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Healthy choices: Supercomputing the flu vaccine

Speed read
  • Choice of vaccines proves to be a cost-effective health management strategy
  • Agent-based models enable risk assessment analysis
  • Processing power of Bridges supercomputer broadens the researcher's ability to compare geographically

Each year, influenza hospitalizes about 226,000 Americans and kills an average of 24,000. But less than half of children and adults under age 65 get vaccinated. An international collaboration looked to the Pittsburgh Supercomputing Center (PSC) to do something about it.

Collaborators from PSC, the University of Pittsburgh and Soongsil University in the Republic of Korea wanted to find out whether offering different types of vaccination — the familiar injected vaccine or two types of ‘needle sparing’ vaccines — would reduce flu cases and make vaccination more cost effective.

<strong>Choice works.</strong> An army nurse attends patients at Walter Reed Hospital, Washington, DC, during the great Influenza Pandemic of 1918-1919. Recent research harnesses high-performance computing to discover that choice of vaccine yields the most effective health and cost benefits over the long term.

Previous work by the group had shown that offering adults and children a choice of vaccines would increase the number vaccinated, but not how effective or cost-effective that increase would be.

“The latest paper caps a series of studies that have looked at the question of vaccine choice from the point of view of simple statistical models to more sophisticated ‘agent-based’ models,” explains Jay DePasse of PSC’s Public Health Applications Group. “The increased computational power of the Bridges system allowed us to build on our earlier work with a massive, agent-based simulation.”

They built on earlier, simpler models using a tool called agent-based modeling (ABM). This method simulates individual people in an area as they go to work or school or socialize, watching how the virus spreads and how vaccination affects that spread.

Using Olympus, PSC’s dedicated public health supercomputer, the scientists first determined that vaccine choice would, on the average, reduce cases and bring down the cost per dose of vaccination in the Washington, D.C., population.

We were able to say, ‘Well, we have the computational power, let's go for it!’ ~ Jay Depasse

They showed that offering vaccine choice reduced flu cases in both adults (who got the choice of a traditional injection versus a very-small-needle intradermal injection) and children (whose ‘virtual parents’ chose between traditional and inhaled intranasal vaccines).

Their study also revealed that the decreased costs due to illness offset the extra expense of offering more vaccines, reducing the overall societal cost of influenza. While offering choice to adults and to children separately helped, choice for both groups provided the best protection and lowest costs.

The group then moved their computations to the larger, Bridges system at PSC, allocated through the Extreme Science and Engineering Discovery Environment (XSEDE). Bridges enabled them to expand their model to multiple regions of the country with very different populations.

(Look here for an interactive view of the Bridges supercomputer.)

“One of the reasons we used an agent-based model is it tests the indirect effects. Say I get vaccinated; that has an impact on whether my kids are going to get the flu. But it’s computationally expensive,” says DePasse. “(Using Bridges) we were able to say, ‘Well we have the computational power, let's go for it.’ That adds to the realism of the simulation.” 

The new work, published in Vaccine in July, 2017 reproduced the results seen in the D.C. study, and Bridges’ power allowed the scientists to test a wider range of assumptions about increased coverage and virus spread, showing that even moderate increases in coverage due to offering more choices can reduce costs and decrease influenza cases by 5,600 to 35,000 people across all five counties.

The group is now continuing their work on an upgraded Olympus, which has incorporated many of the hardware innovations of Bridges.

Read the original article by the Pittsburgh Supercomputing Center here.

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