Philadelphia Health Commissioner Dr. Tom Farley

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The flight manifest contained 40 names when it arrived on Dr. Stephen Alles’ desk: people who were known to have recently passed through the cradle of the coronavirus outbreak in Wuhan and were now slipping into the hum of daily life in pre-pandemic Philadelphia.

It was a Friday, six weeks before the city would identify its first positive case.

Jan. 24: Zero confirmed cases of the coronavirus in Philadelphia

For the 54-year-old director of disease control and his team at the city health department, contact tracing was not a foreign concept.

They’d knocked on doors during the Ebola and H1N1 epidemics in years past. Just last summer, they’d hunted the trail of hepatitis A through the streets of Kensington. No matter the threat, the practice involves identifying potential carriers before it spreads further into the community. How different could this be?

The next day, the passenger log grew to 72 names, and continued to climb. “It rapidly got up to 100,” Alles said.

Philly appeared to be on better footing than New York and Los Angeles, where formidably larger flight manifests contained thousands of passengers. Alles and a team of 30 trackers worked through the weekend, relying on Mandarin translators to communicate with many Chinese nationals who’d traveled through Hubei province. The language barrier presented challenges. Phone numbers didn’t work. Some didn’t pick up. Those who did were told to monitor for symptoms like a fever and dry cough, and quarantine for two weeks if needed.

One night when Alles was on call, the health department’s hotline began to explode.

“I was up entirely through the night,” Alles said. “The phone did not stop ringing with emergency departments wanting to know how to handle a suspect patient.”

Within days, the list of travelers with suspected contact grew to 500 names. While not revealed until March, health officials were observing several people “under investigation” throughout the month of February. They were tracking cases linked to other imported cases. Philly’s patient zero was imminent.

March 10: One confirmed case in Philadelphia

March 14: 8 cases; Mayor Jim Kenney tells the city to ‘go out and have dinner

March 16: Nevermind, the mayor says, issuing a stay-at-home order

When Mayor Jim Kenney’s stay-at-home order went into effect, the Philadelphia Department of Public Health enacted its own transformation.

Instead of a background bureaucracy best known for shutting down restaurants, it became the city’s figurehead in the fight against the pandemic. Health Commissioner Dr. Tom Farley began appearing daily in the public spotlight, while his team of 1,500 employees worked around the clock — often with limited resources and little enforcement power — to track, contain and prevent further spread.

To manage the new role, a coronavirus crisis response unit was formed, following a command structure developed out of a series of deadly California wildfires in the 1970s.

The goal of the restructure: reduce barriers between government agencies that allow them to act more quickly. Led by Alles, who is known as the incident commander, the 200-member team has played a leading hand in every story around the city’s response since early March, from running the city’s quarantine sites to conducting autopsies to leading the recent push to restart contact tracing.

In over a dozen interviews with Billy Penn, senior officials on the command team recounted their thoughts on the all-hours response, including perceived successes and missteps. As the “curve” retreats, efforts have shifted to avoiding a possible second surge as the city moves toward re-opening.

The marathon isn’t over, and lives are still on the line.

“We’re in this for months,” Alles regularly tells his team. “More months than you think.”

The drive-through testing site outside Citizens Bank Park Credit: Emma Lee/WHYY

March 25: 342 confirmed cases, one confirmed death

Late last year, officials in the Philadelphia region participated in a mockup of a different kind of public health disaster.

Dubbed “Frankenthrax,” the months-long simulation was meant to improve the medical response from federal, state and local agencies in the event of a bioterrorist attack.

As a final test, officials set up an emergency response site where they would distribute the doxycycline or ciprofloxacin, antibiotics used to combat the Anthrax attack in 2001. They chose a familiar venue for the hypothetical emergency:

Citizen Banks Park.

“Four or five months later, we find ourselves down here again and running the drive-through test site,” said Jessica Caum, director of logistics and planning for the health department’s coronavirus response team.

