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FOR SEVERAL YEARS NOW, nations worldwide have been gearing up to handle the pandemic that was anticipated if the highly contagious and deadly H5N1 “avian” flu mutated to a form that would transmit from person to person. Last year, the pandemic finally arrived, but not from the expected quarter. Rather, it came when a different strain—the H1N1—spread quickly around the globe after surfacing in Mexico. The experience highlighted persistent gaps in the world’s ability to respond to a pandemic and exposed new ones.

Observers give the federal government its highest marks—and some of its lowest—in the area of risk communication, which requires not only accurate information but also a consistent, unified message and candor about exactly what leaders do not know.

Col. Randy Larsen, U.S. Air Force (Retired), executive director of the U.S. Commission for the Prevention of Weapons of Mass Destruction Proliferation and Terrorism, praises the Centers for Disease Control and Prevention (CDC) and other lead federal agencies for unifying their message and for striking the right tone given the threat: a disease that was highly contagious but not highly virulent. “I think that last spring, CDC Director Dr. Thomas Frieden did a good job of not yelling ‘fire’ in a theater, but not saying it’s not a threat,” explains Larsen.

It was during H1N1’s second wave in late summer and early fall that risk communication suffered, especially the government’s communication of the timeframe for vaccine delivery and its ability to assure the public that the vaccine itself was safe.

As early as May, U.S. public-health scholars warned that a new vaccine for novel H1N1 would not be available at all until early fall and would not be available in adequate volumes for all high-risk populations until later in the season. “We’ve known for some time that vaccine supply was going to be a problem,” says Mario Possamai, CPP, who was a senior advisor to Canada’s SARS Commission from 2003 through 2007. Yet people from various risk groups showed up at points of delivery, and their numbers greatly exceeded supplies. The result was long lines, frustration, and a sense of pervasive government failure.

Observers also give the government low marks on countering questions about the safety of the new H1N1 vaccine—questions experts say are unfounded given the demonstrated safety of the nearly identical seasonal flu vaccines administered to millions each year. A November CNN/Opinion Research poll found that 55 percent of the country’s adult population did not want to get the H1N1 vaccine, and half said one reason was concerns about side effects.

The vaccine-safety issue presents a straightforward comparison of risk, explains Jennifer Nuzzo, an associate at the University of Pittsburgh Medical Center’s (UPMC) Center for Biosecurity. The U.S. Department of Health and Human Services (HHS) and its partners “could have done a better job explaining the safety of the vaccine,” she says.

Perhaps the most conspicuous gap in global capacity to respond to pandemic disease is the roughly six months required for manufacturers to produce large volumes of influenza vaccines for a novel strain like H1N1 using flu grown in chicken eggs. The U.S. government has also failed, experts agree, to develop adequate domestic vaccine production capacity. Only one of the government’s five suppliers, Sanofi Pasteur, produces vaccine in the United States.

With issues of speed and domestic capacity in mind, HHS is focusing funding on another option: cell-culture flu vaccine manufacture in which the flu virus is grown in a culture of cells, typically mammalian liver cells. Early this year, HHS awarded vaccine manufacturer Novartis Vaccines and Diagnostics, Inc., a $487 million contract to build a facility in Holly Springs, North Carolina, scheduled for completion this year.

When refined, cell-based manufacturing is expected to provide vaccine manufacture that is scalable and faster than egg-based manufacture. Cultivation and quality control, however, still pose hurdles.

Larsen also lists situational awareness among the greatest remaining shortfalls in U.S. pandemic response. “We have none,” he says, calling the federal government’s figure for annual deaths from seasonal flu, which falls into a range of between 36,000 and 100,000, “a guess.”

“If the president asked the CDC today how many people are sick, they could not tell him,” Larsen says.

According to a 2009 UPMC issue brief, CDC conducts disease surveillance through 150 public health laboratories nationwide. These labs report on both the number of respiratory lab samples they received and how many of them tested positive for flu. A small portion of those specimens is forwarded to CDC for typing.

Broader estimates come from CDC tracking of influenza-like illness through the U.S. Outpatient Influenza-like Illness Surveillance Network (ILINet), through which 1,400 outpatient care sites report incidences of patients exhibiting flu-like symptoms, according to UPMC. But ILINet’s data is based on symptoms that may or may not actually be caused by flu. Similarly, CDC tracks deaths in 122 cities caused by pneumonia and influenza, but not the exact virology of the deaths.

The government’s data is coarse enough that businesses should collect data themselves about communities throughout their supply chains, says Possamai. “You’d do it the same way you’d engage in competitive intelligence,” he says. “You liaise with your plants; you follow the media; you have a contact at the local school board; you have a contact at the local public health department. You develop your own sources to give you actual empirical data.”

Larsen says that the best bet for complete, real-time tracking of disease outbreaks like H1N1 is nationwide adoption of electronic medical records (EMRs), which are used in Britain. Congress incentivized a shift to EMRs in one of the stimulus packages passed last year, but it has not mandated their adoption.

The H1N1 pandemic’s final chapter has not been written, but thus far, experts say this virus could have been far worse. “I think that we are very lucky that we are facing what we are now facing,” Nuzzo says.