MacCannell says he did everything he could to get the crisis under control: he and his team developed protocols to help public health labs launch new sequencing programs; developed plans to collaborate with commercial laboratories, which have a much larger overall capacity; and set up a consortium of scientists across the country to collaborate and pool resources. But those efforts are only stopgaps, he admits, and in any event, the approval and funding required to get started was delayed by many months. “There was a big gap between what we expected and what we actually saw,” says MacCannell. “Not just at the federal level, but at every step from there.”
Genomic surveillance is one of many shortcomings that plague the disease surveillance system that the CDC presides over. These deficiencies are invisible to anyone who does not work in the field, because at first glance the system makes sense. Public health emergencies identified at the local level are reported to state health officials and then, if necessary, forwarded to the CDC, where officials analyze the information, issue guidelines, and coordinate federal action. There is a specific system for the 120 or so “reportable diseases” – like Lyme disease and hepatitis – all of which agree are serious enough to warrant immediate action, and another for “syndromic surveillance,” according to the epidemiologist Search the emergency room in real time can search data on symptoms of concern. But under this broad structure there is often chaos.
As the coronavirus turned into a full blown pandemic, CDC scientists struggled to answer even basic questions about what the disease looked like or where or how it spread.
The system itself is profoundly disjointed and the technology behind it is less mature than many American households. State health departments are not meaningfully linked, nor are hospitals, clinics, laboratories and local health authorities. The CDC maintains more than 100 separate disease-specific computer systems (a by-product of the agency’s funding silos), and many of them cannot communicate with one another. Critical data is often passed from health care facilities to health authorities through a tortured process that can include handwritten notes, manual spreadsheets, fax machines, and mail. It is not uncommon for basic information such as race, ethnicity, age, or address to be missing from clinical reports. It’s also not uncommon for these reports to wane at the state or local level without ever getting to federal officials. Even the most serious illnesses, which should be logged within 24 hours of their discovery and reported to the CDC in good time, are not necessarily routed systematically into this chain. “That depends on the jurisdiction,” Janet Hamilton, executive director of the State and Territorial Epidemiologists Council, recently told me. “Some regions have robust health departments and good reporting, while others do not.”
Disease surveillance is also hampered by the uneven patchwork of surveillance programs across the country and the need to negotiate data sharing and other arrangements with each state separately. Antibiotic resistance, respiratory infections and other pathogens are being monitored robustly in some areas and very poorly or not at all in others (for example, respiratory infections are monitored more closely in the Four Corners region than elsewhere), partly because the agency does not have the ability or authority to obtain all of the data it needs every community. Hanage compares the entire apparatus with a Rube Goldberg machine. “There is nothing central,” he says. “Random patchwork collaborations were initiated and transformed and are now having an overwhelming impact on our understanding of public health. Don’t let that criticize the people who did these things because the alternative couldn’t have been anything. But the result is something without a rational plan behind it. “
The loopholes make it difficult to track even known diseases and barely get a grip on new ones. During a recent romaine lettuce E. coli outbreak, officials were forced to make billion-dollar life or death decisions about which products to pull from which shelves in which regions of the country, based on data that included screenshots and text-messages to epidemiologists and health authorities. During the 2019 Vaping Injury (or Evali) outbreak, doctors faxed hundreds of pages of medical records directly to local health officials in some cases. Epidemiologists could hardly process the data in this format, let alone analyze it for clues. “There’s no pre-built process when something like a vaping injury or Zika or SARS-CoV-2 comes up,” says Hamilton. “There are 64 different public health jurisdictions in this country, and each will have their own ideas about what information should be collected and shared.”
In 2020, as the coronavirus went from a few isolated outbreaks to a full-blown pandemic, CDC scientists struggled to answer even basic questions about what the disease itself looked like or where or how it spread. “We were asked who is being hospitalized, who are the severe cases, what are the characteristics, and it was so frustrating,” Anne Schuchat, the agency’s deputy director, told a panel of colleagues last fall. “People went out to check graphs manually. I felt like the health sector has this data. It’s in their system. Can we work with them? ”The agency was unable to reliably track the number of tests or cases across the country. It also struggled to update hospital records, which include things like bed availability and ventilator supplies. The Trump administration hired a private contractor to collect this data on charges of political favoritism. And when multiple vaccines were eventually deployed, the agency was unable to monitor supplies or keep a close eye on waste.