90 Days on the Front Line

“We got one”

It was February 27, and Dr. Lea Starita didn’t have time to think. She just took off running.

Though not the typical way this genome scientist navigated the hallways at work, the news she had to share was of such importance, it more than justified her hurried gait. Time was of the essence — and she knew they’d already lost enough of it.

Arriving at her intended destination, a colleague’s office in the University of Washington Health Sciences building in Seattle, Starita delivered her bombshell: “We got one. What do we do?”

For months, Starita, UW Medicine infectious disease researcher Dr. Helen Chu and their fellow researchers at the Seattle Flu Study — a collaborative effort led by the Brotman Baty Institute in association with UW Medicine, Fred Hutchinson Cancer Research Center, Seattle Children’s and the Institute for Disease Modeling — had been mailing out and analyzing nasal swabs from people across the Seattle area. They hoped these user-submitted samples would help them track how the seasonal flu and other respiratory infections spread in the community.

But the sample that Starita rushed to tell Chu and her other colleagues about that day in late February wasn’t positive for influenza — it was positive for SARS-CoV-2, the new coronavirus that was sweeping across the world.

More than a month prior, on January 20, Washington became home to the first confirmed COVID-19 case in the United States. Around two dozen more cases were reported in the country following that, but none were in Washington. Public opinion was this was a disease related mostly to travel, and the average person’s risk of infection was likely low.

The Seattle Flu Study’s positive result in a patient who had no recent travel history, however, indicated something more dire: SARS-CoV-2 was in the Seattle area, spreading undetected.

“The people who present to the hospital are the tip of the iceberg. What about the people who might not feel so good and are staying at home with a cold? It made us wonder what else was out there,” explained Starita, a research assistant professor of genome sciences at the University of Washington School of Medicine and co-director of the Brotman Baty Institute Advanced Technology Lab.

National headlines fixated on the shortage of COVID-19 tests in the United States, but the Seattle Flu Study group had already developed a COVID-19 test by early February, completely separate from their influenza one, after they first learned about the new disease.

The problem was their research lab was not yet certified for clinical testing. Technically, the researchers could test the nasal swab samples they had collected for their flu study and report the results for influenza, but they weren’t allowed to report the results for SARS-CoV-2 tests.

At the end of February, after two weeks of back and forth with state and federal agencies, they decided they couldn’t wait for federal approval any longer. They began testing their nasal swab samples for COVID-19 on a research basis. Only a few hundred samples in, they recorded their first positive.

Back in her colleague’s office, Starita, Chu and the other Seattle Flu Study researchers discussed their next steps.

“We weren’t sure what kind of cascade it was going to trigger and what was going to happen after we found one,” Starita said.

Ultimately, they decided the ethical thing to do was to inform local public health officials. That evening, their positive COVID-19 result hit the news.

Two days later, Washington recorded its first known death due to COVID-19 and Gov. Jay Inslee declared a state of emergency. Within a week, the number of confirmed cases in the state topped 100. Washington would soon become the first epicenter for COVID-19 in the United States.

JANUARY & FEBRUARY

A mysterious pneumonia of unknown cause

In the early days of January, before COVID-19 even had a name, many people around the world were aglow with the fresh potential of a new year. Medical information networks, though, were lighting up.

Authorities in China were reporting dozens of cases of a mysterious pneumonia of unknown cause in Wuhan, a sprawling city of 11 million.

Across the Pacific Ocean in Seattle, Dr. Alex Greninger read the news with the interest of a self-proclaimed “RNA virus nerd.” He had been part of the team working on the SARS epidemic at the World Health Organization (WHO) in 2004, and these new reports piqued his professional curiosity.

“For people like me who are really interested in RNA viruses, this is what we’re all about,” said Greninger, assistant director of the UW Medicine Virology Lab.

At the time, he didn’t know how the pneumonia was transmitted or if it was even caused by a virus. Still, Greninger decided due diligence was in order. He fired off an email on January 6 telling his colleagues that they should probably make a test just to be prepared. If nothing came of it, he figured they’d at least have something for research purposes.

Shortly after, the world learned the pneumonia was actually caused by a new human coronavirus, SARS-CoV-2. It would be another five weeks before the WHO gave the resulting respiratory illness a name: COVID-19.

Growing concern at home

By the end of January, before most of the community was concerned about a COVID-19 outbreak, UW Medicine infectious disease experts were already in full-on preparation mode.

“When we first heard about cases of COVID-19 developing in China, all of us started thinking about how this is going to impact our community and how we needed to start to prepare,” explained Dr. Seth Cohen, medical director of infection prevention and control at UW Medical Center.

