CRISPR Pioneer Opens Bay Area Lab to Test for Coronavirus

A team of academic and industry researchers led by Jennifer Doudna, the researcher best known for her role in the discovery of the gene editing technology called CRISPR, has turned a 2,500-square-foot scientific laboratory into a facility for running medical tests to detect the novel coronavirus that causes COVID-19.

The laboratory, which plans to serve hospitals in the San Francisco Bay Area, says it will be able to process more than 1,000 patient samples a day with a 24-hour turnaround, Doudna announced Monday. The lab will ramp up to processing 3,000 samples a day if necessary.

“This is a big, big issue here in the U.S.,” said Doudna. “We need to ramp up testing very fast. It’s been problematic for various reasons. And so we are building and implementing a clinical testing laboratory on the UC Berkeley campus to do exactly that.”

The effort is one more sign of the desperation in major metropolitan areas to ramp up testing for the coronavirus, called SARS-CoV-2. Two weeks ago, the U.S. had only processed 42,000 tests over the course of the coronavirus pandemic, according to the Covid Tracking Project, a volunteer effort. As of this week, the total number of test results returned has risen to nearly 900,000.

Doudna’s effort isn’t the first in academia. The Broad Institute in Cambridge, Mass., began processing test results last week, and said it would be able to process 2,000 tests a day with a 12-hour turnaround.

The new lab is housed at the University of California, Berkeley’s Innovative Genomics Institute, where Doudna is the executive director. It is being run by more than 50 volunteers from Berkeley and its environs, including the chief scientific officer of lab equipment giant Thermo Fisher, team members from Salesforce, the head of commercial at laboratory information analysis firm Third Wave Analytics, and workers from Hamilton Corp., a maker of laboratory robots, two of which are used in the laboratory.

“It’s unbelievable to see how fast this is coming together and people writing software just overnight to put such a complicated pipeline in place and ensure that it’s secure,” Doudna said. “It’s really quite amazing.”

Doudna said that the Food and Drug Administration and the state of California had been willing to relax normal rules to get the effort going. The lab aims to have certification under the Clinical Laboratory Improvement Amendments (or CLIA) program, the federal regulator of diagnostic labs, by next week, at which point it will begin testing samples. At first, the laboratory will test 300 samples at once, at first working with UC Berkeley’s medical center.

The effort to develop a test began on March 13. The Genomics Institute had been planning to use the space for experiments involving CRISPR, but it already met the safety specifications a laboratory would need in order to handle a contagious virus like SARS-CoV-2.

The test is based on the COVID-19 test developed by ThermoFisher, which has received emergency clearance from regulators. and uses  a process to conduct the polymerase chain reaction, the basis for all the widely used tests to detect the virus. But  the researchers designed a way to use the test on two Hamilton laboratory robots that allowed them to automate the process.

“The throughput numbers assume only one thing: that Thermo supplies and kits do not run out,” said Fyodor Urnov, the genomics institute’s scientific director. He said that the group has already paid a hefty sum for 10,000 of the kits.

Doudna said that her group did a survey of local laboratories, and said that a number of them were running the testing reactions manually.

“Think about that,” she said. “They have no robotics at all. And their turnaround times as a result are up to seven days.”

There is no way, she said, that a manual approach could meet current capacity needs. (Many larger labs are using ready-made systems, such as those made by Roche, Hologic, or ThermoFisher, that are automated.)

“We’ve never faced this before, where clinical labs needed to very quickly be able to ramp up a test so fast,” Doudna said.

This story was originally published by STAT, an online publication of Boston Globe Media that covers health, medicine, and scientific discovery.