The world relies on systems like COVID and influenza surveillance programmes, which depend heavily on human intervention. Groups of experts must convene to determine when a pathogen has evolved enough to be classified as a new variant. This process is not only slow but also prone to delays in decision-making, particularly for less-publicized diseases.
Enter the Cambridge system, which eliminates this bottleneck. In the journal Nature, researchers from the university describe a method that uses genetic sequencing data from infected individuals to identify and track new variants of pathogens. This system acts like a genetic “family tree,” automatically categorizing emerging strains based on their genetic changes and transmissibility.
“Our new method provides a way to show, surprisingly quickly, whether there are new transmissible variants of pathogens circulating in populations... and it can be used for a huge range of bacteria and viruses,” said Dr. Noémie Lefrancq, the first author of the study, who developed the system during her time at Cambridge’s Department of Genetics.
Lefrancq (now based at ETH Zurich) added, “We can even use it to start predicting how new variants are going to take over, which means decisions can quickly be made about how to respond.”
Wide Application
This isn't just about tracking known threats like COVID-19 or influenza, it’s a versatile tool that can be applied to virtually any pathogen. The system requires only a small number of samples to reveal what’s circulating in a population, making it a particularly valuable resource for regions with limited access to healthcare infrastructure.
Using genetic data, it objectively identifies new variants in real-time, removing the need for expert consensus.
“Our method provides a completely objective way of spotting new strains of disease-causing bugs by analyzing their genetics and how they’re spreading in the population,” said Professor Julian Parkhill, a researcher from Cambridge’s Department of Veterinary Medicine and a key contributor to the study.
This means fewer delays and faster responses—a critical factor in preventing outbreaks from becoming epidemics or even pandemics.
Fighting Vaccine-Evading Variants
One of the system’s most promising applications is its ability to detect variants that could evade vaccines or resist antibiotics. This is a game-changer for both prevention and treatment.
For instance...
Vaccine Development: If a new strain is identified as vaccine-resistant, scientists can adapt vaccines more quickly to target it effectively.
Antibiotic Resistance: The system can flag drug-resistant bacteria, enabling healthcare providers to adjust treatments before resistance spreads.
How It Works
At its core, the system uses genetic sequencing data to map out how pathogens are mutating and spreading. Think of it like a detective tracing a suspect’s movements, not just identifying where they’ve been but predicting their next steps.
This “family tree” approach categorizes variants based on:
Genetic Changes: How much a pathogen’s DNA or RNA has changed.
Transmissibility: How easily it spreads among humans.
What sets this system apart is its ability to do all this in resource-poor settings, where healthcare infrastructure is often stretched thin. Just a handful of samples can yield actionable insights, making it an equitable tool for global health.
While this study is a significant step forward, the researchers acknowledge that more work is needed. “To fully realize its potential, we recommend a longer-term effectiveness trial,” said theteam. Still, the possibilities are exciting, a way to level the playing field in fighting infectious diseases, no matter where they emerge.
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