ATLANTA » As the government shutdown moves into its second week, there’s virtually no activity in the federal labs in Atlanta where, each fall, researchers test thousands of samples of flu virus.

As the season of coughs, sneezes and sniffles kicks into gear, boxes of samples sent from across the country to the Centers for Disease Control and Prevention will pile up in storage facilities. Offices at the nation’s premier flu-fighting agency, where experts normally crunch numbers and issue weekly updates, will sit vacant.

Consequently, CDC officials say, outbreaks could go unnoticed. Mutant strains of flu — such as the H1N1 that caused a world pandemic in 2009 — could spread before the new threat they pose is recognized. And just how well this year’s flu shots are working won’t be definitively answered.

”I’m worried about what we don’t know," CDC Director Dr. Tom Frieden told The Atlanta Journal-Constitution.

About 6,000 of CDC’s 10,000 workers in Atlanta have been sent home, including about 270 of the 320 flu surveillance staff.

Frieden made the call to furlough them after consulting with the White House Office of Management and Budget. He said he is simply following the law, a century-old mandate called the Antideficiency Act, which holds sway over the federal shutdown.

At this point, in his judgment, he said, flu surveillance did not rise to the standard of protecting against "an imminent threat to health."

Some infectious disease experts question that determination.

”From a public health standpoint, there could be a strong argument that this is an essential function for CDC and the public health," said Dr. Andrew Pavia, chief of pediatric infectious disease at the University of Utah. "The longer you stumble along in the dark, the more the danger."

Frieden didn’t disagree, likening the CDC’s flu surveillance program to a boat at sea. If it strays off course for a short time, it may not get badly lost. But as time passes, the chances increase of tragedy.

Therefore, Frieden said, he is reassessing the decision on a daily basis, and could change his mind within a week or two.

For the moment, there appears to be no imminent threat. It’s still early in the flu season, which runs from September through May. Both national and state health officials say there is an abundance of flu vaccine available.

But the flu is an unpredictable and fast-moving foe. Last year, for instance, the flu season hit uncommonly early and hard. In prevention efforts, weeks, even days, can count.

If the shutdown continues and the flu trackers stay idle, experts say, a sudden uptick in cases or a newly emergent bug could get out in front of the nation’s detection and treatment apparatus. And if that happens, more people could ultimately sicken and die.

”The world doesn’t stop because the government decides to stop," said Dr. Carlos del Rio, chairman of Emory University’s global health department. "The virus doesn’t stop dividing or transmitting."

The absence of the national detection system places far more of a burden on state health departments to spot trouble. At the same time, 46,000 state and local health positions have been lost across the country in the past four years, CDC officials said.

Most state health departments have the capacity to recognize an outbreak of influenza, but they may not be able to identify a new or resistant strain, said Dr. Larry Madoff, an infectious disease physician and editor of the online public health site ProMED.

The Georgia Department of Public Health continues to collect data on flu in the state, and expects to release its first report of the season this week, said spokeswoman Nancy Nydam.

”There has been some flu activity in the state — nothing out of the ordinary," she said.

Georgia state labs can do some testing to identify what flu is going around, but the CDC alone can nail down essential details such as its genetic makeup.

More than that, the CDC plays a critical role in understanding the trends of flu across the country, as well as communicating between states to target regional outbreaks. It is the CDC that ensures an area hard hit with the flu gets enough of the antiviral treatment drugs.

The textbook demonstration of how crucial the CDC’s role can be came in April 2009 with the emergence of a new strain of H1N1, which became a world pandemic.

It took just two cases, spotted a couple of days apart in April in California, to set off alarms in Atlanta. Within days, the CDC had determined that a new strain, transmitted person-to-person, had emerged.

Within two weeks, the CDC had identified cases in California, Texas, New York, Kansas, Ohio, Mexico and Canada. It had begun laying groundwork for developing a vaccine, issued public health alerts, and transmitted the complete genetic sequence of the new virus to researchers worldwide.

It had also determined which antiviral drugs were effective against this new flu, begun releasing government stockpiles of those drugs, and developed a test that labs throughout the country could use to identify the new strain.

By the time the fall flu season rolled around, an effective vaccine was commercially available, although production problems delayed full-scale distribution.

The CDC later estimated that the vaccination campaign, which reached more than 80 million Americans, prevented about 1 million hospitalizations and saved roughly 300 lives in the U.S. Many more lives would have been saved and hospitalizations prevented if the new vaccine had been made available earlier, CDC officials said.

Even in the midst of the shutdown, some work continues at the CDC, such as protecting the agency’s stock of dangerous agents, such as Ebola, anthrax and smallpox. Programs with "mandatory dollars" also continue, such as vaccination programs for childhood diseases, as well as those with multi-year budgets that don’t depend on this funding cycle, such as global AIDS and malaria programs.

But other surveillance programs have been reduced or largely shut down. Staff in quarantine stations at international airports have been cut to bare bones.

”In the worst case, we could miss an infectious disease coming into the country," said CDC spokeswoman Barbara Reynolds.

In addition, the CDC is doing far less to spot outbreaks of food-borne illness such as salmonella and E coli.

In a memo to workers who remain on duty, Frieden expressed his concern about the damage to research projects left untended by those on furlough.

”I remain both frustrated and concerned about CDC’s ability to protect the health and safety of the public," he wrote.

If other agencies identify a threat, the agency will respond, he told the AJC. For example, the CDC dispatched a team to Arizona after a 5-year-old boy died of Rocky Mountain spotted fever.

But without CDC’s national surveillance system, identifying these dangers becomes a greater challenge.

”How can we respond to an emergency, if we can’t find the emergency?" Frieden said.