University of Guelph decision support system could predict the next pandemic

Influenza virus that jumps from pigs or poultry to humans could be catastrophic

By Lilian Schaer for Livestock Research Innovation Corporation

For Shayan Sharif, the next pandemic was always a question of when and not if.

And the Associate Dean of Research and Graduate Studies at the Ontario Veterinary College and professor in the University of Guelph’s Department of Pathobiology was fairly certain the culprit would be an influenza virus that could jump from animals, like poultry and pigs, to humans.

The most recent influenza pandemic happened in 2009. Caused by the H1N1 influenza virus, it is considered to have been relatively mild, with a global death toll estimated by the U.S. Centres for Disease Control to be approximately 284,000.

A little more than a decade later, the world was plunged into the next pandemic, driven by SARS-COV2, the coronavirus that causes COVID-19. By end of October 2021, the global case count was nearing 250 million with just over five million casualties, and the virus continues to rage in many parts of the world.

The COVID-19 experience has left Sharif more convinced than ever of the need to be proactive and forward-thinking when it comes to pandemic preparedness and prevention – and of the risk pigs and poultry in particular pose as potential hosts for an influenza-driven pandemic.

That’s because for some highly virulent avian influenza viruses transmitted to humans, the fatality rate could be as high as 30 to 50% of infected people, compared to the approximately 2% of confirmed COVID-19 cases.

And although the world has learned a lot through this pandemic, one thing Sharif believes hasn’t progressed is a general understanding of pandemics themselves – how, why, when and where they happen.

Boosting that understanding is what he says will help the world avoid or at least minimize the impacts of future pandemics, especially ones that affect both humans and livestock and could have much more catastrophic global impacts.

“If I were to put a coronavirus head-to-head with an influenza virus, hands down influenza is harder to control. Viruses are very sneaky and they know every single vulnerability in our systems and in our communities, and how to exploit our immune systems to their own advantage,” Sharif explains. “That’s why I’m concerned about future pandemics.”

He’s particularly worried about a livestock virus that could jump to humans and then back to livestock, wreaking havoc on people, their food sources and in some cases, their livelihoods. And if it’s a virus with the capacity to cause greater mortality in younger populations, who also happen to make up the majority of the global workforce, that could have catastrophic impacts on society and the economy.

This was a leading reason why Sharif teamed up with Prof. Rozita Dara, associate professor and data strategy director at Guelph’s School of Computer Science to create a Decision Support System (DSS) that uses data from various sources to predict when and where an influenza virus can emerge.

To date, they’ve focused their work on avian influenza, but it could be adapted to influenza of swine origin, as well as to other species and other diseases.

“We created a system that will have various components like social media posts, poultry farm density, regional climate and weather data, animal transportation and the flight paths of wild birds,” Sharif says. “Using machine learning, we can pull all of this together and predict fairly accurately not only which regions are at risk of occurrence of outbreaks, but what decisions can help mitigate the impacts.”

Using data from southeast Asia, Sharif and Dara’s pilot DSS system has been tested in that part of the world for regional risk prediction of avian influenza outbreaks.

Now, they are seeking funding to determine what is needed to adapt the system to the Ontario and Canadian poultry industries for use here at home. That includes being able to collect and validate data used to assess and manage disease risk, for example.
They’re also seeking the expertise of organizations like the Feather Board Command Centre in Ontario, which plays a key role in foreign animal disease response for poultry producers, and the Canadian Food Inspection Agency, which has federal jurisdiction over livestock disease outbreak response.

To date, the DSS project has received funding support from the Canadian Poultry Research Council, Egg Farmers of Canada, the Ontario Ministry of Agriculture, Food and Rural Affairs, the Natural Sciences and Engineering Research Council and the University of Guelph’s Food From Thought project.

This article is provided by Livestock Research Innovation Corporation as part of LRIC’s ongoing efforts to report on Canadian livestock research developments and outcomes. It was published in the December 2021 edition of Ontario Hog Farmer.