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How San Francisco plans to trace every coronavirus case and contact

Assembling a team to identity and isolate infections could be a crucial step in getting the city back to work.
April 8, 2020
Medical personnel obtain samples at a drive-thru coronavirus testing station in San Francisco.
Medical personnel obtain samples at a drive-thru coronavirus testing station in San Francisco.JUSTIN SULLIVAN/GETTY IMAGES

In one of the first such efforts in the country, San Francisco is assembling a task force to interview and trace the interactions of every person who tests positive for covid-19. The goal is to find who gave it to them and whom they may have given it to, in the hopes of isolating infected patients, alerting those potentially exposed, and ultimately halting transmissions.

The Department of Public Health is supplementing its own staff with dozens of researchers, medical students, and others from the University of California, San Francisco and may pull in workers from other city departments. City health workers have already been contact tracing on a small level, but they plan to significantly scale up the effort over the next few weeks. The team includes about 40 people and could rise as high as 150.

The task force will interview every patient who tests positive and provide necessary support to ensure that all are completely isolating themselves, down to helping them find and get to shelter if necessary. They also expect to reach out to between three and five people that patients came into contact with in the preceding days. They’ll alert them they may have been exposed, ask them to limit their contacts, and either encourage them to go in for a test or bring one to them. Those who test positive will trigger additional rounds of interviews and contact tracing.

“We basically realized that if we ever hope to move beyond shelter in place, we need a robust containment strategy that’s sustainable and can identify every new case and contact,” says Michael Reid, an assistant professor of infectious diseases at UCSF, who is coordinating the university’s contributions to the effort. “And that needs to be in place at least, in the medium term, until we’ve got a vaccine.”

The Bay Area took some of the earliest and most aggressive actions in the US to slow the outbreak, and seems to have succeeded in flattening the curve of the disease. But the region is still reporting hundreds of new cases per day, and the death toll is rising.

The novel coronavirus is highly contagious, with each infected person passing it on to between two and three others, on average, absent social distancing measures. If covid-19 has a reproduction number of 3, toward the top of estimates, one positive case can turn into more than 59,000 in 10 rounds of infections, Reid notes. “So you have to reach out to other contacts as quickly as possible and tell them to stay … at home,” he says.

Other places, notably including Massachusetts, are also setting up major tracing efforts, to identify and contact thousands of residents who may have been exposed. But how the Bay Area does it, and whether that effort can help slow the current spread and prevent major additional outbreaks, could provide crucial lessons—or warnings.

An early, aggressive response

The San Francisco Bay Area saw some of the first covid-19 cases in the US as well as early signs it was spreading in the community, with a case of unknown origin on February 26. On March 16, six counties ordered nearly seven million residents to mostly stay in their homes for weeks. Three days later, California became the first to roll out such measures statewide, as Governor Gavin Newsom ordered nearly 40 million people to shelter in place.

The measures appear to have helped. Daily deaths across California could peak as early as next week and reach zero by mid-May, according the state-by-state modeling at the University of Washington. New case counts in San Francisco, where more than 600 people have tested positive and nine have died, appear to have slowed down in recent days.

But the Bay Area’s success in slowing the spread may also mean that a large portion of its population isn’t immune, making the area especially susceptible to reintroduction of the disease from areas that didn’t respond quickly to the dangers, like Texas, says George Rutherford, an epidemiologist at UCSF. “We’re going to have to follow trace counts like a hawk,” he says.

Ramping up testing will also be critical for effective contact tracing, as researchers will need to be able to test everyone with symptoms as well as everyone they came into contact with, and obtain results quickly. To support that effort and contain the outbreak locally, San Francisco may need to be able to test as many as 130,000 cases per month, Rutherford estimates.

It’s not clear how many tests the city can process currently, but the number is rapidly building. A partnership between UCSF and the Chan Zuckerberg Biohub is now processing 2,000 samples per day and striving for 4,000 (60,000 to 120,000 per month). A number of other groups are also conducting tests, including the Zuckerberg San Francisco General Hospital, the Health Department’s public labs, and commercial operations like Kaiser Permanente and the California Public Medical Center.

The role of technology

Contact tracing is mostly an arduous manual task, which means it often can’t capture every infection and contact during peak moments of outbreaks. But there are some tools and technologies that can help.

The San Francisco task force will use an online and phone-based contact tracing application developed by Dimagi, based in Cambridge, Massachusetts, to manage cases and ongoing care. Among other things, it will send daily text messages to potentially exposed people, asking if they’ve developed symptoms. If so, it’ll flag workers to follow up and provide additional guidance.

The team will also ask patients for permission to look at their phone location data, which can help to provide a fuller picture of where they’ve been and moments when they may have been in crowded areas. But without access to population-wide phone data, the team won’t be able to see every time they crossed paths with others, or who those people were.

Nations like China and South Korea took more aggressive steps to closely monitor the movements of their populations amid the pandemic, requiring citizens to download apps and tapping into sources of personal data, respectively. These efforts effectively allowed those countries to automate and massively scale contact tracing efforts.

China reportedly identified more than 700,000 people who had been in contact with infected and suspected cases, and identified tens of thousands of infections.

Given privacy laws and concerns, however, there are greater limits on what kind of location data US health officials can use. The federal government and research groups are exploring a variety of ways to set up voluntary and anonymized digital contact tracing, using mobile phones, apps, and other tools. Among other things, these could tell people if they’ve walked within close proximity of an infected person.

But it’s not clear whether a critical mass of the population will ever hear about or choose to download these apps, says Ryan Calo, a University of Washington law professor who focuses on digital privacy issues. If few people enroll themselves in such tracing efforts, it could at least undermine their effectiveness and may even give some users a false sense of confidence about where they can safely go out in public, he says.

Continued social distancing

Even if regions do rapidly ramp up contact tracing and testing, and infections and deaths decline, life there won’t simply swing back to normal anytime soon.

Rutherford says that if the Bay Area hopes to relax its shelter-in-place rules, it’ll have to replace those mitigation measures with “containment on steroids.” Among other actions, he says, high-risk populations like the elderly should continue to stay at home, and the rest of the population should wear masks in public and continue to stay six feet apart. Buildings, workplaces, and restaurants will need to take precautions to keep people safe and separated as well, clearing out tables, staggering shifts, and providing hand sanitizer at the door.

Regions may also need to conduct widespread testing of another sort— antibody tests that indicate if people were previously infected—to develop a better understanding of how big secondary outbreaks could be and what kinds of ongoing efforts will be required before relaxing other rules, says William Miller, a professor of epidemiology at Ohio State University.

Antibody testing is just beginning to get under way in the US, through efforts by the Centers for Disease Control and Prevention, Stanford University, and one county in Colorado, among others.

But even with all these measures, cases will likely continue to flare up on occasion. If areas hope to keep infections low and save as many lives as possible, people and politicians will need to be ready and willing to quickly toggle between stricter and looser measures, possibly for many months to come.

“We can go back to normal when everybody has a vaccine in their arm,” Rutherford says, “and not until then.”

Correction: An earlier version of this story said that San Francisco librarians were already involved in this effort. The department has not been formally asked to contribute at this point, according to a spokesperson.

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