As medical doctors across the nation scramble to diagnose instances of COVID-19, scientists on the College of California, Berkeley’s Modern Genomics Institute (IGI) are creating from scratch a diagnostic lab with the potential to course of greater than 1,000 affected person samples per day.
This pop-up laboratory, the trouble of a singular volunteer staff of educational and company companions, will present desperately wanted testing capability within the Bay Space for these with COVID-19 signs and likewise assist public well being officers assess how widespread the epidemic is.
“The UC Berkeley team is racing to address this critical public health situation by establishing a testing lab that will be immediately impactful in our community, while also generating data that contributes to understanding the spread of the SARS-CoV-2 virus,” stated Jennifer Doudna, professor of molecular and cell biology and of chemistry and IGI govt director. SARS-CoV-2 is the coronavirus that causes COVID-19.
Because of the emergency modification of state and federal laws and California’s declared state of emergency, the IGI was in a position to companion with clinicians at College Well being Companies, UC Berkeley’s pupil well being heart, and each native and nationwide corporations to herald the robotic and analytical tools wanted, set up a protected and sturdy pipeline for medical pattern consumption and processing, receive the required regulatory approvals and prepare a crew of extremely expert scientists accustomed to conducting elementary analysis to investigate affected person swabs with a quick-turnaround purpose of lower than 24 hours.
The scientists — greater than 50 volunteers from UC Berkeley, UC San Francisco and native information administration corporations — plan to check their very first viral samples early this week and goal for certification underneath the Medical Laboratory Enchancment Amendments (CLIA) program by subsequent week.
Whereas the testing lab will focus initially on samples from college students and different members of the UC Berkeley neighborhood, the staff is already coordinating with medical facilities across the East Bay to ultimately supply speedy turnaround to additionally meet their diagnostic wants.
“We mobilized a team of talented academic scientists, partnered with experts from companies and pulled together, in a matter of a few days, a group that is operating like a biotech company. It is really a remarkable story,” stated Doudna, who can be a Howard Hughes Medical Institute investigator.
“This is just an amazing opportunity. … The lab side of things has been so reliant on human manual work that this would be a game-changer in a lot of ways.” — Man Nicolette, UC Berkeley’s assistant vice chancellor for College Well being Companies
The lab will run testing primarily based on a course of authorised by the Meals and Drug Administration, however with increased throughput than many business labs, a few of which nonetheless should run samples manually, one after the other. The high-throughput machines, some sourced from campus analysis labs, can take a look at greater than 300 samples without delay and supply the diagnostic end in lower than 4 hours from receipt of affected person swabs. Utilizing robotics and a streamlined course of, the IGI pop-up lab will quickly carry out 1,000 exams every day, with the flexibility to ramp as much as 3,000 exams per day if obligatory.
“We are implementing an existing test in a way that leverages robotics and rapid turnaround times so that we can deliver results quickly to medical centers around the East Bay and provide a critical service to our community in this time of need,” Doudna stated.
“This is just an amazing opportunity,” stated Man Nicolette, UC Berkeley’s assistant vice chancellor for College Well being Companies. “I am amazed at how quickly Berkeley was able to mobilize and to take advantage of the newer rules in order to innovate more quickly. The lab side of things has been so reliant on human manual work that this would be a game-changer in a lot of ways.”
Given limitations on the variety of take a look at kits accessible in California and evolving pointers on who ought to be examined, medical employees at UHS’s Tang Middle need to date despatched out solely a few dozen swabs from college students for testing by native business labs. One was returned as constructive for the SARS-CoV-2 virus that causes COVID-19. However in accordance with Nicolette, turnaround within the Bay Space has diverse extensively and might exceed per week, leaving symptomatic sufferers and clinicians uncertain of their standing, typically creating anxiousness.
He’s optimistic that the on-campus diagnostic lab will permit a lot wider testing that may present a greater image of how prevalent the virus is, on condition that many individuals endure gentle or no signs, but may be contagious. Massive-scale testing has been key to the flexibility of different international locations to manage the unfold of illness by figuring out contaminated people, he stated.
“There are other aspects of broader testing that would be so clinically powerful,” he stated. “We could make better decisions about health, about work, about possibly how long we need to continue to socially distance, based on what we find.”
The ability of automation and robotics
The IGI’s scientific director for expertise and translation, Fyodor Urnov, performed a significant position in mobilizing assets — tools, individuals and cash — after a March 13 assembly of 59 individuals throughout the institute. The essential approach wanted to check for a virus — isolating RNA from a pattern and amplifying it utilizing the polymerase chain response (PCR) — is routine in dozens of labs at most universities. The important thing, Urnov stated, was to shortly determine learn how to scale and automate the method for medical use.
UC Berkeley labs possessing high-throughput PCR machines donated their tools to the trigger, whereas IGI established robotic pattern dealing with in addition to safe information administration.
“We threw our R&D (research and development) mindset into understanding how we can scale it up and accelerate it, because we understood this fundamental need of the medical community,” stated Urnov, a professor of molecular and cell biology who spent 15 years within the biotech trade earlier than coming to UC Berkeley. “Who we are as scientists really connected to an unmet need.”
Medical testing of affected person samples is extremely regulated, requiring CLIA certification not solely of lab scientists, however of the particular laboratory area, tools and high quality management procedures. Whereas the Tang Middle has two CLIA-certified lab scientists, the middle doesn’t have a Biosafety Stage 2 (BSL2) lab required for testing viruses like SARS-CoV-2.
Because of the brand new laws, nevertheless, the Tang Middle’s certification is being prolonged to the BSL2 lab within the IGI, and the scientists who volunteered to do the testing are actually taking an accelerated coaching program to have the ability to function the tools 24/7, if obligatory.
Except for quick turnaround, Urnov stated, the principle focus is accuracy, one thing that dogged the Facilities for Illness Management and Prevention’s unique take a look at kits and delayed widespread testing for a crucial month firstly of the epidemic in the US.
“We have controls for our controls,” he stated. ”Lots of work has gone into guaranteeing that we’re correct after we inform clinicians whether or not their affected person is constructive or destructive.”
As Urnov and his staff ramp up diagnostics, different researchers at UC Berkeley have damaged into a couple of dozen “rapid research response teams” to deal with different COVID-related analysis initiatives, together with attainable improved diagnostics, new medication to deal with the an infection and methods to ship medication to sufferers.
“We are talking about a group of more than 100 people who are actively participating in research projects, including people from UCSF, Stanford and the Gladstone Institutes,” Doudna stated. “These longer-term projects address the ongoing need to understand this family of viruses and to prepare for future outbreaks now.”