Dr. Santiago Neme, an infectious disease expert and medical director of UW Medical Center – Northwest, also jumped into outbreak planning early on.

“I used to lead the infection control program at UW Medical Center – Northwest and transitioned out of that role in 2017,” Neme said. “But when we heard those early reports of COVID-19 in December, I thought, ‘I’m going to start joining our monthly infection prevention calls again, just in case.’”

Then after the first COVID-19 case made landfall in late January, Dr. John Lynch, medical director of infection prevention and employee health at Harborview Medical Center, received a call from Public Health — Seattle & King County. Could they activate Harborview’s home assessment team?

The team, a carryover from UW Medicine’s past pandemic preparations for Ebola, got to work. On evenings and weekends, five members traveled to the homes of potential COVID-19 patients, swabbing noses and sending the samples off to the Centers for Disease Control and Prevention (CDC) for testing.

“We went to a hotel outside the airport, apartment buildings, people’s houses. Pretty much the entire infection control team here was working extraordinarily long hours,” Lynch recalled.

Back in the early days of January, he too had read the reports of the mysterious pneumonia, but assumed — or perhaps hoped — the public health authorities in China would be able to contain the illness as they had similar outbreaks in the past.

But now that SARS-CoV-2 had been identified and COVID-19 had already spread to South Korea, Italy and Iran, his concern was only growing.

“We really ramped up our evaluation and awareness of our personal protective equipment setup. We were taking very seriously the work that was needed to develop plans, policies and protocols, and we started meeting daily across UW Medicine to develop all those policies and protocols to prepare for all those people who could show up in our clinics,” Lynch said.

Neme recalled that time period as one of constant activity, tweaking and retweaking policies and then communicating them to hospital staff. 

“It was a flurry of updates because the information was constantly evolving,” he said. “And, on top of that, we wanted to make sure the policies were medically sound, approved and implemented throughout the system. Having the same protocols across our system was critical to our safety and effectiveness.”

By the last weekend in February, when the implications of the Seattle Flu Study’s positive test result had the region reeling, everything seemed to go off the rails at once: A home assessment they performed on a King County woman who returned from Daegu, South Korea, was positive for COVID-19. A patient who passed away at Harborview that week was also positive. So was another patient who had been admitted to UW Medicine’s Valley Medical Center in Renton. And now Life Care Center, a nursing home in Kirkland, was reporting positives among its residents.

UW Medicine set up a formal incident command team to help its employees and hospitals navigate what would soon explode into a pandemic. 

Lynch worked through Friday evening and Saturday, finally making it back to his home at 1 a.m. on Sunday.

It was only March 1, and things would soon get much worse.

MARCH

Testing takes off

Dressed in a button-down shirt and gray zip-up hoodie, Greninger looked at the cluster of microphones and television cameras before him. It was March 4, and he was tired from weeks of nonstop work. But he and the head of the UW Medicine Virology Division, Dr. Keith Jerome, were meeting with members of the media to share a glimmer of good news: they finally had an authorized COVID-19 test.

Turns out, Greninger’s early prudence about preparing a test had been spot on. His team had developed one by mid-January, but theirs spent weeks in limbo with the CDC and Food and Drug Administration (FDA) over paperwork, lab certifications and positive control material. Although both the Seattle Flu Study and the Virology Division are associated with UW Medicine, each lab and test needed to go through its own separate set of certifications and approvals.

“I usually never use the phone, but I was making 70 calls a day, waking up early to start on the East Coast, trying to call the CDC, asking for feedback from the FDA,” Greninger recalled.

It seemed as if everyone in the Department of Laboratory Medicine descended on their lab to help out. They processed specimens, sorted through the FedEx shipments that piled up in the hallways and made calls to the hundreds of patients who tested positive. UW Medicine CEO Paul Ramsey put out a call to lab technicians and researchers to drop their work and volunteer. One of Greninger’s graduate school friends even flew up from San Francisco to chip in.

“In early March, our lab was 70% of the U.S. testing capacity. It wasn’t just UW Medicine patients. We were doing testing for hospitals in Connecticut, California and Oregon,” Greninger recalled.

And they weren’t the only ones trying to tackle testing. By mid-March, Starita and her Seattle Flu Study colleagues were preparing to launch the next iteration of their swab-and-send program, this time focusing on COVID-19 instead of the seasonal flu. It was called the greater Seattle Coronavirus Assessment Network (SCAN).

It took them more than three weeks and 400 pages of paperwork — what Starita described as a feat in itself — to move their work to a lab certified for clinical testing.

On March 23, they formally launched SCAN, in coordination with Public Health — Seattle & King County.

