The genetic material found within a virus is essential for its ability to replicate and spread. Understanding how this genetic material changes as the virus spreads is crucial to developing drug treatments and vaccines.
A research team led by Techna Institute Scientist Dr. Bo Wang has designed an innovative application that can track the changes that occur to the genetics of the SARS-CoV-2 virus as it spreads.
“Mutations in the virus could affect how well a vaccine or treatment works,” says Dr. Wang. “We needed a tool to monitor these changes—similar to how we have other tools for tracking infection cases.”
Developed by Dr. Wang’s doctoral student Hassaan Maan, the new web application, named the COVID-19 Genotyping Tool (CGT), summarizes and analyzes data from around the world. Genetic sequences are pulled from a global repository and compared based on their similarity. Researchers can sort the data by country, continent, collection date and travel history to see if the virus is evolving in time or by geographic region.
The CGT can also be used to directly compare in-house data against globally sourced data. Artificial intelligence algorithms let researchers situate their local data within the global picture in a matter of minutes.
In addition to helping keep a close eye on the virus, analysis from the CGT will help uncover the transmission history of the virus. Patterns in genetic variations will help identify outbreak epicentres and key transmission events. This information can then be used to guide public health policy decisions and efforts toward managing the pandemic.
This work was supported by the Vector Institute for Artificial Intelligence, Sunnybrook Health Sciences Centre, McMaster University, the Public Health Agency of Canada, the University of Manitoba, the CIFAR AI Chairs Program and the generous support of donors.
Maan H, Mbareche H, Raphenya AR, Banerjee A, Nasir JA, Kozak RA, Knox N, Mubareka S, McArthur AG, Wang B. Genotyping SARS-CoV-2 through an interactive web application. Lancet Digital Health. 2020 June 12. doi: 10.1016/S2589-7500(20)30140-0.
Results from the CGT reveal distinct clusters of SARS-CoV-2 subtypes, which likely correspond to outbreak epicentres. Here, genetic sequences from different geographic regions (coloured circles) are represented in two dimensions, with their distance indicating similarity.