The Centers for Disease Control and Prevention confirmed Friday that key public health functions, including influenza surveillance and updated fall vaccine guidance, would be paused or scaled back as the federal government shutdown entered its second day. Roughly two-thirds of the agency's workforce faced furlough.

The lapse in appropriations began October 1 after Congress failed to pass a funding measure. The Department of Health and Human Services said essential activities protecting life and property would continue, but routine data publication and non-emergency communications would be suspended until funding resumed.

The timing coincides with the start of respiratory virus season. The CDC's FluView report and weekly surveillance dashboards, which clinicians and state health departments rely on to track influenza, COVID-19 and RSV activity, were among the products affected.

State epidemiologists in several jurisdictions said they would depend more heavily on local laboratory networks during the gap. Public health organizations warned that reduced federal monitoring could leave clinicians with less visibility as vaccination campaigns ramp up.

The American Public Health Association said the disruption arrived at the worst possible moment, with pharmacies and clinics beginning fall flu and COVID-19 immunization drives across the country. Food and Drug Administration reviews funded by user fees were expected to continue, but the agency cautioned that new outbreak investigations and inspections could slow if the impasse persisted into the following week.