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.
“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.”
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 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;
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.
Asian locales reacted swiftly to the threat of COVID-19 by leveraging lessons learned from previous pandemics and making use of serology testing in aggressive contact tracing
America’s healthcare leaders in government, hospitals, clinical pathology, and medical laboratories can learn important lessons from the swift responses to the early outbreaks of COVID-19 in countries like Taiwan and South Korea and in cities like Singapore and Hong Kong.
Strategies such as early intervention, commitment to tracing contacts of infected people within two hours, quarantines, and social distancing all contributed to significantly curtailing the spread of the latest coronavirus pandemic within their borders, The New York Times (NYT) reported.
Another response common to the efforts of these countries and cities was the speedy introduction of clinical laboratory tests for SARS-CoV-2, the novel coronavirus that causes coronavirus disease 2019 (COVID-19), supported by the testing of tens of thousands of people in the earliest stages of the outbreaks in their communities. And that preparation and experience is paying off as those countries and cities continue to address the spread of COVID-19.
‘We Look at SARS as the Dress Rehearsal’
“Maybe it’s because of our Asian context, but our community
is sort of primed for this. We will keep fighting, because isolation and
quarantine work,” Lalitha
Kurupatham, Deputy Director of the Communicable Diseases Division in
Singapore, told the NYT. “During peacetime, we plan for epidemics like
this.”
Clinical laboratory leaders and pathologists may recall that Hong Kong was the site of the 2003 severe acute respiratory syndrome (SARS) epidemic. About 8,096 people worldwide were infected, and 774 died from SARS, according to the World Health Organization (WHO). In Hong Kong, 299 died out of 1,755 cases. However, Singapore had just 238 cases and 33 deaths.
To what does Singapore attribute the country’s lower
COVID-19 infection/death rate today?
“We can look at SARS as the dress rehearsal. The experience was raw, and very, very visceral. And on the back of it, better systems were put in place,” Jeremy Lim, MD, Co-Director of the Leadership Institute for Global Health Transformation at the National University of Singapore, told TIME.
“It’s a mix of carrots and sticks that have so far helped us. The US should learn from Singapore’s response and then adapt what is useful,” Lim added.
Singapore Debuts Serology Testing for COVID-19 Tracking
As microbiologists and infectious diseases doctors know, serology tests work by identifying antibodies that are the sources of infection. In the case of COVID-19, these tests may have aided in the surveillance of people infected with the coronavirus.
This is one lesson the US is learning.
“CDC (Centers for Disease Control and Prevention) has developed two serological tests that we’re evaluating right now, so we can get an idea through surveillance what’s the extent of this outbreak and how many people really are infected,” Robert Redfield, MD, CDC Director, told STAT.
The graphic above, which is based on data from the federal Centers for Disease Control and Prevention, illustrates how contact tracing is accomplished. “We believe this is the first time in the world where these particular tests have been used in this context of contact tracing,” Danielle Anderson, PhD, Scientific Director, Duke-NUS Medical School ABSL3 Laboratory, told Science. (Graphic copyright: CDC/Carl Fredrik Sjöland.)
‘Leaving No Stone Unturned’
As of March 27, Singapore (located about 2,374 miles from
mainland China with a population of 5.7 million) had reported 732 COVID-19
cases and two deaths, while Hong Kong had reported 518 cases and four deaths.
According to Time, in its effort to battle and treat
COVID-19, Singapore took the following steps:
Clinical laboratory testing for COVID-19 of all
people presenting with “influenza-like” and pneumonia symptoms;
Contact tracing of each infected person,
including interviews, review of flight manifests, and police involvement;
Using locally developed test to find antibodies
after COVID-19 clears;
Ran ads on page one of newspapers urging people
with mild symptoms to see a doctor; and
Government paid $100 Singapore dollars per day to
quarantined self-employed people.
The Singapore government’s WhatsApp account shares updates on the coronavirus, and Singapore citizens acquire wearable stickers after having their temperature checked at building entrances, Wired reported. The article also noted teams of healthcare workers are kept separate in hospitals—just in case some workers have to be quarantined.
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Meanwhile, in Hong Kong, citizens donned face masks and
pressured the government to respond to the COVID-19 outbreak. Officials subsequently
tightened borders with mainland China and took other action, the NYT reported.
Once the COVID-19 genetic sequence became available, national medical laboratory networks in Singapore, Hong Kong, and Japan developed their own diagnostic tests, reported The Lancet, which noted that the countries also expanded capacity for testing and changed financing systems, so people would not have to pay for the tests. In Singapore, the government pays for hospitalization as well, noted The Lancet.
Lessons Learned
The US has far less experience with pandemics, as compared to the Asian locales that were affected by the H1N1 influenza (Spanish Flu) of 1918-1920 and the H5N1 influenza (Avian Flu) of 1957-1958.
And, controversially, National Security Council (NSC) officials in 2018 discontinued the federal US Pandemic Response Unit, moving the NSC employees into other government departments, Associated Press reported.
According to the March 26 US Coronavirus Task Force’s televised
news conference, 550,000 COVID-19 tests have been completed nationwide and
results suggest 86% of those tested are negative for the disease.
The fast-moving virus and rapidly developing story are placing
medical laboratory testing in the global spotlight. Pathologists and clinical laboratory
leaders have a unique opportunity to advance the profession, as well as improving
the diagnosis of COVID-19 and the health of patients.
