The dynamics of pathogen genetic diversity, including the emergence of fitter lineages, are crucial for disease ecology and public health. However, identifying these lineages and estimating their fitness is challenging and seldom done outside of densely sampled systems.
Researchers have developed a new method to identify more infectious variants of viruses and bacteria, such as those causing flu, COVID-19, whooping cough, and tuberculosis. The approach uses samples from infected individuals to monitor pathogens in real-time, enabling the rapid identification of variants that evade vaccines or resist antibiotics.
This could aid in developing more effective vaccines and inform treatment decisions. Analyzing genetic sequencing data helps track the genetic changes driving the emergence of new variants, offering insights into how different variants spread in human populations.
Current systems for monitoring emerging variants of infectious diseases, such as those for COVID and influenza, are limited. The new technique represents a significant advancement, moving beyond the traditional method where experts decide when a pathogen has evolved enough to be classified as a new variant.
This approach automatically identifies new variants based on genetic changes and their spread in the population by creating “family trees,” eliminating the need for expert intervention. It can be applied to a wide range of viruses and bacteria, requiring only a small number of samples from infected individuals, making it especially valuable for use in resource-limited settings.
“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.
Lefrancq, who is 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.”
“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,” said Professor Julian Parkhill, a researcher in the University of Cambridge’s Department of Veterinary Medicine who was involved in the study.
The researchers applied their new technique to analyze samples of *Bordetella pertussis*, the bacteria responsible for whooping cough, which is currently experiencing its worst outbreaks in 25 years. The method quickly identified three previously undetected variants circulating in the population.
Professor Sylvain Brisse, Head of the National Reference Center for Whooping Cough at Institut Pasteur, highlighted the method’s timeliness, given the rising cases of whooping cough and the concerning emergence of antimicrobial-resistant strains.
In a second test, the team analyzed Mycobacterium tuberculosis, the bacteria that causes tuberculosis, and identified two variants with antibiotic resistance that are spreading in the population.
Professor Henrik Salje, a senior author of the report at the University of Cambridge’s Department of Genetics, said, “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.”
“If we see a rapid expansion of an antibiotic-resistant variant, then we could change the antibiotic prescribed to people infected to try and limit the spread of that variant.”
The researchers say this work is essential in the larger jigsaw of any public health response to infectious disease.
Bacteria and viruses, like those responsible for COVID-19, constantly evolve to spread more effectively. During the pandemic, this led to the emergence of new strains, such as Omicron, which evolved from the original Wuhan strain and spread more rapidly. These changes in the genetic makeup of pathogens help them adapt, particularly by evading the immune system, even in vaccinated individuals.
“This work could become a key tool in global infectious disease surveillance, providing insights that could dramatically alter how governments respond,” said Salje.
Journal Reference:
- Lefrancq, N. et al.: ‘Learning the fitness dynamics of pathogens from phylogenies.’ January 2025, Nature. DOI: 10.1038/s41586-024-08309-9