UC Berkeley scientists spin up a robotic COVID-19 testing lab

As doctors close to the state scramble to diagnose instances of COVID-19, scientists at the University of California, Berkeley’s Ground breaking Genomics Institute (IGI) are making from scratch a diagnostic lab with the capability to method extra than 1,000 patient samples for every working day.

This pop-up laboratory, the energy of a one of a kind volunteer staff of tutorial and company partners, will give desperately necessary testing capability in the Bay Area for those people with COVID-19 signs or symptoms and also help public overall health officers evaluate how widespread the epidemic is.

Postdoctoral fellows Jenny Hamilton and Enrique Lin Shiao with an automated liquid-managing robot (Hamilton STARlet) that will be utilised to evaluate swabs from people to diagnose COVID-19. Hamilton and Shiao volunteered to teach to turn into CLIA certified so as to method patient samples. When examining authentic samples from people, they would be wearing whole individual protecting devices (PPE), such as mask, face protect, robe and gloves. Impression credit history: Max & Jules Pictures

“The UC Berkeley staff is racing to tackle this important public overall health circumstance by setting up a testing lab that will be straight away impactful in our neighborhood, whilst also producing data that contributes to understanding the distribute of the SARS-CoV-two virus,” stated Jennifer Doudna, professor of molecular and mobile biology and of chemistry and IGI govt director. SARS-CoV-two is the coronavirus that triggers COVID-19.

Many thanks to the emergency modification of condition and federal rules and California’s declared condition of emergency, the IGI was ready to associate with clinicians at University Health Companies, UC Berkeley’s university student overall health heart, and the two regional and national organizations to provide in the robotic and analytical devices necessary, set up a risk-free and robust pipeline for clinical sample consumption and processing, get hold of the needed regulatory approvals and teach a crew of very proficient scientists accustomed to conducting essential investigation to evaluate patient swabs with a rapid-turnaround aim of significantly less than 24 hrs.

A sketch of the coronavirus, dubbed SARS-CoV-two, that triggers COVID-19. The brighter blobs encompassing the virus are the “spike” proteins that give coronaviruses their identify and which permit the virus to enter cells. The lighter orange blobs are other proteins embedded in the viral envelope.Impression credit history: Desiree Ho

The scientists — extra than 50 volunteers from UC Berkeley, UC San Francisco and regional data management organizations — strategy to exam their 1st actual viral samples early this week and intention for certification beneath the Scientific Laboratory Advancement Amendments (CLIA) program by up coming week.

When the testing lab will emphasis originally on samples from learners and other customers of the UC Berkeley neighborhood, the staff is currently coordinating with health-related facilities close to the East Bay to at some point provide immediate turnaround to also meet their diagnostic requirements.

“We mobilized a staff of gifted tutorial scientists, partnered with gurus from organizations and pulled collectively, in a subject of a couple of days, a team that is running like a biotech organization. It is seriously a remarkable story,” stated Doudna, who is also a Howard Hughes Clinical Institute investigator.

The lab will operate testing primarily based on a method authorized by the Food and Drug Administration, but with bigger throughput than quite a few industrial labs, some of which even now must operate samples manually, one particular at a time. The higher-throughput equipment, some sourced from campus investigation labs, can exam extra than 300 samples at once and give the diagnostic outcome in significantly less than 4 hrs from receipt of patient swabs. Using robotics and a streamlined method, the IGI pop-up lab will shortly complete 1,000 checks daily, with the capacity to ramp up to three,000 checks for every working day if vital.

“We are implementing an current exam in a way that leverages robotics and immediate turnaround situations so that we can provide final results quickly to health-related facilities close to the East Bay and give a important provider to our neighborhood in this time of require,” Doudna stated.

“This is just an astounding prospect,” stated Person Nicolette, UC Berkeley’s assistant vice chancellor for University Health Companies. “I am stunned at how quickly Berkeley was ready to mobilize and to just take edge of the more recent policies in buy to innovate extra quickly. The lab side of issues has been so reliant on human guide function that this would be a match changer in a good deal of methods.”

Given constraints on the range of exam kits readily available in California and evolving rules on who should be examined, health-related personnel at UHS’s Tang Heart have to date sent out only a couple of dozen swabs from learners for testing by regional industrial labs. A person was returned as optimistic for the SARS-CoV-two virus that triggers COVID-19. But according to Nicolette, turnaround in the Bay Area has varied extensively and can exceed a week, leaving symptomatic people and clinicians doubtful of their position, generally making anxiety.

He is optimistic that the on-campus diagnostic lab will permit a great deal wider testing that will give a far better image of how common the virus is, given that quite a few persons put up with mild or no signs or symptoms, nevertheless can be contagious. Huge-scale testing has been important to the capacity of other countries to command the distribute of disorder by pinpointing infected folks, he stated.

“There are other facets of broader testing that would be so clinically potent,” he stated. “We could make far better conclusions about overall health, about function, about perhaps how long we require to keep on to socially length, primarily based on what we discover.”

The power of automation and robotics

The IGI’s scientific director for technological innovation and translation, Fyodor Urnov, played a significant function in mobilizing sources — devices, persons and income — right after a March 13 assembly of 59 persons inside the institute. The basic strategy necessary to exam for a virus — isolating RNA from a sample and amplifying it using the polymerase chain response (PCR) — is program in dozens of labs at most universities. The important, Urnov stated, was to quickly figure out how to scale and automate the method for clinical use.

Dirk Hockemeyer, an associate professor of molecular and mobile biology, testing techniques in the pipeline that will be utilised to evaluate patient samples. When testing actual patient swabs, he will don whole PPE. Impression credit history: Max & Jules Pictures

UC Berkeley labs possessing higher-throughput PCR equipment donated their devices to the result in, whilst IGI proven robotic sample managing as effectively as protected data management.

“We threw our R&D (investigation and development) mentality into understanding how we can scale it up and accelerate it, simply because we comprehended this essential require of the health-related neighborhood,” stated Urnov, a professor of molecular and mobile biology who put in 15 a long time in the biotech field right before coming to UC Berkeley. “Who we are as scientists seriously connected to an unmet require.”

Scientific testing of patient samples is very regulated, necessitating CLIA certification not only of lab scientists, but of the actual laboratory area, devices and excellent command methods. When the Tang Heart has two CLIA-certified lab scientists, the heart does not have a Biosafety Amount two (BSL2) lab needed for testing viruses like SARS-CoV-two.

Many thanks to the new rules, however, the Tang Center’s certification is being prolonged to the BSL2 lab in the IGI, and the scientists who volunteered to do the testing are now taking an accelerated instruction program to be ready to operate the devices 24/seven, if vital.

Apart from quickly turnaround, Urnov stated, the major emphasis is precision, something that dogged the Facilities for Condition Manage and Prevention’s first exam kits and delayed widespread testing for a important thirty day period at the starting of the epidemic in the United States.

“We have controls for our controls,” he stated. ”A good deal of function has absent into ensuring that we are correct when we inform clinicians regardless of whether their patient is optimistic or negative.”

As Urnov and his staff ramp up diagnostics, other scientists at UC Berkeley have damaged into about a dozen “rapid investigation reaction teams” to emphasis on other COVID-associated investigation tasks, such as feasible enhanced diagnostics, new prescription drugs to deal with the infection and methods to provide prescription drugs to people.

“We are chatting about a team of extra than 100 persons who are actively collaborating in investigation tasks, such as persons from UCSF, Stanford and the Gladstone Institutes,” Doudna stated. “These for a longer time-time period tasks tackle the ongoing require to have an understanding of this household of viruses and to put together for long run outbreaks now.”

Supply: UC Berkeley