Tracking Covid Variants: Innovators Develop Software for Real-Time Monitoring

Tracking Covid Variants: Innovators Develop Software for Real-Time Monitoring

2023-10-02 10:08:00
Software Developer Yatish Turakhia Recognized for COVID-19 Variant Tracking Tool

Even at the beginning of the corona pandemic in 2020, scientists knew that it would be crucial to track the virus’s mutations. Because new strains can mean an even more severe course of the disease. Yatish Turakhia, then a postdoctoral fellow at the Genomics Institute at the University of California, Santa Cruz, helped develop software to track Covid variants by merging them into a family tree of all known SARS-CoV variants within minutes of submitting each new sample. 2 genomes classified. For his work, Turakhia is now one of the winners of the “Innovators under 35” competition, which the US edition of MIT Technology Review organizes annually. Also among them is Sharon Li, the AI security researcher who also received the title “Innovator of the Year”.

The tool called UShER, which has been accessible online since 2021, now records more than 15 million viral sequences, with new ones being added almost every day. It helps researchers and health authorities discover new strains, give them names and track their development. This allows them to monitor the virus worldwide in real time and precisely.

Recently, the team developed another software tool called RIPPLES that examines UShER’s extensive family tree structure and determines whether certain “branches” of Covid variants are so-called recombinations – genetically different hybrid variants. For example, a recombination could take over part of its genome from the Delta variant and another part from the Omicron variant. Because they essentially have two “parents,” recombinations are both rarer and more difficult to identify.

Before developing RIPPLES, scientists could only identify potential recombinations by remembering targeted mutations they had discovered in other variants. RIPPLES automates this process and allows experts to reconstruct the evolutionary history of the virus. It also helps them figure out whether a previously unknown sequence is a truly independent mutation or a combination of existing variants.

“Our understanding of the spread of the coronavirus would be less developed without Yatish’s work,” says David Haussler, scientific director of the UCSC Genomics Institute, who worked with Turakhia on the project. “Its algorithm shows how the virus developed in all genetic details.”

Since the tool was released in 2022, RIPPLES has helped uncover hundreds of new SARS-CoV-2 recombinations. “I only started working on it during the pandemic just because I wanted to be useful,” says Turakhia. “Now when we get a new sequence, experts have already used UShER to train models that can predict whether or not this new variant will be more contagious and immune invasive than Omicron. And that’s just based on this large database.”

UshER and RIPPLES were born out of the need to detect Covid. But they could also help scientists combat outbreaks of other pathogens. Yatish Turakhia and his team are already using them to track respiratory syncytial virus, also known as RSV, and monkeypox. They will soon also want to record tuberculosis and flu. Both infections are difficult to track because their strains are more genetically diverse than those of most diseases, which is why flu, for example, requires a new vaccination every year. The team is making good progress with both pathogens, says Turakhia.

“In the future, we will develop tools that are basically suitable for any pathogen. That is our goal,” he adds. “We want to get the pathogens under better control and develop vaccines that respond better to the development of the pathogens and can therefore save human lives.”

Yatish Turakhia is one of the winners of the “Innovators under 35” competition. The competition, hosted by the US edition of MIT Technology Review, recognizes young people who are driving innovation.]
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