The Centers for Disease Control and Prevention began furloughing a large share of its workforce on Wednesday as the federal government entered a partial shutdown, suspending routine influenza and respiratory virus surveillance at the start of the new fiscal year. The Department of Health and Human Services confirmed the reductions in a contingency notice.

The shutdown followed a congressional deadlock over spending legislation that expired at midnight on September 30. Under HHS lapse plans, agencies including the CDC, the National Institutes of Health and the Food and Drug Administration retain only staff deemed essential for the protection of life and property, while thousands of other employees are placed on unpaid leave.

CDC officials said core outbreak response and laboratory functions would continue, but weekly influenza reporting through the FluView system and non-emergency data updates would be paused. The NIH said it would admit no new patients to its Clinical Center trials except in cases of immediate medical need and would halt processing of new research grants.

Public health groups, including the American Public Health Association and the Association of State and Territorial Health Officials, warned that the timing was especially damaging as respiratory virus season began. Gaps in national surveillance would leave state health departments with less warning ahead of expected flu, RSV and COVID-19 activity.

FDA leadership said user-fee-funded activities, including much of drug and device review, would continue in the near term. A prolonged lapse would eventually slow approvals, and agency leaders urged Congress to restore funding quickly.

"A shutdown at the start of respiratory season is the worst possible time to go blind on the data," said a former CDC official quoted by the Association of State and Territorial Health Officials.