At clinical virology lab, 1 million COVID-19 tests and counting

Stanford Medicine processed its 1 millionth COVID-19 PCR test on Feb. 10 — a milestone representing nearly 80,000 hours of work by a laboratory group that initially consisted of only 20 people.

Since the pandemic began, the clinical virology lab at Stanford Medicine has processed more than five times as many diagnostic tests as it normally would have over a two-year period.

Stanford Medicine was one of the first academic medical centers in the country to receive emergency use authorization from the Food and Drug Administration for its coronavirus PCR test, placing the laboratory’s technicians, researchers and scientists center stage in an effort to contain an unknown, rapidly evolving global health crisis. 

Initially, the test was used mostly for patients at Stanford Medicine’s adult and pediatric hospitals with worrying symptoms of the new respiratory virus. But within days, the laboratory began to provide testing services to other medical facilities in Northern California. By April 1, 2020, the laboratory had conducted 10,000 tests, accounting for about one-third of all the tests in California. But that was only the beginning.

Testing 24/7

As the weeks and months marched on, the laboratory’s staff ballooned to include around 60 technicians and scientists who worked around the clock, seven days a week, to rapidly deliver test results not just to patients but also to health care workers, first responders, community members, schoolteachers and nursing home residents. 

In addition to processing tests, the researchers brought in new sequencing equipment, initiated new testing strategies and monitored the rise and fall of viral variants in the Bay Area — all while maintaining an impressive turnaround time of about 24 hours for nonurgent tests and about an hour for emergency requests.

“Laboratory staff have worked incredibly hard throughout the pandemic,” said Benjamin Pinsky, MD, PhD, medical director of the clinical virology laboratory. “The demands of the past two years have been relentless, but they have been so resilient and determined to deliver the timely results needed to appropriately care for our patients while also protecting those caring for them. They are the real stars of this story.” 

Not over yet

Unfortunately, that story’s not over yet. 

During the height of the recent omicron surge, the lab processed 20,000 tests in seven days, one quarter of which were positive for COVID-19. More recently, the laboratory was processing between 1,000 and 1,500 tests per day, of which about 10% were positive. 

“It’s a relief to see the numbers dropping,” Pinsky said. “But it’s important to stay on our toes and continue screening for the next new variant.” 

Viral variants are the reason there’s more to testing than just delivering a positive or negative result. Since the beginning of 2021, the laboratory has tracked the presence of mutations unique to variants of concern identified by the global scientific community. Doing so has allowed the lab to guide treatment decisions for infected people.

“This gives us a very quick picture of what’s circulating in California, almost in real time,” Pinsky said. “We watched as omicron very quickly replaced the delta variant in our patient population over a period of about three weeks in December.” 

He added, “These variants have very different susceptibilities to the monoclonal antibodies used as therapies, so we worked closely with our infusion center during that transition to help them know when to switch from one panel of antibodies to another that would be more effective for our patients.”

Additional efforts

In addition to monitoring variants, the laboratory scientists and members of Pinsky’s research group have designed novel strategies to identify not just the presence of the virus, but also to track how the immune system responds to infection. 

They were the first in the country to offer what’s called a minus strand test to detect an actively replicating virus. They also devised ways to measure the levels and activity of antibodies that arise after infection or, more recently, after vaccination. And, the lab is examining the response of immune cells called T cells to vaccines and infection. 

Steadfast support from the Stanford Health Care administration has been key to the lab’s success, Pinsky said. In particular, the acquisition of multiple sequencing machines and platforms allowed for flexible workflows that can dodge supply-chain problems. 

“We’ve had sufficient staffing and developed very efficient workflows,” Pinsky said. “Our early preparations left us less reliant on any one supplier.”

But behind every workflow are workers dedicated to keeping patients, community members and health care professionals safe. And, on Feb. 10, not even their masks and face shields could hide their proud smiles. 

“This milestone represents a lot of blood, sweat and tears,” said Jennifer Fralick, administrative director of laboratory services. “It’s a perfect example of how Stanford Medicine has supported its community during the past two years. In the beginning, no one knew much about this virus, but the lab staff wanted to help. They were working overtime, double time and just weren’t leaving. And they continue to have boots on the ground.”