A tale of two labs on the forefront of COVID-19 testing

February 2020 might seem a lifetime ago, but that’s when UW Medicine researchers were the first to report community spread of the novel coronavirus in the United States. They knew the discovery had massive implications, even if the general public couldn’t yet fathom them. But what happened next was months, even years, in the making.

The Seattle area is known as a medical research powerhouse, and Jeff Brotman, the late founder of Costco, had always envisioned an entity that would take advantage of the unique research strengths of our region.

“One of Jeff’s passions was breaking down walls between investigators and between institutions,” says Jay Shendure, MD, PhD, UW Medicine genome scientist and director of the Brotman Baty Institute for Precision Medicine.

Brotman’s longtime friend, Dan Baty, shared that vision. In 2017, thanks to the philanthropic leadership of Jeff and Susan Brotman and Dan and Pam Baty, the Brotman Baty Institute for Precision Medicine (BBI) was launched. It would combine the research strengths of its three co-founding institutions: UW Medicine, Fred Hutchinson Cancer Research Center and Seattle Children’s.

Soon after, another local visionary, Bill Gates, foresaw the need to better prepare cities for the possibility of a pandemic. Fortunately, a few key investigators were already laying the groundwork.

Mike Famulare, PhD, a principal research scientist at the Institute for Disease Modeling, and his colleagues had suggested a pilot for a respiratory disease testing platform that could monitor seasonal transmission of viruses and help prepare for a pandemic. At the same time, Trevor Bedford, PhD, a researcher with Fred Hutch and Nextstrain, was discussing how to accelerate genomic sequencing of pathogens and better map their spread.

Working together with Gates Ventures (Gates’ private office), the Bill & Melinda Gates Foundation, and Dr. Paul Ramsey, CEO of UW Medicine, the teams eventually joined forces. The Seattle Flu Study was launched by the BBI in 2018 with funding from Gates Ventures.

“Given that the Seattle Flu Study involved investigators from several institutions, this was kind of the poster child for the BBI,” says Shendure, one of nine principal investigators for the study. They chose to focus on influenza viruses not only because they are seasonal, but also because many in the field saw respiratory viruses as a likely source of the next pandemic.

The Seattle Coronavirus Assessment Network — or SCAN — is a first-of-its-kind, at-home virus testing program that will improve our understanding of how COVID-19 spreads.

The virus arrives

The Seattle Flu Study began to pay off immediately. Researchers discovered that the physical distancing forced by Seattle’s massive snowstorm in early 2019 led to a dip in transmission of nearly all respiratory pathogens.

In the second year, a more efficient and convenient approach for testing — “swab-and-send” — was developed by Helen Chu, MD, Fel ’12, MPH ’12, associate professor of medicine, Division of Allergy and Infectious Diseases at the UW School of Medicine, and lead clinician of the Seattle Flu Study. Participants self-swab their nose and send the sample back to the lab, allowing researchers to detect less severe cases of illness.

As COVID-19 emerged, Lea Starita, PhD, UW Medicine research assistant professor of genome sciences and co-director of the BBI Advanced Technology Lab and one of the principal investigators of the Seattle Flu Study, added SARS-CoV-2 to the panel of respiratory pathogens that the study was testing for.

No one expected what happened next: On February 27 of this year, the Seattle Flu Study team discovered that the novel coronavirus was already circulating in our community. It was the first report of community spread in the U.S. “The Seattle Flu Study was meant to help us prepare for a possible pandemic, but we assumed that would be years from now,” says Shendure. “It happened in year two.”

Seattle Flu Study researchers were the first to develop and utilize an approach to testing called “swab-and-send” that allows people to test themselves for respiratory viruses from the comfort of their homes. The self-testing kits are mailed back to the lab for processing.

Swift public health action and collaboration

The BBI team responded immediately. Investigators worked with the Washington State Department of Health, the Centers for Disease Control, and Public Health — Seattle & King County to figure out how to transition their research and resources into effective public health action.

On March 23, 2020, Seattle Coronavirus Assessment Network (SCAN) was launched as a collaboration with Public Health — Seattle & King County and with funding from Gates Ventures. “Gates Ventures was able to give us this surge of funding when we needed it for testing and expanding capacity. Their vision and what they helped create provided the infrastructure for this whole thing to happen,” says Starita.

By using the swab-and-send home test developed for the Seattle Flu Study, SCAN researchers are able to develop a better understanding of how the new coronavirus behaves and is transmitted in our region. As of early July, SCAN has sent over 17,500 free testing kits to people in the region who are symptomatic and asymptomatic.

