Researchers have developed a new way to identify 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 to enable rapid and automatic identification of microbes evading vaccines. This could inform the development of more effective vaccines to prevent disease.
The approach can also quickly detect emerging antibiotic-resistant variants. This could inform the choice of treatment for infected people and try to limit the spread of the disease.
It uses genetic sequencing data to provide information on the genetic changes driving 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 variants of infectious diseases, outside of established COVID and flu surveillance programs. The technique is a major advance over the existing approach to these diseases, which relies on groups of experts to decide when a circulating bacteria or virus has changed enough to be designated a new variant.
By creating “family trees,” the new approach automatically identifies new variants based on the extent of a pathogen’s genetic changes and how easily it spreads through the human population, eliminating the need to summon 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 people, are needed to reveal the variants circulating in a population. This makes it particularly useful in resource-poor settings.
The report is published today in the journal Nature.
“Our new method can show, surprisingly quickly, whether there are new transmissible variants of pathogens circulating in populations – and it can be used for a wide range of bacteria and viruses,” said Dr. Noémie Lefrancq, first author of the report. , who carried out the work at 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 to detect new strains of insect pathogens, by analyzing their genetics and how they spread through the population. This means we can quickly and effectively spot the emergence of new, highly transmissible strains,” said Professor Julian Parkhill, a researcher in the Department of Veterinary Medicine at the University of Cambridge who took part in the study.
Test 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 epidemics in 25 years. It immediately identified three new variants circulating in the population that had not been detected before.
“This new method proves to be very timely for the pertussis agent, which justifies enhanced surveillance, given its 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 the Pasteur Institute, which provided bioresources and expertise on genomic analyzes and epidemiology of Bordetella pertussis.
In a second test, they analyzed samples of Mycobacterium tuberculosis, the bacteria that causes tuberculosis. It showed that two antibiotic-resistant variants 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 be specifically targeted against these variants, to make it as effective as possible,” said Professor Henrik Salje in the Department of Genetics at the University of Cambridge, lead author of the report.
He added: “If we see a rapid expansion of an antibiotic-resistant variant, then we might change the antibiotic prescribed to infected people, to try to limit the spread of that variant. »
The researchers say this work is an important piece of the broader puzzle of any public health response to infectious diseases.
A constant threat
Bacteria and viruses that cause disease 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. Underlying this evolution are changes in the genetic makeup of pathogens.
Pathogens evolve through genetic changes that make them better able to spread. Scientists are particularly concerned about genetic changes that allow pathogens to evade our immune systems and cause disease even if 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 information it provides could completely change the way governments respond,” Salje said.
