Later, the CDC said it would continue to collect data about the flu, although it acknowledged it would face difficulties.
"Under a shutdown, CDC's capacity to track and respond to disease outbreaks will be impacted. Flu surveillance, for example, will continue to collect data being reported by states, hospitals, etc.," the CDC told CNBC. "However, our staff resources are limited, which means it will take longer to review, analyze, and report out information needed for public health action."
A research note on the potential impact of a shutdown, by investment firm Cowen, added a note of caution. "For a short shutdown, say a week or less, there is not a lot of effect save perhaps CDC which may not be able to track flu and other disease tracking and NIH [National Institutes of Health] which could be barred from enrolling people in clinical trials," the Friday note said.
Influenza this season has been more widespread and peaking earlier in effects than in recent years. So far this season, 30 children have died from the flu, and hospitalizations related to influenza rose last week.
"Flu is everywhere in the U.S. right now," Dr. Dan Jernigan, director of the influenza division in CDC's National Center for Immunization and Respiratory Diseases, said during a conference call on Jan. 12. "There's lots of flu in lots of places," Jernigan said.
"Our team that does this kind of surveillance studies has been doing this particular thing for 13 years, and this is the first year we had the entire continental U.S. be the same color on the graph, meaning there's widespread activity in all of the continental U.S. at this point. It is in a lot of places and causing a lot of flu," he said.
Harold Wimmer, CEO of the American Lung Association, cited the flu in urging a deal to avoid a shutdown.
"In the midst of a national flu epidemic, the President and Congress are hurtling toward a federal shutdown at midnight on Friday," Wimmer said in a statement.
"Such a shutdown could harm the urgent response needed from the Centers for Disease Control and Prevention and other public health agencies to this epidemic."