When COVID-19 began to spread in early 2020, scientists quickly realized that the Monitoring the mutation of the virus is essential for public health as new strains emerge that put people at greater risk. Yatish Turakhia, then a postdoc at the Genomics Institute at the University of California, Santa Cruz (UCSC), helped develop a computer tool called UShER to track these coronavirus variants by searching for them, within minutes for each new sample to be sent, to a family. tree of all known SARS-CoV-2 genomes.
The tool, is available online Since 2021, it has registered more than 15 million viral followers, and scientists are expanding it every day. This helps them and public health officials find new strains, give them names and track their evolution. It also allows them to monitor the virus in real time on a global scale with a high degree of accuracy.
Recently, the team developed another computer tool, called RIPPLES, which examines the structure of the UShER family tree and investigated whether certain “branches” of variants could be recombinant, that is, genetically distinct hybrid variants. A recombinant can, for example, get part of its genome from a delta variant and another part from an omicron. Because they have two “parents”, recombinants are rarer and harder to identify.
Before the development of RIPPLES, the only way scientists could identify possible recombinants was to remember the mutations they saw in other variants. RIPPLES automates that process and empowers experts reconstructing the evolutionary history of the virus. It also helps them determine whether the previously unseen sequence is a truly independent mutation or a combination of existing variants.
“Our global understanding of how the coronavirus spreads would have been severely compromised without Yatish’s work,” said David Haussler, scientific director of the UCSC Genomics Institute, who worked with Turakhia on the project. “The product of their algorithm, which no one else can do, is a global image of how the virus spread all the genetic details of the entire planet.
Since the launch of the tool in 2022, RIPPLES has helped revealed hundreds of recombinants new SARS-CoV-2. “I started working on it during the pandemic just because I wanted to be useful,” said Turakhia (31 years old). “Now, when we get a new sequence, people use UShER to train models that can predict whether the new variant will be more transmissible and immunologically invasive than omicron or not, just based on this available data.”
Although both tools were born out of the need to track the coronavirus, they also help scientists management of outbreaks of other pathogens. Turakhia and his team have already used it to track respiratory syncytial virus (RSV) and monkeypox. Soon, they plan to add tuberculosis and influenza, both of which are difficult to track. Its strains are more genetically diverse than most diseases, and tuberculosis also has a larger genome because it is a bacterium. But the team is already seeing good results, Turakhia continued.
“In the future, we will create tools that can be generalized to any pathogen that exists: that is our goal,” he added. “We want to better manage pathogens and develop more reactive vaccines how pathogens evolve, and thereby save lives,” he concluded.