Michael Nagle / Bloomberg via Getty Images
In early February, the Centers for Disease Control and Prevention were looking for ways to stop the new coronavirus before it got out of hand in the United States.
The agency has selected six cities for sentinel surveillance – a sort of early warning system to detect whether the coronavirus is spreading freely. The idea was to find the virus among patients who had mild respiratory symptoms and no known travel risk factors – patients who were not tested according to CDC guidelines at the time.
To speed up the project, the CDC planned for cities to build on their well-established flu testing programs. Patient samples were already tested for influenza strains. The agency would provide coronavirus tests for a subset of these patients to see if the coronavirus epidemic spreads undetected.
But this quick start of the project was far from being fast in most places. Five weeks later – contrary to statements by senior CDC officials – only one of these cities had the results of the coronavirus tests in hand, according to an NPR survey.
Difficulties with CDC coronavirus testing, logistical problems, clashes between state and federal authorities, and even fear of hospitals being stigmatized as a source of infection – all of this costs precious time to control the spread coronavirus in the United States, according to sources at NPR.
Once the monitoring project started, its early warning arrived too late for some cities. Others appear to have received the alert just in time – or at least early enough to significantly reduce the death toll.
As they obtained evidence that the virus was moving much faster than they had imagined, California city health officials were able to use the information to convince officials to issue orders for most of the residents. residents – earlier than a week or more than other places, at a time when the relentless community spread of the virus had already started.
“It feels like you’ve wasted time,” says Jennifer Nuzzo, epidemiologist at the Bloomberg School of Public Health at Johns Hopkins University. “Since we learned that this disease spreads – and spreads effectively – between humans, we should have been able to resist sentinel tests in the United States. “
Virus under the radar: how the surveillance project started
On February 13 of this year, the Secretary of Health and Social Services, Alex Azar, made an announcement before a Senate committee.
Five cities, he said – Chicago, Los Angeles, New York, San Francisco and Seattle – would start testing for coronavirus in people who didn’t follow strict CDC guidelines for testing. Honolulu was added to this list of cities a week later. The goal was to find out if the coronavirus was spreading without being detected.
At that time, in February, the CDC had only performed a few dozen tests a day at its headquarters in Atlanta. Beyond that, public health laboratories were unable to process CDC test kits because the kits were defective.
As a result – apart from the new surveillance experience – the only patients who could be tested had to be symptomatic of COVID-19 and had either traveled to Hubei Province in China or had been in contact with a confirmed person infected with coronavirus . Hospital patients who had recently traveled to any part of China could also be tested.
J. Scott Applewhite / AP
The six cities were selected because of the high likelihood of emerging coronavirus cases and because, in partnership with the CDC, they had already implemented influenza surveillance programs. Each flu season, cities with such programs test hundreds of samples of patients with mild respiratory symptoms for various strains of flu. They report their results to the CDC to help track where the flu spreads and what strains are spread.
To adapt this system to the current pandemic, samples of patients whose test for influenza was negative would be eligible for a coronavirus test. Since public health labs could not run CDC tests, the federal agency offered to test them at its headquarters in Atlanta.
“We recognize that there was a situation where we didn’t have as many tests as we wanted in the United States,” said Dr. Joseph Bresee, deputy incident manager at the CDC. “But for any sentinel site, we guaranteed tests. “
Officials hoped to use surveillance tests to more accurately assess the speed at which the coronavirus had already spread – and to do so quickly.
“The results of this monitoring would be an early warning signal to trigger a change in our response strategy,” Dr Nancy Messonnier of the CDC announced to the press on February 14. “This is just the starting point, and we plan to expand to more sites in the coming weeks until we have national oversight. ”
A month later, on March 11, senior health officials assured Congress that surveillance tests were underway.
“The CDC has already started this in six sentinel cities and will extend it to many other cities,” said Dr. Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases, to the House Oversight and Reform Committee. “We need to know how many people – to the best of our ability – are infected, as we say,” under the radar. ” ”
Here’s the thing: some of these sentinel cities were still having trouble launching their testing programs.
Chicago goes first
Chicago was the first in the CDC project to test its influenza patients for coronavirus, starting March 2 in five hospitals, as well as several other Illinois counties.
This had an advantage. The Illinois State Public Health Laboratory was the first in the United States to be able to process CDC test kits, starting in mid-February – somehow avoiding defective test kits that have gone to other states.
