Artificial Intelligence used to design brand new viruses

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Health and science correspondent

Artificial Intelligence has been used to design brand new viruses that are fully functional and can replicate in the laboratory, say US researchers.

It is the first time whole genomes have been successfully designed by AI.

The resulting 16 novel viruses were created to infect bacteria and pose no threat to people.

The breakthrough has been labelled a "very significant turning point" in science that could unlock a new era for treating disease. But experts have also warned AI-designed viruses raise "urgent" safety and security concerns.

AI tools are rapidly advancing and have already been used to design new antibiotics.

But that is relatively simple compared with designing a new viable virus from scratch.

"This is a next step in the complexity that's designable by generative AI, this is the first time generative AI has been used to design a complete genome, it's something that can replicate and have other functions inside cells… this was new territory for us," Brian Hie, assistant professor at Stanford University, told the BBC.

The technology works similarly to large language models, like ChatGPT, which predict sequences of text.

In this instance the AI models, known as Evo1 and Evo2, predict the language of life rather than words.

The AI models were trained on genetic codes from viruses, bacteria, plants and people.

They were then refined to produce a type of virus, known as a bacteriophage, which infect only specific species of bacteria.

The Stanford researchers picked the most promising 302 AI designs and synthesised them in the lab. Of these, 16 proved effective at killing E. coli bacteria.

Samuel King, a PhD student in the lab, said they realised the phage were working in the early hours of the morning.

The phage were placed on petri dishes growing a layer of bacteria on them and the scientists waited for signs their new viruses were enjoying the feast.

"We were starting to see these clear spots and it was just extremely exciting," says King. When the results were shared with the wider team "the room spontaneously burst into applause", Hie recalls.

Developing new phage could lead to new ways of treating infections that have become resistant to antibiotics.

But the breakthrough also points to the ability of AI to design new biology that goes beyond the natural world – what is known as synthetic biology.

Hie argues this has the potential to "massively improve human health" by developing new drugs and therapies.

But concerns have already been raised that the same technology could be used maliciously to create new diseases.

In a commentary accompanying the publication in the journal Science, Dr Thomas Inglesby and Dr Moritz Hanke from the Center for Health Security at Johns Hopkins University wrote that the findings raise "urgent biosafety and biosecurity questions".

They said it was no longer a question of "whether generative viral genome design will exist" but whether it can be used without "enabling serious harm".

For example, they said new viruses with the potential to cause disease "should not be pursued".

The researchers themselves took steps to maximise safety. They excluded viruses that could infect complex organisms from the training database, performed the research on phage rather than viruses that infect people and it all took place in a secure laboratory.

Hie argues even existing safeguards go a long way towards "ensuring that the technology is used for good".

Viruses are not alive and it would take another significant leap for AI to generate living organisms.

The genetic code of the phage is around 5,400 base pairs (letters) long. The smallest genome of a living cell is around 500,000 base pairs. The human genome is three billion base pairs.

Hie says "it would probably be a lot of work, but not impossible" to attempt some simple organisms and they were "definitely interested in working towards" that.

Prof Marc Güell, from the synthetic biology lab at Pompeu Fabra University in Spain, said the study was a "very significant turning point" because for the "first time in history, we are beginning to design biology on a computer".

He said it "allows us to dream of exciting possibilities for tackling humanity's greatest challenges" such as developing phages to tackle disease, enzymes to treat genetic disorders and antibodies that could be used in immunotherapy.

Prof Patrick Cai, chair of synthetic genomics at the Manchester Institute of Biotechnology, said the study was an "important milestone".

"The significance extends far beyond phages – it suggests that genome language models are beginning to learn the design principles encoded by evolution, opening the door to AI-assisted genome writing."