Powerful Tool Detects Fast-Spreading SARS-COV-2 Variants

Throughout the course of the COVID-19 pandemic, new variants of SARS-CoV-2 have emerged, each demonstrating increased transmissibility. Viruses can mutate in ways that enhance their ability to infect hosts, either by increasing viral load or evading immune responses. Rapid detection of these mutations is crucial to understanding viral biology and identifying new variants that may require further investigation. Quickly identifying mutations that contribute to higher transmission rates can aid in outbreak control and help spot potential immune escape variants. However, determining how individual mutations influence viral transmission has proven to be a difficult task. To overcome this challenge, researchers have developed a tool capable of detecting SARS-CoV-2 variants with high transmission potential before they become widespread.

A team of scientists, led by the Peter Doherty Institute for Infection and Immunity (Doherty Institute, Melbourne, Australia) and the University of Pittsburgh (Pittsburgh, PA, USA), analyzed millions of viral genome sequences from around the world. Their work revealed specific mutations that give SARS-CoV-2 a significant advantage in spreading. While many of these mutations were found in the virus’s spike protein, which is responsible for allowing the virus to enter human cells and is targeted by antibodies, the researchers also discovered important mutations in less-studied regions of the virus.

These mutations play a role in enhancing the virus's ability to bind to human cells, evade immune responses, or alter protein structure. Unlike previous methods, this new model, highlighted in Nature Communications, uses genomic surveillance data to accurately identify the mutations driving the spread of certain variants, even when these mutations appear in only a small fraction of cases. While the model was developed specifically for SARS-CoV-2, the researchers believe it can be adapted to track the transmission of other pathogens, such as influenza.

“Our method is like a magnifying glass for viral evolution, helping public health systems spot and monitor highly transmissible variants before they become widespread,” said Associate Professor John Barton from the University of Pittsburgh, co-lead author of the study. “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.”