Thanks to research supported by the Government of Canada's Genomics Research and Development Initiative (GRDI), Canada's multibillion-dollar pork industry has a new level of protection from the potentially disastrous impacts of African Swine Fever (ASF).
While it poses no danger to humans, ASF is a highly contagious disease for which there is currently no vaccine or treatment. Over the past 5 years alone, outbreaks in Europe, Asia and Africa have resulted in the death or destruction of well over 10 million pigs.Footnote 1 The disease has yet to appear in Canada, but it is getting closer: outbreaks were reported in the Dominican Republic and Haiti in 2021.Footnote 2
At the Canadian Food Inspection Agency (CFIA), which works with partners across the country to guard against the entry of foreign animal diseases, research scientist Dr. Oliver Lung says prevention is essential.
Practice prevention—but be prepared
"Canada has rigorous import restrictions and controls to help prevent the introduction of ASF in Canada," says Dr. Lung. "Even then, there's always a risk something could slip through. A real concern is illegal imports.”
"There's a very good reason pork products of any kind should not be brought into Canada," adds Dr. Lung, who heads the Genomics Unit at the National Centre for Foreign Animal Disease (NCFAD), the CFIA's Winnipeg laboratory. "The virus that causes ASF, for example, is very stable and can survive a lot of processing. It could arrive in something as apparently innocuous as a pork sausage."
Given the risk, and the magnitude of the potential impacts on an industry that generates some $24 billion in economic activity for CanadiansFootnote 3, Dr. Lung says it's critical to be ready to respond should ASF be found in Canada. "With any infectious disease, the sooner you can obtain a positive and detailed identification, the sooner and better you will be able to respond with measures to contain the infection."
From slow to fast—very fast
“Infections like this can spread very quickly, and existing tests for ASF can be improved to allow us to acquire detailed genetic strain information in less time," says Dr. Lung. "Just confirming the presence of ASF in a sample takes at least two hours, and many more hours to even begin to get the kind of genetic data you need to guide a truly effective response—tracking where the infection may have originated, for example, or whether ASF infections in different locations are from the same or different sources."
With the support of GRDI funding, Dr. Lung and his team at the Winnipeg lab have developed new laboratory, IM/IT and analytical processes that automatically transfer and analyze genomic data acquired through nanopore sequencing, a third-generation genomics technology, creating a new testing method for ASF that starts producing detailed genetic information of a particular strain in a matter of minutes after the start of sequencing. This new diagnostic tool supports rapid response to a possible outbreak which can help mitigate the severity of impacts of the disease.
"We can now accomplish in 2 hours what used to take 12 or more hours," says Dr. Lung. "Not just confirming whether the virus is actually ASF, but acquiring a complete or near-complete genome, allowing us to begin comparisons with ASF that's been sequenced elsewhere—a key step in figuring out where the infection originated. And, since short fragments of the genome are available within minutes, we get even more of a head start in our investigation."
National importance
At the British Columbia Ministry of Agriculture, Food & Fisheries Animal Health Centre, Head of Virology & Molecular Diagnostics Dr. Tomy Joseph says there is no question that ASF poses a significant threat and that the research led by Dr. Lung will help to ensure Canada is better prepared to meet the threat.
"A reliable and rapid diagnostic method is extremely important for early warning, timely intervention and monitoring of this disease," says Dr. Joseph. "That's why the research led by Dr. Lung is so valuable. The nanopore sequencing method developed by Dr. Lung and his team is a very powerful tool for accurate and timely detection and characterization of ASF."
International implications
The World Organisation for Animal Health (WOAH) has officially recognized the CFIA's NCFAD in Winnipeg as a WOAH Reference Laboratory for ASF. This designation by the WOAH is a sign of Canada's scientific excellence and demonstrates Canada's increasing ability, capacity, and readiness to detect and respond to an outbreak of ASF as well as support global efforts to manage the disease.
The NCFAD is already using the nanopore sequencing-based test method to support genomic characterization of ASF virus samples collected in other countries that don't have access to the technology. With their international collaborators, the NCFAD is contributing to the building of a library of ASF genomes that can be used to support investigations of future outbreaks in countries where ASF is a recurring threat, as well as increase Canada's readiness to respond to ASF should it be detected in this country.