Unlike other types of COVID-19 testing, which often required an appointment from a doctor, SCAN was able to provide a testing option for people at their homes, opening up access to those who may not have been able to get a test otherwise. A key goal of the study was to distribute swabs to every part of the county as well as among those who had symptoms and those who had none to ensure a representative sample.

“We only had the infrastructure to send out and receive 400 swab kits a day, and we were trying to make it more equitable by spreading it out on the county. By doing that, we could provide a really important service and help reach underserved communities,” Starita said.

Racing to keep up

Although testing had cleared its initial hurdles, the situation in area hospitals was growing grim. By late March, Washington’s confirmed COVID-19 cases topped 2,000, and UW Medicine had admitted more than 40 patients to its acute care and intensive care units.

UW Medical Center – Northwest, in particular, was heavily impacted early on in the pandemic as patients from Life Care Center and other assisted-living facilities were admitted with COVID-19.

To accommodate the influx, the hospital campus converted three of its floors into COVID-19 units. Hospital staff were redeployed from other areas like surgery to help patient care teams with the important task of safely putting on and taking off personal protective equipment (PPE). And palliative care specialists huddled together with families in the emergency department to have difficult but necessary conversations about end-of-life care for their loved ones.

Meanwhile, supplies of face masks and eye shields — equipment essential for keeping front-line workers safe — were running low everywhere.

Members of incident command collaborated with UW Medicine’s supply chain team to quickly establish new strategies for obtaining, conserving, tracking and distributing PPE.

“We wanted to not only make sure we had enough PPE but also enough ventilators and beds and all those things that make a hospital work,” Neme said. “As a team, we looked into the possibility of reprocessing equipment and making sure everyone understood our PPE guidelines and the rationale behind them.” 

Across the organization, employees jumped in to help. Pharmacists at UW Medical Center began whipping up batches of hand sanitizer to supplement the hospitals’ supply, while researchers used 3D printers to make face shield visors for front-line workers.

At Harborview, Lynch and his infection control team pulled all-nighters to try and keep up. Each evening, one would take a turn sleeping on a camping cot in the hospital office so someone would be available at the hospital if needed. When it wasn’t their turn for an overnight shift, other team members would still be working until 1 a.m. each day — only to be back at it six hours later.

The scene inside the hospital was equally surreal and strange. Some units were eerily empty, with elective surgeries delayed and in-person appointments transitioned to virtual visits. Meanwhile, Harborview’s COVID-19 floors buzzed with near-constant activity.

In the hallways, equipment-laden crash carts lined the walls. Medical staff pulled on gloves, donned protective gowns and slipped on powered air purifying respirator (PAPR) hoods to prepare to enter a patient’s room. Within the negative-pressure rooms, critically ill patients lay still, hooked up to a dizzying array of tubes and wires.

Nurses and doctors rotated in and out, providing care to patients around the clock. Some patients would finally turn a corner and improve. Others would take a turn for the worse, requiring them to be hooked up to ventilators to help them breathe. And for a heartbreaking number, their conditions would deteriorate so much a nurse would have to video call their loved ones so they could say a final goodbye.

“It was brutal and extremely hard. We saw more infections each day, and the proportions of positive test results were also more than they were previous weeks. When I looked at those general trends, I saw signs that the surge was still ahead of us,” Lynch said.

Predicting the pandemic

When would that surge hit? How large would the peak get? And, most importantly, would hospitals have enough space, staff and resources to respond?

Dr. Christopher Murray, director of the Institute for Health Metrics and Evaluation (IHME) at UW Medicine, was thinking about all of this and then some.

Once an executive director at WHO, Murray had plenty of experience with outbreaks like this one. He and others at IHME watched the COVID-19 outbreak unfold from the beginning, knowing there was a chance it could be contained but also a chance it could explode.

“We didn’t leap into the fray at first, but then the tipping point came when we saw the outbreak in Italy, then Washington and at the Life Care Center in Kirkland,” Murray recalled.

That’s when UW Medicine officials made a request: Could IHME model what would happen to their hospital system during the COVID-19 pandemic?

It would require IHME to invent a completely new type of model, so Murray put out a call for volunteers. Of the 500 people who work at the institute, nearly 100 joined the COVID-19 team.

“We rapidly pivoted from our usual work to doing a lot more work on this challenge because it was so pressing,” Murray said.

It would normally take them up to a year to build a statistical model that could predict the growth, magnitude and duration of an infection. But in this case, it took the IHME team 10 days to launch their model for UW Medicine hospitals and another 10 days to expand it to the rest of the United States.

Their model confirmed what Lynch had predicted. The worst was still yet to come.