“Being able to do the tests locally has certainly made it more feasible and realistic to be able to do sentinel surveillance,” said Dr. Jennifer Layden, chief medical officer of the Chicago Department of Public Health.
During the first week of testing, 95 emergency patients were all tested negative for the coronavirus. But by the second week, 5% of the patients were positive.
“We were surprised by the number of positives,” says Layden. “The identification of community transmission let us know that this was happening and changed our protocols on which we should consider testing for COVID-19. “
But in the middle of the two-week project, sampling more of the mild cases for surveillance became difficult, state officials said, as chemicals used in the tests began to run out.
“We want to expand our sentinel surveillance to look for the spread in the community,” said Dr. Ngozi Ezike, director of the Illinois Department of Public Health, at a media briefing. March 8. “And so that means you would need more reagents. “
Eventually, the city and state waited to follow up on the results of surveillance tests for a full week; a statewide shelter order came into effect on March 21. The city quickly became a viral spread hotspot, seeing a rapid increase in coronavirus cases that are just beginning to flatten.
Success in Los Angeles after a false start
With a high volume of travelers arriving from China every day, Los Angeles health officials suspected at the end of January that a wave of coronavirus cases was heading towards them. The city’s first documented case appeared on January 26 – a traveler from Wuhan, China – and officials feared infection could fall through the cracks.
“We wanted to try to identify the people who could have been missed by the CDC screening criteria at that time,” said Dr. Prabhu Gounder, medical director of the respiratory diseases department of the public health department of Los Angeles County.
Los Angeles County health officials have identified five hospitals for the surveillance project that serve large populations of Chinese immigrants to the area. After discussions, they began to draft a study protocol with one of these hospitals.
Gounder said the hospital’s medical staff were supportive, but the hospital’s board was not – remember, only one case of coronavirus had been confirmed in the county at that time.
“They had a very different perspective,” said Gounder of the hospital’s board of directors. “They were concerned that if the second case in LA County was related to this hospital, there would be some stigma that could be bad for the hospital in terms of anxiety among healthcare workers about exposure and also of the potential of the patients must be anxious and fear of being exposed to COVID when coming to this hospital. ”
Los Angeles health officials refused to identify the specific hospital because they agreed to keep the discussions confidential. NPR contacted several hospitals and confirmed that discussions with the Los Angeles County public health department had taken place, but could not verify which hospital board had these concerns.
Gounder says efforts to find the coronavirus in the general community have been stalled for several weeks in the area, until another hospital is called – Los Angeles County + USC Medical Center, in Los Angeles.
“This is a leading indicator,” said Dr. Brad Spellberg, chief medical officer of Los Angeles County + USC Medical Center. “If you don’t watch it, you miss the canary in the coal mine. You wait for the coal mine to collapse on you. “
Spellberg Hospital had prepared its own emergency plan to be ready to accommodate a sudden and large influx of COVID-19 patients. But not being able to test mild cases for the disease was like “flying blind,” he said. His hospital therefore partnered with the county to conduct surveillance tests for patients with mild respiratory symptoms at the hospital and its affiliated emergency care center – although Spellberg said there was controversy in within his institution concerning the testing of mild cases.
“There was huge resistance,” says Spellberg. The hospital had just obtained a small number of tests from a private laboratory – Quest Diagnostics – and had sent them to the sickest patients, which was in line with CDC general guidelines at the time. “The whole system was like,” You lose our tests. Don’t do this. “”
Damian Dovarganes / AP
However, testing at the county medical center hospital and related clinics began on March 12, and results began to return a few days later. For four days, the researchers learned something that alarmed them: up to 5% of the patients tested had coronavirus.
“It spreads silently in the community, and we didn’t even know it,” says Spellberg. “They were people who went to work, to social events, to wander the community for days and days. “
“We were all a little surprised and alarmed,” says Gounder. “It was the first real firm data point we had that confirmed our suspicions. “
This discovery marked a watershed in the response of the LA County coronavirus. Until then, health workers have been trying to contain the virus, using contact tracing to meticulously track down anyone who may have been exposed. But when a virus spreads without being detected, this type of containment strategy alone is insufficient, according to epidemiologists.
Three days after the Los Angeles surveillance study was completed, Los Angeles mayor Eric Garcetti added a new strategy, ordering residents to stay at home, with a few exceptions. So far, county hospitals have not been overwhelmed by COVID-19 patients.
