The scenario played out last spring when “swine flu” suddenly became a household name. As public health agencies sprung emergency policies into place, scientists set about tracing the new H1N1 virus back to its source, following it from person to person and eventually to the animals where it originated. Understanding how the virus’ genes mutated in pigs could help scientists determine how it jumped to humans, and give clues as to the most effective ways to fight the disease. But in the time it took to reconstruct the origins of swine flu, thousands and thousands of people were were newly infected with the virus.
Fortunately, last year’s novel H1N1 virus ended up fizzling out into a run-of-the-mill flu – still deadly in a small percentage of people, but not the runaway killer it threatened to be in its earliest days. But we might not be so lucky with the next disease to jump from animals to humans, so monitoring potential threats before they crossover is a scientific priority. While the genetic sequences of more and more organisms are cataloged every day, the viruses, bacteria and parasites those organisms living inside those animals have barely been characterized.
That knowledge gap is the target of the Emerging Pathogens Project, a collaboration between scientists at the University of Chicago and the Field Museum announced Tuesday morning at the museum’s very cool DNA Discovery Center. Blending the centuries-old practice of gathering animal specimens on field expeditions and the bleeding-edge technology of large-scale genomics, the project hopes to give scientists advance warning and knowledge about tomorrow’s epidemics.
“We plan to treat each one of these animals as an ecosystem in and of itself,” said Shannon Hackett, head of the bird division at the Field Museum and co-leader of the project. “We’re really interested in what lives in and on these organisms.”
Those animal ecosystems were collected during an expedition last fall in the African country of Malawi, a trip that brought back roughly 1,100 bird and mammal specimens. A sampling of those (pictured above) were on display at the announcement of the project; just one shelf from the tens of thousands that store critters of all types in the museum’s vast collection facilities. In categorizing those specimens, the museum has moved increasingly to genetic analysis, but the Emerging Pathogens Project brings those efforts to a much larger scale.
That’s possible thanks to the genomics infrastructure established by Kevin White, director of the University’s Institute of Genomics and Systems Biology and Hackett’s leadership partner in the Emerging Pathogens Project. Having previously launched massive projects to study genetic regulation and the genetic makeup of tumors, White said there was still time to take on another scientific challenge. Gesturing at the DNA laboratory that was the backdrop for Tuesday’s event, White aid that the high-throughput sequencing technology now available could do an amount of work equivalent to several million of such labs.
“A few years ago, this project wouldn’t have been possible at all,” White said. “The amount of data that we can produce has been rising exponentially over the past few years. At this point, we happen to be at an inflection point where we actually produce more data than we can handle in most computer systems.”
That means the sequencing – which begins this summer – is only part of the genomic story, as computational biologists will then start sifting through the flood of data to create a “baseline” of pathogen genetics in the population. If a pathogen crosses over to humans in the future, scientists can quickly compare the new virus to its previous forms in animals to look for vulnerabilities to target with treatments. Even if such an outbreak never occurs from this population, the genetic information can be tracked to observe how climate change and other ecological processes modify pathogens over time.
Of course, none of that data would be possible without the original data points – the 1,100 specimens, from bats and mice to chickens and finches. Jason Weckstein, a research scientist in the museum’s Zoology Department and a member of the expedition, talked about taking blood and tissue from each animal, using a portable field lab to freeze samples and make microscope slides. Weckstein, who studies bird parasites, said that as much as 70 percent of life on Earth is made up of parasitic organisms, yet very little is known about their biology. A new flood of genomic data can help shine some light on that mysterious world, the scientists said.
Understanding parasites and other unwelcome travelers more thoroughly may not pay off with immediate results for modern health care – as Hackett said at the event, “we’re not going to find the next Ebola virus.” But the project could be a crucial, proactive tool should humans find themselves under attack by something nasty, new and microscopic in the future.
“This project is all about potential,” White said. “The potential for understanding biodiversity, for understanding new pathogens, and the potential for the application of new technologies.”