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 contains 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.

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.

“Our global understanding of how covid spreads would have been severely compromised without Yatish’s work,” says David Haussler, scientific director of UC Santa Cruz 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.”