A fresh AI tool that forecasts viral mutations has the potential to steer COVID-19 treatment and preparations for future pandemics. EVEscape, created by the brains at Harvard Medical School and Oxford University, aced its tests by accurately foreseeing the most troublesome and common SARS-CoV-2 virus variants that cropped up during the pandemic.
A recent report in Nature spilled the beans on some really cool findings. EVEscape’s predictions turned out to be more spot-on than messing around with experiments, and it did the job quicker and slicker than those time-consuming lab tests. Plus, it nailed down which treatments might not be so hot at tackling the new variants.
The predictions are already helping with keeping tabs on the pandemic. The researchers have been putting out lists of the most troubling new SARS-CoV-2 strains every two weeks for more than a year. They’re also sharing these findings with groups like the World Health Organization (WHO).
“There are still thousands of new strains emerging each month — too many to experimentally test,” Pascal Notin, an Oxford University researcher who co-authored the study, told TNW. “EVEscape allows us to rapidly determine the threat level of the new strains.”
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EVEscape could shape how vaccines are made
Notin and his team have taken EVEscape for a spin and accurately guessed the mutations of HIV and the flu. They’re currently giving the tool a whirl on less famous troublemakers that might trigger pandemics, like Nipah and Lassa.
In the future, the researchers see EVEscape playing a big role in shaping how vaccines are made. Right now, vaccines and treatments are tested by looking back at past pandemic mutations, but EVEscape could change that.
EVEscape might step up to the plate and give us a heads-up on where the virus is headed next. That could be a game-changer, potentially leading to the development of vaccines that can stand up to any variant.
The fresh tool relies on a fancy model known as EVE, short for the Evolutionary model of Variant Effect. At first, EVE was designed to forecast the chances of genetic mutations causing human diseases, like cancer. But when COVID-19 started showing off its mutation skills and dodging treatments, the researchers tweaked their model to tackle SARS-CoV-2.
Generative models are the way to go
Generative models are the go-to choice for this task, and one of their standout skills is figuring out whether mutations will mess with the viral protein’s “fitness.” This “fitness” is all about ensuring the protein stays in good shape, doing its job by being functional, folding correctly, and latching onto the host cell receptor.
To make its predictions, EVE goes to school on some special protein sequences. These sequences have managed to keep themselves in tip-top shape for thousands to millions of years, and EVE learns from them to get a good grip on things.
“By doing so, it has to implicitly learn the biochemical constraints that underpin functional sequences,” Nodin explained. “We can subsequently leverage that understanding to predict whether new mutated forms for the protein — whether they are human or viral proteins — will be functional themselves.”
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EVEscape’s modular design is a big plus
EVEscape’s ability to adapt is all thanks to its straightforward nature. It gets its smarts from a dataset that’s all about viral protein sequences and their structure. This means it can be used for any virus right from the get-go when a pandemic hits.
Nodin stated that this represents a significant enhancement compared to approaches that usually require waiting for widely accessible pandemic antibodies for testing.
Another ace up EVEscape’s sleeve is its modular design. If newer, stronger generative models come onto the scene, you can quickly swap out the existing fitness prediction models.
COVID-19 has broadened EVEscape’s horizons. The pandemic has taught us valuable lessons about AI predictions and handed us a treasure trove of data. With all that info, EVEscape can pull off some pretty spot-on forecasts for lesser-known viruses that we don’t have much data on. That could be a real game-changer in future outbreaks.
