Viral-mutations detection tool may combat future outbreaks

The Peter Doherty Institute for Infection and Immunity (Doherty Institute) — an initiative of The University of Melbourne and The Royal Melbourne Hospital — together with University of Pittsburgh (UP), University of California, Bahria University and The Hong Kong University of Science and Technology have developed a new tool that can detect variants of SARS-CoV-2 with high transmission potential before they become widespread.

The team uncovered the specific mutations that give SARS-CoV-2 a ‘turbo boost’ in its ability to spread. They did this through the analysis of millions of viral genome sequences from around the world; a finding that has the potential to significantly support public health efforts to control outbreaks and help identify new variants that need closer monitoring.

Of these key mutations, many are in the spike protein, which helps the virus enter human cells and is the target of antibodies. Yet the team also found important mutations in other, less-studied parts of the virus; mutations that enhance its ability to bind to human cells, evade the immune system or alter protein structure.

“Among thousands of SARS-CoV-2 mutations, we identified a small number that increase the virus’ ability to spread,” a Laboratory Head at the Doherty Institute, Professor Matthew McKay, said. “Our approach is mathematically simple yet highly effective.”

“Unlike previous techniques, our model leverages genomic surveillance data to pinpoint the exact mutations driving the spread of certain variants, even when they appear in just a small fraction of cases,” McKay explained. The research team also believe that, while this new model focuses exclusively on SARS-CoV-2, it can be adapted to study the transmission of other pathogens, such as influenza.

“This is one of the first practical tools to systematically quantify how individual mutations impact viral transmission on a global scale,” said Associate Professor John Barton, a co-lead researcher from UP. “Our method is like a magnifying glass for viral evolution, helping public health systems spot and monitor highly transmissible variants before they become widespread.

“Not only can we track SARS-CoV-2 more effectively, but our method can also be adapted to study the evolution of other pathogens, helping us stay ahead of future outbreaks. It’s a powerful tool for global efforts to tackle emerging diseases.”

**************************************************

‘Inferring effects of mutations on SARS-CoV-2 transmission from genomic surveillance data’, a 2025 paper about this new tool, has been published open access in Nature Communications and you can read it at doi.org/10.1038/s41467-024-55593-0.

**************************************************

Image credit: iStock.com/Drazen Zigic