Story at a glance

  • BioNTech announced it had partnered with InstaDeep to create an algorithm to quickly flag potential high-risk COVID-19 variants.
  • BioNTech conducted an 11-month study that showed its Early Warning System (EWS) could detect multiple variants flagged by the World Health Organization.
  • The EWS approach is solely dependent on existing data, not a “wait-and-watch" approach.

One pharmaceutical company announced it has developed a method to predict new COVID-19 variants through artificial intelligence to help global efforts in combating the coronavirus pandemic. 

BioNTech announced on Tuesday it had partnered with InstaDeep to develop a computational method that analyzes global sequencing data. Called the Early Warning System (EWS), BioNTech said it combines spike protein structural modeling with artificial intelligence (AI) algorithms to quickly flag potential high-risk COVID-19 variants.  

The company conducted an 11-month study that showed the capabilities of EWS and found it could evaluate new variants within minutes, with the system identifying over 90 percent of the World Health Organization’s designated variants, including variants of concern, interest and variants under monitoring, on average two months in advance. 

The alpha, beta, gamma, theta, eta and omicron variants were all detected by EWS in the same week its sequences were first uploaded. The omicron variant was even ranked as a high-risk variant the same day its sequence became available, according to BioNTech. 


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“Early flagging of potential high-risk variants could be an effective tool to alert researchers, vaccine developers, health authorities and policy makers, thereby providing more time to respond to new variants of concern,” said Ugur Sahin, CEO and co-founder of BioNTech. 

The EWS algorithm assigns variants an immune escape score and a fitness prior score, which represents the variant’s transmissibility potential. Combining these two metrics produces a Pareto score, which BioNTech says is the best assessment of the risk posed by a given virus variant. The higher the score the higher the risk a variant has of impacting global health.  

BioNTech noted that the EWS approach is solely dependent on existing data and is not dependent on a “wait-and-watch" approach. 

“More than 10,000 novel variant sequences are currently discovered every week and human experts simply cannot cope with complex data at this scale," said Karim Beguir, co-founder and CEO of InstaDeep. 

“For the first time, high-risk variants could be detected on the spot, potentially saving months of precious time. We are happy to make our research work publicly available and, most importantly, look forward to its continued real-world impact,” added Beguir. 

BioNTech’s announcement comes as some public health experts warn the next COVID-19 variant is, “just around the corner.” The Centers for Disease Control and Prevention cautions that new variants are expected to occur but taking steps to reduce the spread of viruses by getting a COVID-19 vaccine, wearing a mask and getting regularly tested are the best ways to slow the emergence of new variants.  


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Published on Jan 11, 2022