At the stroke of midnight on Tuesday morning, seven counties in the San Francisco Bay Area went into near-lockdown — ushering in a new reality for biopharma companies and biomedical labs.

The “shelter in place” order, which aims to slow the spread of the coronavirus by mostly confining residents to their homes for at least the next three weeks, offers significant leeway for medical research. Employees of pharma and biotech companies are explicitly allowed to travel to and from work. So too is anyone working in “health care operations,” which leaves the door open for clinical trials to continue. Another exception allows university employees to travel to perform “essential functions,” provided they stay 6 feet away from each other — an apparent carveout for the researchers who maintain cell lines and feed rats in academic biomedical labs.

Still, the order “takes the challenges that people were having with running trials, getting patients, running a company that we started to experience at the beginning of last week — and just ratchets it up 50 notches in a matter of moments,” said Greg Dombal, president and chief operating officer of Halloran Consulting Group.

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“It’s hugely challenging,” said Dombal, who has been advising biotech and pharma companies, including some based or running operations in the Bay Area, on their coronavirus response.

Industry leaders said that the shelter-in-place order may exacerbate cutbacks they’re already seeing — and be a sign of things to come across the country. Lab experiments are being abandoned. Mice are being prevented from breeding. Some hospitals are restricting hours in which patients enrolled in drug trials can get infusions.

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The near-lockdown of the Bay Area may also impact the supply chain, the safety of biopharma employees traveling to and from work, and the protection of supplies and resources within biotech and biomedical manufacturing facilities, said Mike Guerra, CEO of the industry trade group the California Life Sciences Association.

Despite the legal exceptions allowing their researchers to come to work, some Bay Area companies and labs are winding down in-person operations on their own — an acceleration of the work-from-home shift that began earlier this month. The same thing is increasingly happening at research labs across the country, including in the Boston area.

At Unity Biotechnology, the biotech company just south of San Francisco focused on developing drugs targeting a process involved in aging, in-process experiments will be finished and cell cultures frozen, according to a company spokesperson.

At the University of California, Berkeley, Chancellor Carol Christ wrote in a Monday email to the campus community that “labs should ramp down normal operations, and shift to basic maintenance.” Christ specifically noted an exception for “maintenance of certain critical research specimens.”

At Stanford University, a spokesperson on Monday night said the institution was still evaluating the impact of the order.

On Sunday night — before the shelter-in-place order was announced — administrators at UC San Francisco wrote an email to campus researchers ordering labs to shut down “all noncritical research activities” before midnight on Wednesday. In cases requiring in-person management of things like animal lines and liquid nitrogen stocks, each lab or group of labs may assign a “skeleton crew” of one to four people, depending on how many animals are in the lab, the UCSF administrators wrote. They also advised researchers to reduce breeding of lab mice as much as possible.

“We completely understand that these restrictions go against virtually everything we represent as scientists — and it is heartbreaking to tell a scientist to stop doing experiments,” the UCSF administrators wrote.

There was one key exception, however, to the new rules: studies of Covid-19 “that have the potential to mitigate the spread of the pandemic,” the email said.

Although clinical trials can legally proceed under the shelter-in-place order, actually running them may get harder — especially as hospitals get flooded with Covid-19 patients.

In the Bay Area as well as in Boston and the New York area, Dombal said, he’s beginning to see major hospitals that operate as trial sites restrict their hours for his biopharma clients’ clinical studies. Typically, sites are open to administer drug infusions and enroll new patients Monday through Thursday. Now, in some cases, those hours are being restricted to Tuesdays and Wednesdays, in part to allow for more cleaning — taxing staff and limiting infusion chairs, Dombal said.

Dombal said his biopharma clients in the Bay Area fall into two camps when it comes to their reaction to the shelter-in-place order.

Some of them have reacted calmly, saying they expected this. Others, he said, “have immediately hit the panic button — that they’re not going to be able to complete trials, they’re not going to be able to hit enrollment targets, and they’re certainly not going to be able to manage adequately the care that they might be supporting for patients who are on trial.”

Matthew Herper and Damian Garde contributed reporting.

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