Thu. Jan 20th, 2022

According to a study, a new early warning system can predict the highest risk coronavirus variants simply from their genetic code, alerting health authorities and vaccine developers to the potential risks months before they spread.

The artificial intelligence-based program, developed by BioNTech, the German biotechnology group behind the leading Covid-19 vaccine, and the North African AI start-up InstaDeep, identified more than 90 percent of worrying variants, including the highly transmissible Omicron strain, on average two months before their appointment by the World Health Organization.

The results of the study show that the program can evaluate the risks of new variants of their nail proteins within minutes, and monitor them as they develop “almost in real time”, according to the two companies. Ugur Sahin, CEO of BioNTech, said the tool would be made freely available.

“Early flagging of potential high-risk variants could be an effective tool to alert researchers, vaccine developers, health authorities and policymakers, providing more time to respond to new variants of concern,” Sahin said.

The system had a red flag with Omicron on the day its genomic order was first uploaded to the global Gisaid database late last year as the most worrying variant out of more than 70,000 variants discovered between early October and late November is, said the study, which has yet to be peer-reviewed. It was three days before it was classified by the WHO as a variant of concern.

It was also able to flag the Alpha variant, which spread rapidly in the south of England last winter, 65 days before its official designation by the WHO.

“More than 10,000 new variant series are discovered every week and human experts simply cannot handle complex data on this scale,” said Karim Beguir, co-founder and CEO of InstaDeep, in the UK. “For the first time, high-risk variants could be detected on the spot, potentially saving months of precious time.”

Bar graph of difference in days between early warning system detection date and WHO designation of variant as high risk, showing how AI tool will help detect coronavirus concern variants

Most mutations in the Sars-Cov-2 genome are likely to be harmless, but a small portion of the changes to its genetic material could lead to more infectious variants such as Alpha, Delta, and Omicron.

Genomic sequencing, a technique that can detect mutations in the virus’ genetic material, now has a key surveillance tool in the fight against the virus.

Emma Hodcroft, an evolutionary geneticist at the University of Bern, said the early warning system could be “useful” in detecting future variants, but warned that “these predictions are just as good as the information we need to fill in them” .

“A lot of scientists also noticed Omicron on the day it was made available, but we’re still really limited by when we can taste such variants,” she said.

Although South African scientists have sounded the alarm about Omicron, more than 80 percent of the 6.3 million genomes uploaded to Gisaid come from North America and Europe. “We will be held back in how early we can see things unless we extend our Sars-Cov-2 genomic surveillance to more countries to get more reliable data,” Hodcroft added.

Using global sequencing repositories such as Gisaid, the BioNTech / InstaDeep program is able to scan hundreds of thousands of registered virus variants and each variant’s “fitness” – its potential to spread – and its immune escape properties, or its ability to to evade existing immunity, to analyze. to the coronavirus.

These two measures are then combined to create a risk score – a higher score indicates an increased risk that the variant affects global health. Omicron has achieved extremely high on both of these benchmarks. The system also evaluated the IHU or B.1.640.2 variant recently observed in France, and found that it has immune-escaping properties that are relatively similar to Omicron, but with significantly lower fitness, making it less worrying.

Advance warning of a high-risk variant will also help scientists adjust vaccines. BioNTech said it will begin clinical trials of its mRNA-based Omicron vaccine by the end of January. At the JPMorgan Healthcare Conference in San Francisco this week, Sahin said: “We have already started manufacturing for the commercial scale of Omicron vaccine. We expect to be ready for market supply by March 2022, subject to regulatory approval. ”

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