A new method of identifying more infectious variants of viruses or bacteria that begin spreading in humans has been identified by University of Cambridge researchers.
Using samples from infected humans, it allows real-time monitoring of pathogens – including those causing flu, Covid, whooping cough and tuberculosis – and will enable vaccine-evading bugs to be quickly and automatically identified.
Bacteria that causes tuberculosis
The approach could inform the development of vaccines more effective in preventing disease and could also quickly detect emerging variants resistant to antibiotics, helping guide treatment options.
“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 Cambridge’s Department of Genetics and is now based at ETH Zurich. “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.”
The approach uses genetic sequencing data to give information on the genetic changes underlying new variants, which can help explain why variants spread differently in human populations.
There are few systems for monitoring the merging variants of infectious diseases, with the exception of the established surveillance programmes for Covid and flu, which rely on groups of experts deciding when a circulating bacteria or virus has changed enough to be designated a new variant.
However, the new system is a major development on this and creates ‘family trees’.
It designates new variants automatically based on how much a pathogen has changed genetically and how easily it spreads in the human population, which removes the need to convene experts to do this.
Only a small number of samples from infected people are needed to reveal the variants circulating, making it valuable for resource-poor settings.
“Our method provides a completely objective way of spotting new strains of disease-causing bugs, by analysing 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 Prof Julian Parkhill, a researcher in the University of Cambridge’s Department of Veterinary Medicine who was involved in the study, published in Nature.
The technique was tested on samples of Bordetella pertussis, a bacteria that causes whooping cough. Many countries are battling their worst whooping cough outbreaks of the last 25 years and the method identified three new variants 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 Prof Sylvain Brisse, head of the National Reference Center for whooping cough at Institut Pasteur.
The researchers also analysed samples of Mycobacterium tuberculosis, which causes tuberculosis. It identified two variants with resistance to antibiotics.
“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 senior author Prof Henrik Salje, of the 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.
“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.”
The research was primarily funded by the European Research Council.