Researchers have discovered a novel method to identify highly contagious variants of viruses or bacteria that may begin transmission among humans. This includes pathogens responsible for illnesses such as the flu, COVID-19, whooping cough, and tuberculosis.
Researchers have discovered a novel method to identify highly contagious variants of viruses or bacteria that may begin transmission among humans. This includes pathogens responsible for illnesses such as the flu, COVID-19, whooping cough, and tuberculosis.
This innovative technique utilizes samples from infected individuals, allowing real-time tracking of pathogens present in human populations, and enabling rapid identification of vaccine-resistant strains. This information can guide the creation of more effective vaccines.
Additionally, this method can swiftly pinpoint new variants that have developed antibiotic resistance, aiding in the selection of appropriate treatments for infected individuals and efforts to curb disease spread.
By employing genetic sequencing data, it offers insights into the genetic alterations that lead to the emergence of new variants. Understanding these variations is crucial for comprehending why certain strains proliferate more quickly than others in human populations.
Currently, there are very few systems in place to monitor emerging variants of infectious diseases, aside from the recognized surveillance programs for COVID-19 and influenza. This new technique marks a significant enhancement over traditional methods, which have depended on expert panels to determine when a virus or bacterium has changed sufficiently to be classified as a new variant.
The new approach constructs ‘family trees’ that automatically identify new variants based on the genetic alterations in a pathogen and its transmission efficiency, eliminating the need for expert consultations.
It can be applied to a wide variety of viruses and bacteria, requiring only a small number of samples from infected persons to unveil the circulating variants within a population. This characteristic especially benefits regions with limited resources.
The findings are published today in the journal Nature.
“Our new method allows us to quickly determine if there are new transmissible variants of pathogens present in populations, applicable to a broad range of bacteria and viruses,” stated Dr. Noémie Lefrancq, the lead author of the study conducted at the University of Cambridge’s Department of Genetics.
Now affiliated with ETH Zurich, Lefrancq elaborated, “We can even begin to predict how new variants might proliferate, facilitating timely decision-making regarding responses.”
“This method offers a completely impartial way to detect new strains of disease-causing pathogens by examining their genetics and their spread in the population, enabling us to rapidly identify the emergence of highly transmissible strains,” explained Professor Julian Parkhill from the University of Cambridge’s Department of Veterinary Medicine, who contributed to the study.
Evaluating the technique
The researchers applied their new technique on samples of Bordetella pertussis, the bacterium responsible for whooping cough. Many nations are currently facing significant whooping cough outbreaks, the worst seen in the last 25 years. Their approach promptly identified three new previously undetected variants in circulation.
“This innovative method is particularly timely for the whooping cough agent, as it necessitates enhanced surveillance due to its resurgence in various countries and the concerning emergence of antimicrobial-resistant strains,” stated Professor Sylvain Brisse, Head of the National Reference Center for whooping cough at Institut Pasteur, who supplied resources and expertise in genomic analysis and epidemiology of Bordetella pertussis.
In a subsequent test, they examined samples of Mycobacterium tuberculosis, the bacterium that leads to Tuberculosis, revealing the spread of two antibiotic-resistant variants.
“This approach will quickly highlight which pathogen variants are most concerning regarding their potential to cause illness. Consequently, vaccines can be precisely designed to target these variants, maximizing their effectiveness,” remarked Professor Henrik Salje from the University of Cambridge’s Department of Genetics, the study’s senior author.
He continued, “If we observe a fast increase in an antibiotic-resistant variant, we could alter the antibiotic treatment prescribed to infected individuals to help contain the spread of that variant.”
The researchers assert that this work represents a crucial component in the broader public health response to infectious diseases.
A continual threat
Pathogens such as bacteria and viruses are in a constant state of evolution, adapting to spread more efficiently among humans. During the COVID pandemic, new strains emerged, such as the initial Wuhan variant, which was rapidly supplanted by others like Omicron, with enhanced transmission capabilities. These evolutionary changes are driven by genetic alterations in the pathogens.
Pathogens evolve through genetic modifications that improve their transmission. Scientists are particularly concerned about changes that enable pathogens to escape our immune defenses, causing illness even in vaccinated individuals.
“This work could play a vital role in infectious disease surveillance systems worldwide, and the insights it offers may significantly influence government response strategies,” stated Salje.
