PORTLAND, Ore. — Swine flu may have been caught early enough to prevent a serious U.S. epidemic, according to computer models developed by Virginia Tech's Network Dynamics and Simulation Science Laboratory (NDSSL).

Separately, CombiMatrix Corp. announced the availability of a flu chip manufactured for it by STMicroelectronics that it claimed can confirm swine flu infections in four hours.

NDSSL, part of Virginia Tech's Bioinformatics Institute, (Blacksburg, Va.), boasts the world's most power epidemic modeling tool. It is used by the U.S. Department of Health and Human Services (HHS), which has designated swine flu as the "2009 H1N1 flu virus."

"We have done many, many studies with layered interventions where you have social distancing, which includes closing schools and workplaces, and many other actions that involve breaking up a social network to reduce significant contact between individuals," said NDSSL Director Chris Barrett.

"Study after study has shown that social distancing, especially in child populations has a very large effect--as large as if very high efficacy vaccines were given in advance of the outbreak. So closing schools is important, but it can't be a halfway measure such as closing only one school."

Earlier this week, one New York City school was closed after cases of swine flu were confirmed.Other city schools remained open. Two more New York schools closed voluntarily later in the week, but were not ordered to do so.

The World Health Organization has moved its threat level to just one step below a global pandemic.

"So far, only a few schools in New York were closed, because of the outbreak detected there, but our model allows you to simulate not only the results of closing one school, but also the probable results of closing additional schools such as ones where the siblings of those infected are attending," said Stephen Eubank, the NDSSL's deputy director.

U.S. health officials have not been willing to implement the types of social distancing that would likley insure the spread of the flu virus in the U.S. Even if, for example, all U.S. schools were closed and its borders sealed, other countries would have to follow suit to prevent a global pandemic.

"If the virus spirals out of control in other countries, all our measures here will only slow down its spread--even if we closed our borders," said Barrett. "On the other hand, if we could slow it down here for, say, six months, that might be enough time to develop an effective vaccine."

Too little is known about this particular strain of swine flu to quickly develop an effective vaccine. It is known that the H1N1 flu virus has elements of human, pig and avian flu from different parts of the world, forcing NDSSL modelers to use the closest characteristics from previous H1N1 pandemics. The H1N1 designation means that swine flu uses type one hemagglutinin (H) to gain entry into uninfected cells, then use their internal machinery to make copies of itself. The virus then uses type one neuraminidase (N) to exit the infected cell and move on to new ones.

"So far, we haven't even identified the incubation period or how long people are infectious," said Barrett. "We do know that the strains detected in the U.S. appear to be milder than the ones that have already killed in Mexico."

The lab argues that these unknowns increase the value of its models since "we can try different values in the range of things that are possible in our populations, including how many people a day are becoming infected, details of their movement and demographics," Barrett added. "The result is a very detailed range of possibilities, and what interventions would be most likely to prevent the worst-case scenario."

More than 100 U.S. cases of swine flu have been identified so far with one confirmed death.

One of the lab's tools, Simfrastructure, models complex interdependent, socio-technical infrastructures employing multiple simulations. The models are used by policy makers with tools for planning. Another tool, Simdemics, is the supporting modeling environment that can be distributed across large, irregular computer networks.

The high-end computing tools were previously only available to meteorologists, ocean scientists and nuclear engineers, Barrett said.

A simulation for a single large U.S. city takes about 1 second, including a social network of about 20 million nodes on the lab's current hardware. Simfrastructure and Simdemics are running on eight supercomputer clusters totaling 1,200 processors sharing 200 Gbytes of memory and nearly 1 petabyte of mass storage. For larger simulations, the software can also be run on the National Science Foundation's TeraGrid host or the Argonne National Labs "Urgent Computing" resource.