AI-driven surveillance system to combat emerging infectious diseases

AI-driven surveillance system to combat emerging infectious diseases

Researchers have found a new way to identify more infectious variants of viruses or bacteria that spread in humans — including those that cause flu, COVID, whooping cough and tuberculosis.

The new approach uses samples from infected people to provide real-time monitoring of pathogens circulating in human populations and enable rapid and automatic identification of vaccine viruses. This could influence the development of vaccines that are more effective at preventing disease.

The approach can also quickly detect emerging variants with antibiotic resistance. This could influence the choice of treatment for people who become infected - and attempts to contain the spread of the disease.

It uses genetic sequencing 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.

Aside from established COVID and influenza surveillance programs, there are very few systems in place to monitor for emerging infectious disease variants. The technique represents a major advance over the existing approach to treating these diseases, which relied on panels of experts to decide when a circulating bacteria or virus had changed enough to be called 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 through the human population - eliminating the need to convene experts to do this.

It can be used on a wide range of viruses and bacteria and requires only a few samples from infected people to detect variants circulating in a population. This makes it particularly valuable for resource-poor environments.

The report is published in the magazine todayNature.

“Our new method offers a way to 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, lead 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 predict how new variants will take hold, so 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 pathogenic beetles by analyzing their genetics and how they spread through the population. This means we can quickly and effectively detect the emergence of new highly transmissible strains," said Professor Julian Parkhill, a researcher at the University of Cambridge's Institute of Veterinary Medicine, who was involved in the study.

Testing the technology

Using their new technique, the researchers analyzed samples of Bordetella pertussis, the bacterium that causes whooping cough. Many countries are currently experiencing the worst whooping cough outbreaks in the last 25 years. Three new variants were immediately identified that were circulating in the population and were previously undetected.

“The novel method proves to be very timely for the pertussis pathogen, which requires increased surveillance given its current comeback in many countries and the worrying emergence of antimicrobial resistance lines,” said Professor Sylvain Brisse, head of the National Reference Center for Pertussis at the Institut Pasteur, who provided bioresources and expertise on genome analyzes and epidemiology of Bordetella pertussis.

In a second test, they analyzed samples of Mycobacterium tuberculosis, the bacterium that causes tuberculosis. It turned out that two variants with antibiotic resistance are spreading.

"The approach will quickly show which variants of a pathogen are of most concern in terms of disease potential. This means that a vaccine can be targeted against these variants to make it as effective as possible," said Professor Henrik Salje of the Department of Genetics at the University of Cambridge, lead author of the report.

He added: "If we see rapid spread of an antibiotic-resistant variant, we could change the antibiotic prescribed to people infected with it to curb the spread of this 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

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 quickly, but was later overtaken by other variants, including Omicron, which evolved from the original and spread better. This development is based on changes in the genetic makeup of the pathogens.

Pathogens develop through genetic changes that facilitate their spread. Scientists are particularly concerned about genetic changes that allow pathogens to evade our immune systems 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 transform the way governments respond,” Salje said.

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