“The order” Safer at Home “may have come into effect just in time to avoid a situation in New York,” said Spellberg.
Seattle and CDC clash on first tests
As King County, Washington health officials began discussions with the CDC in early February, state health officials had a suggestion: the Seattle flu study, a Research project which already collected samples from patients with respiratory symptoms, could be exploited to check for the coronavirus.
“It was a surveillance system that was operational,” said Dr. Scott Lindquist, Washington State epidemiologist for communicable diseases. “My point was, why don’t we use these samples? It was operational – let’s do it. “
But as a research project, the Seattle Flu Study’s coronavirus test – developed by the study researchers – was not yet authorized by the Food and Drug Administration, and the laboratory used for the study did not was not certified to perform clinical work for patients. (The FDA did not allow laboratories outside the CDC to handle coronavirus testing until the end of February.)
“The CDC and FDA would not allow us to use these samples,” says Lindquist. “I kept asking,” Can’t we just [get] an exception?’ ”
Sensing an increasing urgency, the researchers conducting the flu study still tested samples for the coronavirus and discovered on February 28 a teenager from Snohomish County with an alleged diagnosis of COVID-19 who had not traveled in a countries with a known coronavirus epidemic who had not had contact with a patient who was positive for the virus.
Meanwhile, King County, Washington health officials continued to seek other partnerships with sentinel surveillance tests, as the CDC suggested – clinics that would collect samples to send to CDC laboratories at Atlanta for treatment. But the county had a number of logistical issues to resolve, such as finding the right populations to test, setting up a system to inform patients, and organizing methods of collecting and transporting samples to a site where they could be assessed. . This approach never worked.
Ultimately, the researchers running the Seattle Flu Study obtained the necessary approvals to start the surveillance tests, so the county chose to partner with them. The surveillance study officially started on March 23.
Lindquist says sentinel tests earlier than this would have been very helpful in the weeks following the state’s first confirmed case on January 21. Researchers have since discovered that the virus probably spread for weeks without being detected during this period.
“It could have let us know it was here before we faced outbreaks and transmission in long-term care facilities,” said Lindquist. “But we missed this period. “
Surveillance elsewhere: faux pas and success
The pattern of slow starts or delays that affected Chicago, Los Angeles and Seattle also plagued the other three cities in the CDC’s monitoring project.
By the time New York City started its surveillance tests, it was far too late to provide an early warning. NPR could not get details of New York’s experience with the project, but city health officials confirmed that in March, New York had taken its first samples for the project – from more than 500 patients.
On March 23, the day New York sent these first samples to the CDC for analysis, the city already had more than 12,000 cases of coronavirus. By the time it obtained preliminary test results on March 31, showing that 6.6% of patients were positive, the city’s epidemic was out of control – with more than 900 deaths and increasing.
Hawaii started surveillance relatively early, compared to its first recorded case, and results so far suggest that it may have paid off. The state began testing community spread with the CDC project in mid-March. It wasn’t long after the first case of COVID-19 in Hawaii was confirmed on March 6 by a passenger returning from the Grand Princess cruise ship.
During the first week of these tests, the state did not find any cases of spread in the community (according to data finally published on March 27) and found a case the following week. Hawaii issued its home stay order to begin March 25. Since then, Hawaii has tested more than 1,000 samples through its influenza surveillance network. As of April 17, 2.1% of these cases had returned positive for the coronavirus.
San Francisco, after having preliminary discussions with the CDC, has not started sentinel surveillance tests. A spokesman for the San Francisco Department of Public Health told NPR that it was not the city’s decision, but ultimately the project “did not materialize”. The city did not provide any other details.
Silicon Valley starts its own surveillance
Besides the CDC’s six cities of origin, some other communities were keen to establish their own surveillance tests. But they too were in trouble.
For example, about 30 miles south of San Francisco, in the heart of Silicon Valley, Santa Clara County saw its first travel-related coronavirus case on January 31.
The county was not on the CDC’s original list of six test sites because it is not part of the agency’s influenza surveillance network. Santa Clara County health officials had discussed the possibility of starting the sentinel surveillance tests themselves, but – as was a problem in Seattle and New York – the county health laboratory initially could not not run CDC test kits.
In late February, the county found its first example of community spread.
