Scientists develop new tool to uncover patterns in coronavirus mutations

Scientists have developed a method to quickly identify and label mutated versions of the novel coronavirus that causes Covid-19 using information from a global database of testing information, an advance that may aid in the development of therapeutics against the deadly disease.

The new tool, described in the journal PLOS Computational Biology, identifies patterns from volumes of genetic information, and can identify whether the virus has genetically changed.

According to the researchers, including those from Drexel University in the US, the method can be used to categorise viruses with small genetic differences using tags called Informative Subtype Markers (ISM).

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In the current study, they categorised slight genetic variations in the novel coronavirus SARS-CoV-2 and generated labels that are publicly available for scientists worldwide.

"The types of SARS-CoV-2 viruses that we see in tests from Asia and Europe is different than the types we're seeing in America," said Gail Rosen, a co-author of the study from Drexel University.

"Identifying the variations allows us to see how the virus has changed as it has travelled from population to population. It can also show us the areas where social distancing has been successful at isolating Covid-19," Rosen said.

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The ISM tool, according to the scientists, is particularly useful because it does not require analysis of the full genetic sequence of the virus to identify its mutations.

It also identified certain positions in the viral genetic sequence that changed together as the virus spread, the study noted.

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According to the scientists, from early April to the end of the summer, three positions in the SARS-CoV-2 sequence which are in different parts of the genome mutated at the same time.

They said one of these portions is associated with the formation of the spike protein of the virus that enables its entry into healthy cells.

While more investigation is needed on how these simultaneous mutations impact the transmission and severity of the virus, the researchers said, sites that change together can be used to consolidate the subtype label into 11 base molecules.

"It's the equivalent of scanning a barcode instead of typing in the full product code number," Rosen said.

"This allows us to see the very specific fingerprint of Covid-19 from each region around the world, and to look closely at smaller regions to see how it is different," he added.

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In addition to helping scientists understand how the virus is changing and spreading, the scientists believe the method can also reveal the portion of its genetic code that appears to remain resistant to mutations -- a discovery that could be exploited by treatments to combat the virus.

"We're seeing that the spike protein and the part of the virus responsible for packaging its genetic material have developed a few major mutations, but otherwise they are changing at a slower rate," said study co-author Bahrad Sokhansanj from Drexel University.

"Importantly, both are key targets for understanding the body's immune response, identifying antiviral therapeutics, and designing vaccines," Sokhansanj said.