The system to detect new variants is a tool to better respond to infectious disease outbreaks in the future

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Researchers developed a way to detect more viruses and bacteria, including the ones that cause flu, COVID (whooping cough), tuberculosis, and whooping-cough.

This new method uses samples taken from people infected with pathogens to monitor the spread of these bugs in real time. It also allows for automatic identification of vaccine-resistant bugs. It could help to develop vaccines with greater effectiveness in the prevention of disease. This approach is also able to detect new variants that are resistant to antibiotics. It could help determine the best treatment to give infected people and limit the spread.

This tool uses genetic sequence data to reveal the changes in the genome that lead to the appearance of new variations. It is crucial to understand how different variants affect human populations.

Apart from established COVID surveillance and influenza programmes, there are few systems to monitor emerging variants in infectious diseases. This technique represents a significant advance over the current approach, where groups of experts decide whether a virus or bacteria has sufficiently changed to warrant a designation as a variant. The new method,

identifies variants automatically by creating “family trees” based on the amount of genetic change a pathogen underwent and the ease with which it spreads among humans. This eliminates the need for experts. The method can be applied to a wide range of bacteria and viruses. Only a few samples from people infected are required in order to identify the variants that circulate in a given population. It is therefore particularly useful in resource-limited settings.

Nature (19459012) published the report today.

Noemie Léfrancq is the first author of this report. She worked at Cambridge University’s Department of Genetics. Lefrancq added that she is now based in Zurich and has been a part of the research at the University of Cambridge Department of Veterinary Medicine. Test of the technique.

Researchers used the new technique to analyze samples from Bordetella Pertussis bacteria, which causes whooping-cough. Many countries have experienced their worst outbreaks of whooping-cough in the past 25 years. The study immediately detected three previously unknown variants that were circulating among the population. Sylvain Brise, the Head of the National Reference Center at Institut Pasteur for Whooping Cough, provided expertise and bioresources on Bordetella Pertussis genome analyses and epidemiology. They analysed Mycobacterium tuberculosis samples, which is the bacteria responsible for Tuberculosis. The study showed two resistant variants to antibiotics were spreading. Henrik Salje, Professor at the Department of Genetics of Cambridge University and senior author of this report said:

“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,” .

Salje added that “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.”

The researchers said this work was an important part of any larger puzzle in public health responses to infectious diseases.

Constant threat

The bacteria and viruses responsible for disease are always evolving. They become faster and more effective at spreading. This led to new strains emerging during the COVID Pandemic: The original Wuhan strain was spread quickly, but it was soon overtaken and surpassed by variants such as Omicron which were developed from the original strain. This evolution is a result of changes to the genetic makeup of pathogens. Genetic changes make pathogens more effective at spreading. Scientists worry about the genetic changes which allow pathogens evade immunity and spread disease even though we are vaccinated. Salje said

“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,” .

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