“We urgently needed to know how much [community spread] that was happening, “says Dr. George Han, assistant health administrator at the Santa Clara County Public Health Department.
On March 5, with the help of a CDC field intervention team, Santa Clara County tested a sample of patients with mild symptoms in four emergency care centers and found that 11% were positive for the coronavirus. Two days after the testing was completed, Santa Clara and five other counties in the Bay Area issued home housing orders to residents.
” Those data [from the sentinel testing] was instrumental in informing this decision because it was one of the few relatively unbiased sources of data we could rely on, “said Han.” It was, I think, a key point we had to have in ordering . “
The action has been widely recognized so far for preventing an overwhelming outbreak of COVID-19 cases in the region.
Santa Clara health officials say that if the CDC test kits had worked earlier in February, they would have started sentinel surveillance even earlier – and potentially prevented even more deaths. The county recently learned that a resident died of COVID-19 on February 6, earlier than the first deaths previously known and reported. The discovery suggests that the virus was already circulating in Santa Clara County in late January.
What was won and lost in a few crucial weeks
As coronavirus epidemics have exploded in the United States, epidemiologists say that communities that ordered social distance and home shelter earlier than others may have significantly limited the number of infections and deaths .
“A week or two can make a big difference,” said Dr. Arthur Reingold, epidemiologist at the University of California, Berkeley’s School of Public Health. “The sooner you do it, the better. “
The CDC says the long delay it took to start sentinel surveillance – up to six weeks in some cities – can be attributed to the logistical challenges of fighting a deadly new virus.
“Deployment in these clinics – both by identifying the clinics that were interested and ready and willing to do so and also simply by preparing them for shipping and sample collection – even if it was similar to the it was different enough that it would take a little longer, “says the CDC’s Bresee.
In addition, Bresee said it was important that safety protocols were in place before the start of projects – health workers testing patients for coronavirus had to receive and wear additional personal protective equipment, for example.
At the time, says Bresee, the CDC was also monitoring other data – such as the number of hospitalizations of people with flu-like symptoms – that suggested cases of coronavirus infections were still limited in February.
“It’s a good question whether this delay of three or four weeks, or more, resulted in a loss of visibility of what was going on,” said Bresee. “But I don’t think so. “
While it is unclear whether previous surveillance tests would have changed the results for tens of thousands of people in hospitals and millions sitting at home, leading epidemiologists say the first weeks of the epidemic were crucial.
“Three weeks is a long time to allow cases to accumulate without knowing it,” said Nuzzo of the Bloomberg School of Public Health. “If we had had sentinel surveillance [activated] in a number of cities – cities where we expect to see cases first – we might have been able to detect it earlier and perhaps intervene before the number of cases exploded. ”
Next steps for communities and the United States
While many cities are eagerly awaiting a time for coronavirus cases to decline, they are already starting to plan new surveillance efforts to anticipate the next wave of new infections.
“We absolutely want to restart sentinel surveillance and we are preparing to do so,” said Layden, the Chicago medical chief. “We want to have a good idea of the level and amount of spread that is happening in our community. “
Some cities plan to set up surveillance projects that test a sample of patients with flu-like symptoms, while others plan to use antibody tests, which check for previous infections instead of active cases, to get a better estimate of the scale of the epidemic. already widespread.
The US government has also identified sentinel tests in its roadmap for the reopening of the country. In this case, the project would go beyond mild cases; it would test people who appear to be in good health. The goal is to find out how many people who do not have symptoms are actually infected and able to spread the virus.
“We will be doing sentinel surveillance in nursing homes, in downtown federal clinics, in Aboriginal populations – to be able to really detect asymptomatic people in the community quickly,” said Dr. Deborah Birx , White House coronavirus. task force, said at a press conference last week as the Trump administration exposed its plan.
Some epidemiologists say this type of national effort could be a chance to get adequate sentinel surveillance – providing the essential information that health officials will need to prevent a second, larger wave of serious illness and death.
“To move forward, we need a national testing strategy, period,” said Nuzzo. “Not just for testing people for clinical purposes, but for testing strategically so that we can understand the amount of disease in the community and how it spreads.” “
Such an effort would require wide availability of coronavirus tests. Although the Trump administration says there is already adequate testing capacity, many parts of the country are still reporting shortages of test supplies, noting that the country is not yet ready to collect critical surveillance data including He will need.