‘A new way to do science’: UC Berkeley, UCSF researchers focus efforts on COVID-19

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While campuses have closed down, scientists at UC Berkeley and UCSF are still conducting research both on campus and virtually.

Researchers from various disciplines are working on projects that may aid the response to the coronavirus. Despite logistical difficulties imposed on research by physical distancing measures, many experts are expediting their research processes and joining national and global networks of researchers to collaborate on projects and share information.

UC Berkeley associate professor Sarah Stanley is working on growing and culturing the live virus in her lab from a clinical isolate imported from Washington.

“What we’re doing is we’re partnering with different labs around campus to enable not only our own research, but also research from other faculty members,” Stanley said.

Specific areas of research these labs are focused on include testing new therapeutics, novel diagnostics and methods for decontaminating personal protective equipment, or PPE.

Stanley’s lab is one of three campus labs that are currently working with the live virus. Given the deadly nature of the virus, Stanley’s research must be done in biosafety level 3 labs, which are used for potentially deadly respiratory pathogens and have a higher level of precaution than most other labs.

After analyzing cell culture models, Stanley also hopes to establish a mouse model on campus to test potential therapeutics.

UCSF professor Nevan Krogan began research related to the coronavirus more than two months ago, attempting to understand how the virus replicates in human cells.

Krogan has since formed the Quantitative Biosciences Institute Coronavirus Research Group, or QCRG, which includes about 20 UCSF labs.

Members of the group are using a method known as host factor targeting, in which they identify which proteins in the host, or the infected species, interact with the virus so they can inhibit these proteins. Based on this information, they created a list of 69 existing drugs that could potentially be used to diminish the virus’s ability to enter the host cell or replicate.

“(Host factor targeting is) a little bit different than what is the traditional antiviral approach like we use for viruses that have been around for a while like HIV, where drugs are targeting the viral proteins themselves,” said Kevan Shokat, a professor at UCSF and UC Berkeley who is working on this project through the QCRG.

Krogan said drugs targeting the virus could face resistance because the virus mutates very quickly, while human genes mutate slower. This makes it such that drugs targeting human genes would face less resistance.

The QCRG sent the list of 69 potential drugs to New York, where the effects of these drugs on the virus were tested, and has narrowed the list down to two promising sets of candidates. Some of these drugs will likely go into clinical trials, according to Krogan.

Prior to the COVID-19 pandemic, Michael Matthay, professor and associate director of Critical Care Medicine at UCSF, focused his research on critically ill patients who develop acute respiratory distress syndrome, or ARDS. Now, he is participating in a collaborative effort with the National Heart, Lung and Blood Institute to establish a clinical trial to test the efficacy of high doses of vitamin C on COVID-19 patients who develop ARDS.

The institute also started a clinical trial to test the impact of the drug hydroxychloroquine, which may have antiviral properties, on cases of COVID-19, according to Matthay.

“We do not know yet whether it could be effective, and there are potential side effects in terms of cardiac issues,” Matthay said. “We just have to know the risk-benefit ratio.”

The trial is being conducted across 50 hospitals with 510 patients.

Other researchers are working to develop ways to assist hospitals with the influx of COVID-19 cases.

UC Berkeley professor Amy Herr is part of N95DECON, a multi-institutional coalition that established a consensus on proper N95 mask sanitation methods.

“Those masks are designed not to be reused at all,” Herr said. “The only reason we’re considering reuse is because of this extraordinary situation that we’re in with shortages of the personal protective equipment.”

N95DECON combed through existing scientific literature, and on April 1, the group published a study on three promising methods of N95 mask decontamination — humid heat, ultraviolet C lighting and hydrogen peroxide vapor. These guidelines align closely with guidelines published by the Centers for Disease Control and Prevention on March 31.

N95DECON is now working on answering questions from health care workers and people interested in helping solve the need for more masks based on CDC guidelines and related scientific literature.

In an effort to form a quick solution to the ventilator shortage, a coalition of scientists has been working on transforming CPAP and BiPAP machines — which are used by people with sleep apnea — into ventilators.

Turning these machines into ventilators is a quick process, according to UC Berkeley associate professor Grace O’Connell, who is a member of the coalition. The team has already sent about 10 ventilators to hospitals. It has also set up an online registry where people can donate unused sleep apnea machines.

The new ventilators work for patients with mild to moderate cases and recovering patients weaning off regular ventilators.

UC Berkeley professor Bin Yu and her team of graduate students and postdoctoral researchers are working with nonprofit Response4Life to help connect hospitals with appropriate supplies, including ventilators and PPE.

The team is curating available data to predict accumulated death counts on a county level throughout the United States and trying to use this data to create a “severity index” for each hospital.

“The situation is very dynamic,” Yu said. “The model can only do so much, and we really try to augment that with other information and human judgment calls.”

Shokat said the research conducted through the QCRG and collaborating institutions in the past couple months would normally take two to three years.

Krogan attributed the fast pace at which the group’s research has developed to greater collaboration across labs on the UCSF campus and globally, as well as other institutions, including pharmaceutical companies. He hopes that this new “infrastructure” for scientific research set in place by COVID-19 is maintained once the pandemic is over.

“I think this is a new way to do science,” Krogan said. “To me, a silver lining here is that we’ve shown when we break down the silos how fast we can move.”

Emma Rooholfada is the lead research and ideas reporter. Contact her at [email protected] and follow her on Twitter at @erooholfada_dc.