A team from Cambridge University, UK, developed a new way to identify variants of viruses or bacteria that start spreading in humans, including flu, COVID-19, whooping cough, and tuberculosis, according to a study published in the journal Nature.
Using samples from infected patients allows researchers to follow in real-time how pathogens are circulating in human populations. Crucially, this enables doctors to identify viruses immune to vaccines and bacteria resistant to antibiotics. This information could be used to treat patients with these variants to limit the spread of the disease. The new procedure uses genetic sequencing to obtain information on the genetic changes underlying new variants. This is key to understanding why different variants spread differently in human populations.
At the moment, there are few ways to monitor emerging variants of infectious diseases apart from the COVID and influenza surveillance programmes. The new method is a significant advance over the existing approach, which relies on experts to subjectively decide when a circulating bacteria or virus has changed enough to be designated a new variant.
Instead of using this subjective method, the authors suggest creating ‘family trees’ to identify new variants based on how much a pathogen has changed genetically and how easily it spreads in the human population. This is more effective and removes the need to convene experts to do this.
What’s more, this can be adapted to use with a broad range of viruses and bacteria and only needs a small number of samples from infected patients to reveal the different variants circulating in a population. This means it can be used in most locations, even with limited resources. “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, first author of the report, who carried out the work at the University of Cambridge’s Department of Genetics. “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.”
“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. This means we can rapidly and effectively spot the emergence of new highly transmissible strains,” added Professor Julian Parkhill, a researcher in the University of Cambridge’s Department of Veterinary Medicine.
To test the method, the team analysed samples of patients with Bordetella pertussis, the bacteria that causes whooping cough. The new method immediately identified three new variants circulating in the population that had been previously undetected. “The novel method proves very timely for the agent of whooping cough, which warrants reinforced surveillance, given its current comeback in many countries and the worrying emergence of antimicrobial resistant lineages,” said Professor Sylvain Brisse, Head of the National Reference Center for whooping cough at Institut Pasteur.
In the second test, they analysed samples of Mycobacterium tuberculosis, the bacteria that causes Tuberculosis. It was identified that two variants that are resistant to antibiotics are currently spreading. “The approach will quickly show which variants of a pathogen are most worrying in terms of the potential to make people ill. This means a vaccine can be specifically targeted against these variants to make it as effective as possible,” said Professor Henrik Salje from the University of Cambridge’s Department of Genetics. “If we see a rapid expansion of an antibiotic-resistant variant, then we could change the antibiotic that’s being prescribed to people infected by it to try and limit the spread of that variant.”
Bacteria and viruses that cause disease are constantly evolving to be better and faster at spreading between us. During the COVID pandemic, for example, multiple variants emerged. The original strain was later overtaken by other variants, including Omicron, which evolved from the original and was better at spreading. “This work has the potential to become an integral part of infectious disease surveillance systems around the world, and the insights it provides could completely change the way governments respond,” concluded Salje.
Lefrancq, N., Duret, L., Bouchez, V. et al. Learning the fitness dynamics of pathogens from phylogenies. Nature 637, 683–690 (2025). https://doi.org/10.1038/s41586-024-08309-9