process and monitor the automated equipment.     

Postdoctoral fellows Jenny Hamilton (left) and Enrique Shao (right) with an automated liquid-handling robot (Hamilton Microlab STAR), which 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 and caption copyright: Max and Jules Photography/UC Berkeley.)

Federal and State Authorities Remove Hurdles

In her article, “Blueprint for a Pop-up SARS-CoV-2 Testing Lab,” published on the medRxiv servers, Doudna summarized “three regulatory developments [that] allowed the IGI to rapidly transition its research laboratory space into a clinical testing facility.

  • “The first was the FDA’s March 16th Policy for Diagnostic Tests for Coronavirus Disease-2019 during the Public Health Emergency. This policy simplified the process for getting authorization for a testing method and workstream.
  • “The second was California Governor Newsom’s Executive Order N-25-20, which modified the requirements for clinical laboratory personnel running diagnostic tests for SARS-CoV-2 in a certified laboratory.
  • “The third was increased flexibility and expediency at the state and federal levels for certification and licensure requirements for clinical laboratory facilities under the Clinical Laboratory Improvement Amendments (CLIA) program. Under these emergency conditions, the California Department of Public Health (CDPH) was willing to temporarily extend—once the appropriate regulatory requirements have been fulfilled—an existing CLIA certificate for high-complexity testing to a non-contiguous building on our university campus.”

“These developments,” wrote Doudna, “enabled us to develop and validate a laboratory-developed test (LDT) for SARS-CoV-2, extend the UC Berkeley Student Health Center’s clinical laboratory license to our laboratory space, and begin testing patient samples.”

Lessons Learned Implementing a Pop-Up COVID-19 Testing Laboratory

“Our procedures for implementing the technical, regulatory, and data management workstreams necessary for clinical sample processing provide a roadmap to others in setting up similar testing centers,” she wrote. 

Learned strategies Doudna says could aid other academic research labs transform to a “SARS-CoV-2 Diagnostic Testing Laboratory include:

  • Leveraging licenses from existing CLIA-certified labs;
  • Following FDA authorized testing procedures;
  • Using online HIPAA training;
  • Managing supply chain “bottlenecks” by using donated equipment;
  • Adopting in-house sample barcoding;
  • Adapting materials, such as sampling tubes, to work with donated equipment;
  • Reaching out for donations of personal protective equipment (PPE).

Cost of equipment and supplies (not including staff) was $550,000, with a per test cost of $24, Doudna noted.  

“As the COVID-19 pandemic continues, our intention is to provide both PCR-based diagnostic testing and to advance research on asymptomatic transmission, analyze virus sequence evolution, and provide benchmarking for new diagnostic technologies,” she added.

Medical laboratory leaders understand that the divide between clinical and research laboratories is not easy to surmount. Nevertheless, UC Berkley’s IGI pulled it off. The lab marshaled resources as it took on the novel coronavirus, quickly developed and validated a test workflow, and assembled and trained staff to analyze tests with fast TAT to providers, students, and area residents. There’s much that can be learned from UC Berkeley IGI’s accomplishments.

—Donna Marie Pocius

Related Information:

Berkeley Scientists Spin Up a Robotic COVID-19 Testing Lab

IGI Launches Major Automated COVID-19 Diagnostic Testing Initiative

Berkeley Lab Pivots from Editing DNA to Processing COVID-10 Tests

Governor Newsom Declares State of Emergency to Help State Prepare for Broader Spread of COVID-19

Governor Newsom Issues New Executive Order Further Enhancing State and Local Government’s Ability to Respond to COVID-19 Pandemic

Jennifer Doudna’s Berkeley Institute Launches COVID-19 Testing Lab

UC Berkeley to Test 5,000 Healthy People in Bay Area for Coronavirus

Blueprint for a Pop-up SARS-CoV-2 Testing Lab

CRISPR Pioneer Doudna Opens Lab to Run COVID-19 Tests