Genomic surveillance is one of many shortcomings plaguing the disease-surveillance system over which the C.D.C. presides. Those shortcomings have been invisible to anyone not working in the field, because at first blush the system makes sense. Public-health emergencies that are identified at the local level are reported up to state health departments and then, when necessary, passed on to the C.D.C., where officials analyze the information, issue guidelines and coordinate federal response efforts. There’s a special system for the 120 or so “notifiable diseases” — like Lyme disease and hepatitis — which everyone agrees are serious enough to warrant immediate action, and another for “syndromic surveillance,” in which epidemiologists can search real-time emergency-room data for symptoms of concern. But beneath that broad structure, chaos often reigns. The system itself is deeply disjointed, and the technology that underpins it is less sophisticated than that found in many American households. State health departments are not connected to one another in any meaningful way, nor are hospitals, clinics, laboratories and local health agencies. The C.D.C. maintains more than 100 separate disease-specific computer systems (a byproduct of the agency’s funding silos), and many of those can’t interface with one another. Crucial data is often shepherded from health care facilities to health departments through a tortured process that can involve handwritten notes, manual spreadsheets, fax machines and snail mail. It’s not uncommon for basic information like race, ethnicity, age or address to be missing from clinical reports. It’s also not uncommon for those reports to languish at the state or local level without ever making their way to federal officials. Even the most serious diseases, which are supposed to be logged within 24 hours of detection and reported to the C.D.C. in a timely way, are not necessarily sent up that chain in any systematic manner. “It depends on the jurisdiction,” Janet Hamilton, executive director of the Council for State and Territorial Epidemiologists, told me recently. “Some regions have robust public health departments and good reporting records, and others don’t.” Disease monitoring is also hampered by the uneven patchwork of surveillance programs across the country and the need to negotiate data sharing and other agreements separately with each state. Antibiotic resistance, respiratory infections and other pathogens are tracked robustly in some areas and very poorly or not at all in others (respiratory infections, for example, are more heavily monitored in the Four Corners region than in other places), in part because the agency does not have the ability, or authority, to get all the data it needs from every community. Hanage likens the entire apparatus to a Rube Goldberg machine. “There’s no central anything,” he says. “Random patchwork collaborations were initiated and transformed and now have an outsize impact on our understanding of public health. That’s not to criticize the people who made those things, because the alternative might have been nothing. But the result is something with no rational plan behind it.”