How software that tracks covid variants could protect us against future outbreaks

Yatish Turakhia is one of MIT Technology Review's 2023 Innovators Under 35.

When covid-19 started spreading in early 2020, scientists quickly realized that tracking how the virus was mutating would be essential for public health as new strains emerged that put people at greater risk. Yatish Turakhia, then a postdoc at UC Santa Cruz's Genomics Institute, helped develop a software tool called UShER to track these covid variants by placing them, within minutes of each new sample's submission, on a family tree of all known SARS-CoV-2 genomes.

The tool, which has been accessible online since 2021, now records more than 15 million viral sequences, and scientists add to it daily. It helps them and public health officials discover new strains, assign them names, and track their evolution. It also allows them to surveil the virus in real time on a global scale with a high degree of precision.

More recently, the team built another software tool, called RIPPLES, which examines UShER's extensive family tree structure and investigates whether specific branches" of variants may be recombinants-genetically distinct hybrid variants. A recombinant could, for example, take one part of its genome from the delta variant and another part from omicron. Because they essentially have two parents," recombinants are both rarer and tougher to identify.

Before the development of RIPPLES, scientists' only method of identifying potential recombinants was by remembering mutations they'd spotted in other variants. RIPPLES automates that process, allowing health experts to reconstruct the virus's evolutionary history. It also helps them work out whether a previously unseen sequence is a truly independent mutation or a combination of existing variants.

Our global understanding of how covid spreads would have been severely compromised without Yatish's work," says David Haussler, scientific director of the UCSC Genomics Institute, who worked with Turakhia on the project. The product of his algorithm, which nobody else could make, is a global picture of how the virus spread in full genetic detail around the entire globe."

Since the tool's release in 2022, RIPPLES has helped reveal hundreds of new SARS-CoV-2 recombinants. I just started working on it during the pandemic solely because I wanted to be useful," says Turakhia, 31. Now, when we get a new sequence, people have already used UShER to train models that can predict whether that new variant will be more transmissible and more immune-invasive than omicron or not, just based on this big data that is available."

While both tools were born from the need to track covid, they could also help scientists handle outbreaks of other pathogens. Turakhia and his team are already using it to track respiratory syncytial virus, also known as RSV, and monkeypox. Soon they plan to add tuberculosis and flu. Both infections are tough to track. Their strains are more genetically diverse than those of most diseases, and tuberculosis also has a much larger genome because it's a bacterium. But the team is already seeing promising results, says Turakhia.

In the future, we are going to create tools which are basically generalized to any pathogen out there-that's basically our goal," he adds. We want to manage the pathogens better, and to develop vaccines that are more reactive to how the pathogens are evolving, and thereby save lives."

Yatish Turakhia is one of MIT Technology Review's 2023 Innovators Under 35. Meet the rest of this year's honorees.