If there is a silver lining to this pandemic, it may be that it has spurred unprecedented levels of collaboration — across health systems, government entities and private foundations. “People are going out of their way to pull down barriers so things can get done,” Shendure says.

There is no shortage of things to be done. With additional support, SCAN investigators hope to expand their research study across the state, expand testing to underrepresented and high-risk groups as well as to family members and close contacts of those who test positive, and help other regions in the country who want to implement similar programs. One thing is for certain: It will take everyone coming together to make it happen.

Meanwhile, in early January 2020, Keith Jerome, MD, PhD, Res. ’97, Fel. ’99, professor of laboratory medicine at the UW School of Medicine, head of the UW Medicine Virology Division and director of the UW Virology Laboratory, didn’t know if the mysterious virus they were tracking in China would ever come to the U.S. In fact, he doubted it would, but he knew it was better to be prepared.

Jerome and his team began working on a test to detect COVID-19. However, in order to get emergency use authorization from the FDA, they needed a sample of the virus. Before they could get viral RNA shipped to their lab, the virus found them.

In late February, amid their own internal testing for respiratory viruses, the lab uncovered the second reported case of community-spread COVID-19 in Washington state — just days after the Seattle Flu Study found the first one.

The UW Department of Laboratory Medicine had to make a big decision and it fell on the shoulders of Geoffrey Baird, MD, Res. ’07, PhD, professor of laboratory medicine at the UW School of Medicine and interim chair of the UW Department of Laboratory Medicine.

“It was clear that the pandemic was going to be significant, and that our testing capacity was going to be instrumental in helping the state weather the storm,” says Baird. “I also realized how much it was going to cost.”

Since early January, Dr. Keith Jerome (pictured right), director of the UW Virology Laboratory, and his team began preparing for the possible arrival of the new coronavirus. In late February, they found the second case of community-spread COVID-19 in Washington.

A shift in thinking

Because the UW Department of Laboratory Medicine is a prominent regional and national reference laboratory, it has a relatively large reserve, which is reinvested back into faculty, staff, instruments, education and test development.

The decision to spend down the reserve in order to ramp up COVID-19 testing was not an easy one. “I had to make the decision knowing that I was potentially harming, or at least borrowing from the future of, a department comprised of well over 100 faculty and 1,400 staff,” says Baird.

However, he is confident that he made the right decision. It led to the UW Virology Lab becoming the state’s largest test provider, able to conduct 8,500 tests a day. For the first few months of the pandemic, the lab provided over 50% of the state’s testing.

Baird had the full support of his colleagues, including Jerome. “This kind of pandemic really does require a shift in thinking,” says Jerome. “We will deal with the costs later. Right now, our first obligation is to the health of the people of Washington.”

Researchers in the UW Virology Laboratory work to process thousands of COVID-19 tests and antibody (serologic) tests. The UW Department of Laboratory Medicine spent down its reserves so the lab could ramp up testing in our state.

A sprint, then a marathon

While the UW Virology Lab continues COVID-19 testing, it’s also working on large-scale serologic tests, or blood tests, that can tell with a high degree of accuracy whether someone has had the virus.

They are also supporting vaccine development and continuing to operate a robust genetic sequencing program. In fact, Jerome notes, not many people know that UW Medicine is one of the largest depositors of coronavirus genomes in the U.S.

All of this work has required tens of millions of dollars. While the department’s reserves are depleted, Baird hopes most of it will be replenished by federal, state and philanthropic dollars. Everyone is incredibly grateful to the donors who have stepped up.

“The sprint of our COVID-19 response is clearly going to be a marathon,” says Baird. “The entire UW Medicine health system faces a financial crisis, as do many health systems, and indeed the whole country. So it will continue to be a challenge to fund our COVID-19 response in the coming months.”

Despite the obstacles, Jerome notes that in retrospect, Seattle was actually a good place for the virus to land first. “Between our program getting ready for testing just in case it came here and groups like Seattle Flu Study looking at the population in a broad way, we were incredibly well-prepared,” he says. “We are built perfectly to respond to something like this.”

By Eleanor Licata
Photography: Dennis Wise


Your generous support helps us respond rapidly and effectively to the COVID-19 pandemic. A gift to the SCAN study improves our understanding of how the novel coronavirus spreads. A gift to the UW Medicine Virology Lab helps researchers continue to test thousands of people every day for active and past COVID-19 infections.