The test site outside the Phillies ballpark was the first to open in the city, and testing remains a focus. Caum helps oversee those efforts. Her planning and logistics team sets up city-run sites like the Liacouras Center surge facility, manages documentation, and, most challengingly, secures needed supplies.

Supply shortages have been one of the defining narratives of the crisis. Inventory records show the city health department is still waiting on hospital gowns and test swabs it ordered over two months ago.

As the cases grew by the hundreds every week, so too did the urgency.

March 30: More than 1,000 people infected with the coronavirus. Nine deaths.

Justin Harlem, the response team’s PPE handler, has spent most of the last two months — or has it been years? — trying to secure supplies in the Wild West economy of international medical supply dealers.

The competition is grueling.

“Every county in every state is competing for these things, every institution,” he said. “The list is endless.”

PPE was just one of many issues. Crucial data was missing about the disproportionate infection rate among the city’s African American population. Monitoring 145 congregate care facilities for outbreaks, from nursing homes to the city’s overpopulated jails, did not prove easy.

Each day represented a unique challenge, and what worked one week sometimes went out the window the next.

In the restructured coronavirus team, Dr. Kristen Feemster oversees clinical management and infection control. Public health guidance, she noted, has continued to shift daily at the federal level. Feemster recalled a meeting in early March when health officials deliberated banning gatherings over 1,000 people. Were they being excessive? Feemster laughs now just thinking about it.

“Things evolved so quickly, and it really was hard to anticipate,” she said. “It’s sometimes a little anxiety-provoking, because we don’t know. We don’t have all the answers.”

The Liacouras Center surge facility Credit: Kimberly Paynter / WHYY

April 7: 4,777 cases, 78 deaths

Restructuring the department to fight the coronavirus brought its own hurdles.

By April, 70% of the department’s staff was working from home. Incident commander Alles said they struggled with outdated technology and streamlining communication between agencies that tend to work in silos. Dr. Kendra Viner, the “special populations” director, said poor communication led to some oversights with patient care and outreach — particularly among people experiencing homeless.

Internally, officials shared a similar frustration felt by epidemiologists across the globe. They had banged their fists on the table about a pandemic for years, but the limited planning in the Philadelphia region couldn’t prepare them for what to come.

“I think you can study a pandemic or epidemics and public health till you’re blue in the face, but you never know what it’s going to be like to actually respond to one until it happens,” said Emily Waterman, state-county liaison for the response team.

April 13: 6,813 cases, 190 deaths

The COVID-19 response team learned to brace for emergencies within emergencies — the things they hadn’t planned for.

At one point, they received an alert that a nursing home was being evacuated over a fire. Hearts nearly stopped: where would they safely house a building full of residents already at high risk? It turned out to be an evacuation at a nearby apartment building, not a long-term care facility.

“There’s such relief in that the worst didn’t happen,” Harlem said.

If it wasn’t the worst, it was still definitely bad. Residents and staff at long-term care facilities represent more than half of the coronavirus deaths and more than a quarter of all COVID-19 cases in Pennsylvania, according to state data. Privately run facilities began carrying out bodybags day and night, while providing little information to residents and their family members.

Since that night in late January when Alles worked the phone, alarms have sounded endlessly on the health department’s hotline, bringing questions about nursing homes and more.

Social distancing isn’t being enforced. People aren’t wearing masks in the park. Where is the PPE? Do something, callers told the health department.

At daily press briefings, Mayor Jim Kenney defers often to his health commissioner. “We’ll reopen when Dr. Farley says we can open,” he repeated this week, asked about the city’s timetable to ease restrictions on businesses.

But for all their efforts leading the city’s response, Philadelphia Department of Public Health can’t always do something.

The department can shutter a five-star restaurant over some mouse droppings in the kitchen. But cracking down on a nursing home or hospital for glaring failures in medical care? Jim Garrow, the health department’s spokesperson, put it this way: “We have more regulatory control over the food that’s served in Philadelphia than the healthcare that’s provided.”

