A&S alumnus Marc Fiume and his team at DNAstack work to upgrade our early COVID-19 warning system

March 15, 2022 by Toronto Star Micah Toub

How can hospitals learn to live with COVID-19?

The pandemic’s toll on our health-care system is clear. Surgeons have performed 560,000 fewer procedures than usual. Nursing staff are facing burnout from working overtime to manage surges, and 77 per cent of those who have dealt directly with COVID-19 patients reported their mental health has worsened.

As the rate of Omicron infections ebbs, vaccine maker Moderna says it expects COVID to become endemic sometime next year. But public health experts have warned that the virus will still be deadly, with unpredictable waves of outbreaks. Even once the virus becomes endemic, we’ll need better ways to contain it and bring relief to health-care staff.

Since we’ll have to live with this virus, the driving question is clear: How do we ensure that our health-care system can cope in the era of ever-present COVID? New technologies are providing some clues.

Upgrade our early warning system

“The two tools that proved to be powerful in response to COVID-19 were general surveillance — so sequencing of the viral genome — and rapid international data sharing,” says Marc Fiume (HBSc 2009, MSc 2011, PhD 2015) CEO of DNAstack, a Toronto health technology company. “You need both and, at the start of the pandemic, we didn’t have an infrastructure for either.”

Scientists look at mutations in the virus’s genome, particularly on the infamous spike protein, to identify new variants of concern. During the pandemic, countries including Canada rapidly expanded their facilities for mass-sequencing of COVID samples, and that capacity will need to be retained to some degree. But Fiume says scientists still need more efficient ways to share data — it sometimes takes months for sequences to be uploaded into global repositories.

DNAstack has created Viral AI, a system for international data sharing, in which each contributor retains ownership and control of their data sets, but partners can query the whole of it. “It’s a faster, more scalable model for how we might share genomics and health data,” says Fiume. A better picture of what’s happening globally should enable faster detection of variants and give vaccine manufacturers a better sense of what to target.

If data-sharing platforms were paired with monitoring of wastewater and airborne pathogens, it could catch signs of danger much earlier across a range of diseases. It could be, Fiume says, “a sort of digital immune system to keep us safe going forward.”

Read the full article here