Canadian Scientists Develop Platform to Track Changes in Genetic Structure of COVID-19 Virus

Jun 15, 2020

The COVID-19 genotyping toolThe COVID-19 genotyping tool Researchers from the University of Toronto and University Health Network have designed an innovative tool for quickly tracking changes in the genetic structure of SARS-CoV-2, the virus that causes COVID-19.

Tracking these genetic changes from person to person will help researchers and clinicians better understand the evolution and transmission of the virus, locally and globally.

"As AI researchers, we're accustomed to working with big data," said Bo Wang, a professor of medical biophysics at U of T and the artificial intelligence lead at the Peter Munk Cardiac Centre, UHN. "The global research community has really embraced the initiative on data sharing during the COVID-19 pandemic; our goal was to design a tool that would help make sense of it."

Wang's doctoral student Hassaan Maan developed the platform, called the COVID-19 genotyping tool or CGT, alongside colleagues from McMaster University and Sunnybrook Health Sciences Centre. The tool offers an online, user-friendly interface where researchers can quickly compare the genome sequence of the SARS-CoV-2 virus in their hospital against the global picture.

The researchers recently published an article on the new application in The Lancet Digital Health.

Professor Bo WangProfessor Bo Wang The analysis enabled by the tool previously took up to a week to perform, but now takes 15 minutes or less with the AI-driven platform. The resulting data will help researchers learn more about how the virus is moving and evolving, said Wang, who holds a Canadian Institute for Advanced Research in Artificial Intelligence Chair at the Vector Institute. That data has direct implications for vaccine design, drug development and the global effort to combat COVID-19.

The researchers used nasal swab samples from more than 20,000 patients with COVID-19, and uploaded virus genome sequences to a database called the Global Initiative on Sharing All Influenza Data.

The tool allowed rapid comparsion of genome sequences from individual hospitals with virus samples from around the world. Results provide insight on where transmission events likely occurred, when outbreaks happened, and most importantly, key changes in the genetic makeup of the virus that can affect its virulence and ability to spread.

The CGT will be particularly helpful in prepartions for a second wave of COVID-19. "As the virus spreads throughout the world, it picks up small mutations along the way," said Maan, who designed the tool to be open-source and globally accessible. "We want to perform surveillance of these mutations in the event a different strain of SARS-CoV-2 arises."

This story was based on a news release from UHN, and files from the office of communications in the Faculty of Medicine at U of T.

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