This was originally published Oct. 1 on Maryn McKenna’s Superbug Blog, hosted by Wired Science. There’s going to be a lot — a lot — of coverage today on the federal shutdown, what it means and how long it might go on. I thought it might be worth quickly highlighting how it affects the parts of the government readers here care most about: public health, global health, food safety and the spread of scary diseases. Most of those government functions are contained within the Cabinet-level Department of Health and Human Services, where 52 percent of the employees have been sent home. So the news is not good. The U.S. Centers for Disease Control and Prevention furloughed 68 percent of its people — not just here in Atlanta, but globally. Yesterday I asked a longtime acquaintance there what was likely to happen and she said:

“I know that we will not be conducting multi-state outbreak investigations. States may continue to find outbreaks, but we won’t be doing the cross-state consultation and laboratory work to link outbreaks that might cross state borders, such as a recent Hep A outbreak. We will not be doing rapid response for vaccine preventable disease cases or outbreaks, such as measles. We won’t be monitoring seasonal influenza activity in the U.S. as flu season begins. “Surveillance for other emerging infectious disease outbreaks, such as H7N9 and MERS, will be weakened. We won’t be doing routine inspections of BSL3 and BSL 4 labs as part of the select agent program. Our work to prevent HIV/STDs and TB in the states using molecular epidemiology will be discontinued.”

Let’s unpack that a little bit. In the U.S., the flu season is beginning. This year’s flu vaccine has been manufactured and is either already in the hands of state and local health departments or with doctors or on its way to them via the commercial middlemen who handle distribution for the manufacturers. (OnTwitter today, Jim Garrow of the Philadelphia Department of Public Health confirmed that they already have an inventory of flu vaccine.) So flu prevention won’t necessarily be harmed — except for those people who don’t get a flu shot unless CDC’s public health campaigns remind them because there won’t be any such campaigns. But flu surveillance, which CDC conducts and also assembles out of data sent to it by health departments and by networks of physicians, is on the shelf. Here’s what CDC’s flu-surveillance homepage looks like right now: (The original page is here.) And here is what that means: We are now at the start of flu season. If this season becomes a bad one — a rogue virus, an uneven epidemic, a concentration of cases in the elderly or the very young or in a particular city or state — we’ll have no way of knowing. And, for what it’s worth, we’ll have no way of directing additional public-health or research help because they’ve all been sent home. In tracking flu, one of the most unpredictable and mutable human-disease viruses around, we have been blinded. And, if the shutdown continues more than a few weeks, then that blindness will also blanket development of next year’s flu vaccine — because, within a few weeks, CDC researchers would start analyzing this year’s northern and southern hemisphere viruses to determine what ought to be included in next year’s vaccine mix. That blindness is not limited to the U.S. CDC loans scientists and sends money to the World Health Organization and to dozens of countries in the industrialized and developing worlds. One of its specialties is helping to track the emergence of new flu viruses that have pandemic potential. That global spyglass has just been shuttered. And, we are less than two weeks from the official beginning of the hajj, the worldwide pilgrimage of observant Muslims to the holy sites of Saudi Arabia — where, if you’ve been following along, MERS has been slowly growing for more than a year. Health planners have been quietly fretting for months that the hajj might allow the spread of MERS outside of the Middle East — a reasonable fear, as that has happened in past hajj seasons with other diseases. But with the shutdown, we lose some of the most accurate tools for finding that out. This enforced ignorance of disease spread isn’t hypothetical. Just this morning, the WHO tweeted that there is a three-country outbreak of more than 200 cases of polio in the Horn of Africa. The top polio-hunters in the worldwide eradication effort, the ones who developed the “molecular clock” that allows the eradication campaign to trace new cases back to their source, work at  — yup, CDC. The shutdown’s risks to health aren’t limited to what CDC does. The Food and Drug Administration has sent home 45 percent of its staff. The ones who remain can do so because they work in programs that receive user fees such as reviews of proposed new pharmaceuticals. Those can continue provided the application for review was already submitted. (New reviews, according to FDA’s statement today, are out of luck.) But food safety — always an underfunded mandate — is in real danger. HHS’s memo on shutdown staffing acknowledged this:

“FDA will be unable to support the majority of its food safety, nutrition, and cosmetics activities. FDA will also have to cease safety activities such as routine establishment inspections, some compliance and enforcement activities, monitoring of imports, notification programs (e.g., food contact substances, infant formula), and the majority of the laboratory research necessary to inform public health decision-making.”

Translated, that means: No foodborne outbreak tracking; no inspection of food imports; no lab research; no publishing of guidance documents. (Food Safety News and Regulatory Focus have more.) At the U.S. Department of Agriculture — which attends to about 15 percent of the U.S. food supply, including meat, compared to FDA’s 85 percent — things are a bit better. Eighty-seven percent of its staff have been retained, including most of the Food Safety and Inspection Service. In its shutdown memo, USDA says FSIS falls under an Office of Management and Budget shutdown category described as “necessary to perform activities necessarily implied by law” (for wonks, that’s No. 3 of the five categories). Thus, they can continue to conduct meat, poultry and egg inspections on-site; that is, at plants and packing houses. However, the agency loses personnel as follows:

“The following headquarters staffs performing the central program guidance, coordination, direction and planning functions described will be furloughed except as minimally required in direct support of Agency field operations:

• Inspection Operations (Office of Field Operations): Responsible for planning, coordinating and directing the Meat, Poultry, and Egg Products Inspection programs. Due to the large numbers of in plant inspection personnel who support excepted activities, most individuals in this area would be excepted and on duty.
• Public Health Science (Office of Public Health Science): The Public Health Science Program is responsible for planning, coordinating and directing all scientific guidance and support in chemistry, epidemiology, pathology, toxicology, nutrition, and parasitological. The Public Health Science Program also performs Agency risk assessments, directs the residue testing program, and also performs activities that address zoonotic diseases. With the exception of the laboratory function within Public Health Science, designations for these functions would be non-excepted, with limited individuals being identified as excepted and on duty. The majority of all Laboratory functions will be excepted.
• International Programs (Office of Field Operations, Office of Policy and Program Development, and Office of Investigation, Enforcement and Audit): The International Programs are responsible for ensuring that meat, poultry, and egg products from foreign countries are safe and wholesome. Program personnel also confer with foreign governments on issues involving imports and exports of meat, poultry and egg products and international food safety standards. A substantial number of these programs other than inspection of imports and certifying products for export would not be excepted.”

I know other Wired colleagues are going to tackle the shutdown’s effect on the rest of the government science apparatus. There is no question, though, that public and global health and food safety are experiencing great impact. Better hope there are no major outbreaks brewing and that no food producer or manufacturer — or food importer in a country with lower standards — decides that now is the time to try to slip something by government-funded detection and response. As of this morning, the protections we rely on are no longer there.