German biotech firm BioNTech and UK-based artificial intelligence (AI) specialists InstaDeep have partnered to develop an early warning system (EWS) for dangerous new COVID-19 variants.

The new computational method combines structural modelling of the viral Spike protein and AI algorithms to flag potential high-risk variants (HRVs) entered into SARS-CoV-2 sequence data repositories within less than a day.

It combines metrics, based on a variant’s fitness and immune escape properties, into a score indicating its risk of impacting global health.

During a trial period, the EWS identified more than 90% of variants designated by the World Health Organisation (WHO) as potentially dangerous, on average two months in advance - including Alpha, Beta, Gamma, Theta, Eta and Omicron.

As part of their collaboration, BioNTech and InstaDeep formed a joint AI Innovation Lab in London and Mainz to advance novel drug discovery and design, protein engineering, manufacturing and supply chain optimisation. 

WHY IT MATTERS

Frequent and wide circulation of the COVID-19 virus increases its likelihood to mutate in parts of its genetic make-up with the potential to change its features. 

Data shows that thousands of new variants are emerging every week at an increasing rate, with a weekly average of registered variants of around 300 in September 2020, 7,000 in August 2021 and 12,000 in December 2021.

While most variants do not impact the course of the pandemic, some pose significantly increased risk. Variants that can bypass neutralization by antibodies pose a risk to individuals who previously had COVID-19 or are vaccinated.

Foreseeing variants with the potential to become HRVs is a challenge for public health authorities, as detection by varied tests in the lab is very time consuming. 

The EWS allows for early detection of these variants and shortens the time that health authorities need to assess their impact and respond in a timely manner. 

THE LARGER CONTEXT 

Last year BioNTech acquired Vienna-based biotech company PhagoMed, which is developing novel synthetic lysin technology for precision antimicrobial treatments.

Meanwhile, Spanish startup Seqera Labs recently announced $5.5 million (€4.7M) in seed funding for its technology enabling scientists to deploy scalable data analysis. The software has been applied to global SARS-CoV-2 sequencing efforts, assisting with the identification and surveillance of variants including Alpha and Delta.

ON THE RECORD

BioNTech MD, CEO and cofounder, Ugur Sahin, said: “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.” 

InstaDeep cofounder and CEO, Karim Beguir, said: “More than 10,000 novel variant sequences are currently discovered every week and human experts simply cannot cope with complex data at this scale. We’ve addressed this challenge by deploying the powerful AI capabilities of InstaDeep’s DeepChain platform combined with BioNTech’s SARS-CoV-2 know-how and technology. For the first time, high-risk variants could be detected on the spot, potentially saving months of precious time.”