Virus variants: Tool that could help scientists better detect mutated germs

A team of scientists from India, Sweden and Japan has developed a new diagnostic tool capable of keeping up with the rapidly changing rates of bacteria and viruses.

At a time when the world has seen first-hand how new germs – like SARS-CoV-2 and its variants – can disrupt life on a massive scale, researchers say. Their new tool can speed up the discovery of new viral and bacterial variants. help fight them quickly and effectively.

The authors wrote in a paper published Wednesday in the scientific journal ACS Infectious Diseases: “The emergence of new zoonotic infections in the human community has increased the burden on global health care system in limiting their spread.”

“In response to the rate at which pathogens evolve, it is essential to improve existing diagnostic methods for early detection and characterization of pathogens at the molecular level.”

This tool, a computer program called AutoPLP, is built on top of the polymerase chain reaction (PCR) test technology used to detect viruses and bacteria based on their genetic material. . PCR tests use nucleic acid probes — short, single-stranded DNA or RNA sequences coded to match a specific pathogen — to diagnose infections by looking for matching DNA or RNA that are related to the pathogen they are testing for.

Rolling circle amplification (RCA) tests work similarly to PCR tests, but are known to be more sensitive than PCR tests because they use a special, more precise type of nucleic acid probe called a drive probe. key (PLP). This makes them useful in detecting mutated genetic sequences, such as those in new viruses and virus variants.

The caveat is that because the padlock probes are so precise, more work is needed to identify the specific genetic sequences for them to target. Additionally, as the pathogen mutates, its gene sequence also changes, forcing scientists to redesign their probe each time.

So researchers Sowmya Ramaswamy Krishnan, Ruben RG Soares, Narayanan Madaboosi and M. Michael Gromiha set out to develop a software program that could keep up with viral and bacterial mutations better than they could. capabilities of human scientists.

AutoPLP automatically designs the PLP to accommodate genetically modified bacteria and viruses, and systematically considers “all the necessary specifications at once to make the whole process easy.” and stronger.”

The program can take the genomic sequence of a similar pathogen as input and run a series of analyzes and database searches, generating a custom set of PLP sequences.

The authors tested the tool by designing probes to detect the rabies virus and drug-resistant strains of Mycobacterium tuberculosis, the bacteria that cause tuberculosis. Probes designed by AutoPLP work faster, more accurately and more easily than previous probes developed to detect these pathogens.

The authors hope the tool will accelerate the discovery of new viral and bacterial variants, and help “fight them quickly and efficiently through accurate molecular diagnostics,” according to a press release. press release released on Wednesday.

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