Researchers have devised a new way to identify more infectious variants of viruses or bacteria that begin to spread in humans, including those that cause flu, 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 insects. This could contribute to the development of vaccines that are more effective in preventing disease.
The approach can also quickly detect emerging variants with antibiotic resistance. This could inform the choice of treatment for people who become infected and try to limit the spread of the disease.
It uses genetic sequencing data to provide information about the genetic changes underlying the emergence of new variants. This is important to help understand why different variants spread differently in human populations.
There are very few systems in place to monitor emerging infectious disease variants, other than established COVID and flu surveillance programs. The technique is a major advance on the existing approach to these diseases, which has relied on groups of experts to decide when a circulating bacteria or virus has changed enough to be designated as a new variant.
By creating ‘family trees’, the new approach automatically identifies new variants based on how much a pathogen has changed genetically and how easily it spreads in the human population, eliminating the need to call in experts to do so.
It can be used for a wide range of viruses and bacteria and only a small number of samples, taken from infected people, are needed to reveal the variants circulating in a population. This makes it particularly valuable for resource-poor settings.
The report is published today in the magazine. Nature.
“Our new method provides a way to show, surprisingly quickly, whether there are new transmissible variants of pathogens circulating in populations, and can be used for a wide range of bacteria and viruses,” said Dr. Noémie Lefrancq, first author of the study. . report, which carried out the work at the Department of Genetics at the University of Cambridge.
Lefrancq, who now works at ETH Zurich, added: “We can even use it to start predicting how new variants are going to take over, meaning decisions can be made quickly about how to respond.”
“Our method provides a completely objective way to detect new strains of disease-causing insects, analyzing their genetics and how they are spreading in the population. This means we can quickly and effectively detect the emergence of new highly transmissible strains,” he said. Professor Julian Parkhill, a researcher at 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 bacteria that causes whooping cough. Many countries are currently experiencing the worst whooping cough outbreaks in 25 years. It immediately identified three new variants circulating among the population that had not been previously detected.
“The new method is very timely for the pertussis agent, which justifies reinforced surveillance, given its current reappearance in many countries and the worrying emergence of antimicrobial-resistant lineages,” said Professor Sylvain Brisse, director of the National Center Reference for whooping cough. at the Institut Pasteur, who provided biological resources and experience in genomic analysis and epidemiology of Bordetella pertussis.
In a second test they analyzed samples of Mycobacterium tuberculosis, the bacteria that causes tuberculosis. It showed that two variants with resistance to antibiotics are spreading.
“This approach will quickly show which variants of a pathogen are of most concern in terms of their potential to make people sick. This means that a vaccine can specifically target these variants, making it as effective as possible,” said Professor Henrik Salje. in Department of Genetics at the University of Cambridge, lead author of the report.
He added: “If we see a rapid spread of an antibiotic-resistant variant, then we could change the antibiotic that is 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 broader 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 rapidly, but was later overtaken by other variants, including Omicron, which evolved from the original and spread better. Behind this evolution are changes in the genetic composition of the 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 system and cause disease even though 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,” Salje said.