Researchers have found a new way to detect more infectious variants of viruses or bacteria that are beginning to spread in humans – including those that cause influenza, COVID, whooping cough and tuberculosis.
The new approach uses samples from infected humans to enable real-time monitoring of pathogens circulating in human populations and enable rapid and automatic identification of vaccine-evading bugs. This could help develop vaccines that are more effective at preventing disease.
The approach can also detect rapidly emerging antibiotic-resistant variants. This could inform the choice of treatment for people who become infected – and try to limit the spread of the disease.
It uses genetic sequence data to provide information about the genetic changes that underlie the emergence of new variants. This is important for understanding why different variants spread differently in human populations.
There are very few systems in place to monitor emerging infectious disease variants, other than the established surveillance programs for COVID and influenza. The technique is a major advance on the existing approach to these diseases, which relies on teams of experts to decide when a circulating bacterium or virus has changed enough to qualify as a new variant.
By creating “family trees”, the new approach automatically identifies new variants based on how much a pathogen has genetically changed and how easily it spreads through the human population – eliminating the need to call in experts to do this.
It can be used for a wide range of viruses and bacteria, and only a small number of samples, taken from infected individuals, are needed to reveal the variants circulating in a population. This makes it especially valuable for resource-poor settings.
The report is published today in the journal Nature.
“Our new method provides a way to show, surprisingly quickly, whether there are new infectious 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 in the Department of Genetics at the University of Cambridge.
We can even use it to start predicting how new variants will take over, meaning decisions can be made quickly about how to respond.”
Dr. Noémie Lefrancq, ETH Zurich
“Our method provides a completely objective way of identifying new strains of disease-causing microbes by analyzing their genetics and how they spread through the population. This means we can quickly and efficiently detect the emergence of new highly contagious strains,” he said. Professor Julian Parkhill, a researcher in the Department of Veterinary Medicine at the University of Cambridge who took part in the study.
Testing the technique
The researchers used their new technique to analyze samples of Bordetella pertussis, the bacterium that causes whooping cough. Many countries are currently experiencing their worst whooping cough outbreaks in 25 years. It immediately identified three new variants circulating in the population that had not been detected before.
“The new method proves very timely for the pertussis agent, which requires enhanced surveillance given its current return in many countries and the alarming emergence of antimicrobial-resistant lineages,” said Professor Sylvain Brisse, Head of the National Reference Center for the whooping cough. at the Institut Pasteur, who provided biological resources and expertise in Bordetella pertussis genomic analyzes and epidemiology.
In a second test, they analyzed samples of Mycobacterium tuberculosis, the bacterium that causes tuberculosis. It showed that two antibiotic-resistant variants are spreading.
“The approach will quickly show which variants of a pathogen are of most concern in terms of the potential to make people sick. This means that a vaccine can be specifically targeted against those variants to make them as effective as possible,” said Professor Henrik Salje at the University of Cambridge’s Department of Genetics, senior author of the report.
He added: “If we see a rapid expansion of an antibiotic-resistant variant, then we could change the antibiotic prescribed to people infected with it to try to limit the spread of that variant.”
The researchers say this work is an important piece in the larger puzzle of any public health response to infectious diseases.
A constant threat
Disease-causing bacteria and viruses are constantly evolving to spread better and faster among us. During the COVID pandemic, this led to the emergence of new strains: the original Wuhan strain spread quickly, but was later overtaken by other variants, including Omicron, which evolved from the original and was better at spreading. Underlying this evolution are changes in the genetic makeup of pathogens.
Pathogens evolve through genetic changes that make them better at spreading. Scientists are particularly concerned about genetic changes that allow pathogens to evade our immune systems and cause disease despite the fact that we are vaccinated against them.
“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,” said Salje.
Source:
Journal Reference:
Lefrancq, N., et al. (2025). Learning the dynamic fitness of pathogens from phylogeny. Nature. doi.org/10.1038/s41586-024-08309-9.
