More than 40,000 people who work at HHS and its various subagencies have been told not to come to work until Congress passes some sort of legislation to fund the federal government, affecting everything from tracking the flu season to clinical trials at the National Institutes of Health.

While the furloughs cover roughly half of the entire HHS workforce, for many programs—including state Medicaid funding, Medicare reimbursement and the Affordable Care Act’s premium support subsidies—it’s business as usual.

According to the department’s contingency plan in case of a shutdown, many activities will continue, including:

• Processing Medicare reimbursements, though a prolonged shutdown could lead to delayed payments to providers.
• Patient care at the NIH Clinical Center.
• Operation of 1,400 community health centers through the Health Resources and Services Administration (HRSA).
• Addressing the IV saline shortage through the Food and Drug Administration.
• Medicaid enrollment, because it is administered by states, not the federal government.

In its separate contingency plan, the Department of Veterans Affairs said only 1,059 of the 337,829 employees in the Veterans Health Administration would be furloughed.

“95.5 percent of VA employees would come to work, and most aspects of VA’s operations would not be impacted,” VA press secretary Curtis Cashour said in a statement.

In the official plan, parts of flu tracking program at the Centers for Disease Control and Prevention (CDC) would be among the services shuttered during the shutdown. States would still track the cases and the CDC would “be collecting data reported by states, hospitals, [and] others and they’ll be reporting that critical information needed for state and local health authorities.” However, the CDC wouldn’t be available to verify samples of the virus or offer advice to state agencies—which more may need given the country is experiencing a severe flu season.

Other HHS functions that would be suspended include:

• NIH clinical trials wouldn’t admit new patients.
• Many grant awards or applications would be held in limbo, such as those through NIH and the Agency for Healthcare Research and Quality (AHRQ).
• AHRQ wouldn’t monitor previously-funded projects “related to health services research initiatives, including research on improving patient safety and reducing healthcare-associated infections.”
• Most of ONC’s responsibilities, like testing, implementation and coordination on health IT standards, or advancing any regulations as required by the 21^st Century Cures Act.

Members of Congress spent much of Sunday, Jan. 21, trying to reach a short-term spending deal before the workweek began but were unable to reach an agreement.

“Talks will continue, but we have yet to reach an agreement on a path forward that would be acceptable for both sides,” Senate Minority Leader Chuck Schumer, D-New York, told POLITICO.