AI System Tracks Emerging infectious Disease

Researchers have developed a novel method for identifying more infectious diseases of viruses or bacteria that spread in humans, including those that cause influenza, COVID, whooping cough, and tuberculosis.

The novel method employs infected human samples to allow for real-time monitoring of infections in human populations, as well as the rapid and automatic identification of vaccine-evading bugs. This could help to produce more effective vaccines for disease prevention.

The technique can also detect new antibiotic-resistant variations fast. This could help to guide treatment decisions for afflicted patients and limit the disease’s spread.

It employs genomic sequencing data to provide information on the genetic alterations that drive the emergence of novel variations. This is crucial for understanding why various variations propagate differently in human populations.

Aside from the established COVID and influenza surveillance programmes, there are few systems in place to monitor new variations of infectious diseases. The strategy is a significant improvement over the previous approach to these diseases, which relied on expert panels to determine when a circulating bacteria or virus had mutated sufficiently to be labeled as a new variant.

It may be used to detect a wide range of viruses and bacteria, and just a small number of samples from infected people are required to identify the variants circulating in a community. This makes it especially beneficial in resource-constrained environments.

The report was published today in the journal Nature.

“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.

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.”

 Dr. Noémie Lefrancq, ETH Zurich

“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 Professor Julian Parkhill, a researcher in the University of Cambridge’s Department of Veterinary Medicine who was involved in the study.

Test the procedure
The researchers applied their novel technique on samples of Bordetella pertussis, the bacteria that causes whooping cough. Many countries are currently seeing the greatest whooping cough outbreaks in the past 25 years. It instantly found three previously unknown variations in the population.

“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 Professor Sylvain Brisse, Head of the National Reference Center for whooping cough at Institut Pasteur, who provided bioresources and expertise on Bordetella pertussis genomic analyses and epidemiology.

In a second test, they examined samples of Mycobacterium tuberculosis, the bacteria that causes tuberculosis. It demonstrated that two antibiotic-resistant varieties are spreading.

“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 Professor Henrik Salje in the University of Cambridge’s Department of Genetics, senior author of the report.

He added: “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.”

According to the researchers, this effort is a critical component of any public health response to infectious disease.

A continual threat.
Bacteria and viruses that cause disease are continually developing to be more effective and faster at spreading between humans. During the COVID pandemic, additional strains emerged: the original Wuhan strain spread quickly but was eventually surpassed by other varieties, including Omicron, which developed from the original and disseminated more effectively. This evolution is driven by changes in the pathogens’ genetic make-up.

Pathogens evolve through genetic alterations that increase their ability to spread. Scientists are particularly concerned about genetic modifications that enable viruses to elude our immune system and cause disease despite being immunized 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,” said Salje.