The department has little leverage over privately run health centers, group homes, shelters or hospitals. They can’t even require these facilities to test their residents, which has raised transparency questions around the testing data that’s been released. They can dispatch officials to the site and make recommendations. Punitive action — like revoking a nursing home’s license, for example — must come from the state or federal level.

A tent outside the the emergency room at the University of Pennsylvania where patients are screened for COVID-19. Credit: Emma Lee/WHYY

April 25: 12,329 cases, 466 deaths

Dr. Claire Newbern returned to the U.S. from her home in New Zealand earlier this year after the deaths of her mother and brother. She intended to remain in the states for a few months, and then return.

Then the pandemic hit.

Philadelphia’s health department, where she had worked twice before, needed an epidemiologist who could run a team tackling data management. Newbern temporarily settled back into Philly with her 10-year-old, juggling her own grief against an exhaustive workload.

“It’s probably not the best way to deal with things, but that’s how I deal with it,” Newbern said.

Under normal circumstances, public health is a nine-to-five job. But thanks to the coronavirus, many officials said they work at least six days a week, often 12 hours a day. Some have taken no full days off since the pandemic began, Alles said.

Those long hours are slowly starting to ease up. Farley said Monday that the city is scaling back its weekend updates in order to give staff some breathing room. Like many others, they’ve struggled to juggle their personal lives against the new realities brought on by the crisis.

“People are working 80 to 100 hours a week,” said Danica Kuncio, who helps oversee the city’s quarantine and isolation sites, “but still making time to pick up somebody’s prescription for them.”

They also deal with angry residents, while trying not to take it personally.

The quarantine sites have temporarily housed over 150 people to date, Kuncio said. But when screening patients, her team has had to turn away many more — and people often want to blame the messenger.

“Saying no is the hardest part of the job,” she said.

Philadelphia Health Commissioner Dr. Tom Farley Credit: Emma Lee / WHYY

May 1: 15,137 cases, 638 deaths

Nearly every health official who spoke with Billy Penn shared the same fear: how is the city going to reopen without new outbreaks popping up?

In general, Philadelphia got lucky. Hospital beds have remained available, even at peak crisis. The surge facility for coronavirus patients at Temple University did not get used as similar sites did elsewhere, and was put on standby as of May 4.

“Our health system hasn’t been overwhelmed,” Alles said.

Pressures are mounting to ease restrictions on certain sectors of the economy.

Still, the city is far from meeting Gov. Tom Wolf’s criteria for moving to the “yellow” phase of his reopening plan. To get to the aggressive mitigation stage, Philly needs to have 50 or fewer cases per 100,000 people over the course of two weeks. Right now, the city is seeing an average of 200 new cases each day — about 350% higher than the benchmark.

May 19: 20,132 cases, 1,049 deaths

Four months after tracking down the Wuhan flight manifests, Philadelphia officials say they have to return back to contact tracing as a key strategy to contain the virus.

A small-scale effort launched in early May with a group of volunteers at the University of Pennsylvania, but to be effective, they’ll need more labor. Tracing requires tons of phone calls to people who may have been exposed, and then contacting people they may have been in touch with.

“This is going to be so much larger than what we were doing initially,” said Dana Perella, who heads the surveillance unit on the department’s coronavirus team.

Most crucially, case numbers need to keep dropping.

While trying their best to communicate the importance of wearing face masks and continuing to socially distance, city health officials say they know nothing will work out as planned, and they’ll have to adapt. The city’s steps and missteps may not reveal themselves in full for years to come.

“We are going to heavily look at this,” Alles said. “Where were the breaches? Where were the gaps?

Max Marin (he/him) was Billy Penn's investigative reporter from 2018 to 2021. A graduate of Temple University, he has produced award-winning journalism on local politics, criminal justice, immigration...