AI tool predicts new viral variants and could improve vaccines

Antibodies attack Covid-19

The UK’s University of Oxford is taking the lead on two collaborative international projects to improve the response to new Covid-19 variants and contribute to future pandemic preparedness.

Researchers at Harvard Medical School (HMS) in the US and the University of Oxford have developed a new artificial intelligence (AI) tool named EVEscape that can predict new viral variants before they emerge.

The scientists say the tool can help inform the development of vaccines and therapies for SARS-CoV-2 and other rapidly mutating viruses.

In a study published on 11 October 2023 in Nature, the researchers showed that had it been deployed at the start of the pandemic, EVEscape would have identified the most concerning variants for SARS-CoV-2.

The University has also launched a new global consortium to research and develop next-generation Covid-19 and flu vaccines, backed by £8 ($9.8) million funding from UK Research and Innovation (UKRI).

The academic and industry consortium has created the IMMPROVE (Immune Memory and Mechanisms of Protection from Vaccines) project to develop better vaccines that will protect against multiple strains of Covid-19.

According to the European Centre for Prevention and Disease Control, the current variants of interest are Omicron variants BA.2.75, XBB.1.5 and variations of the latter including EG.5, FL.1.5.1, XBB.1.16.6, and FE.1, though cases of BA.2.86 are also growing.

EVEscape AI tool

The AI tool has two elements: A model of evolutionary sequences that predicts changes that can occur to a virus, and detailed biological and structural information about the virus.

The researchers are using EVEscape to release a ranking of new variants of SARS-CoV-2 every two weeks.

“We want to know if we can anticipate the variation in viruses and forecast new variants — because if we can, that’s going to be extremely important for designing vaccines and therapies,” said senior author Debora Marks, Associate Professor of Systems Biology in the Blavatnik Institute at HMS.

The scientists first developed the generative model EVE (evolutionary model of variant effect) to predict gene mutations that cause human diseases. As the Covid-19 pandemic progressed, Marks and her team rebuilt EVE into a new tool called EVEscape for the purpose of predicting viral variants.

In the new study, EVEscape outperformed experimental approaches in predicting which Covid-19 mutations would be most prevalent. It could also make predictions more quickly and efficiently than lab-based testing since it didn’t need to wait for relevant antibodies to arise in the population and become available for testing.

The team went on to demonstrate that EVEscape could be generalised to other common viruses, including HIV and influenza, and are testing EVEscape on understudied viruses such as Lassa and Nipah.

Another important application of EVEscape would be to evaluate vaccines and therapies against current and future viral variants. Noor Youssef, a research fellow in the Marks lab, said: “We want to figure out how we can actually design vaccines and therapies that are future-proof.”

The IMMPROVE project

The IMMPROVE research project is headed by Professor Teresa Lambe OBE and Professor Paul Klenerman, both Principal Investigators in the University of Oxford’s Pandemic Sciences Institute.

The research aims to enhance protection against several respiratory pathogens, including influenza and respiratory syncytial virus (RSV). The work will also establish global networks of trained personnel with the scientific tools to better prepare the world for the next pandemic.

Building on past experience accumulated during the Covid-19 pandemic, the consortium will improve understanding of how a protective immune response is induced, how it is maintained, and the role of immunity in the nose and the lungs.

Paul Klenerman, Sidney Truelove Professor, said: “The UK scientific community rose to the challenge of the pandemic and in doing so it brought many different groups together to collaborate in new networks. This consortium continues the spirit of that collaboration to address some of the key remaining challenges, not just for Covid-19, but for vaccines in general.”

The research partners include Babraham Institute, University of Cambridge, University of Birmingham, Imperial College London, London School of Hygiene and Tropical Medicine, University College London, University of Southampton the PITCH consortium (involving researchers in Oxford, Birmingham, Liverpool, Newcastle, and Sheffield Universities), the Sanger Institute, UK Health Security Agency (UKHSA) and the Royal Veterinary College.

Other industry and non-profit partners include AstraZeneca, Sanofi Pasteur, Moderna, Bill & Melinda Gates Foundation and Janssen Pharmaceuticals.

IMMPROVE is one of three projects announced today by UKRI under its Tackling Infections strategic theme, which is investigating future infectious disease threats.

Diana Spencer, Senior Digital Content Editor, Drug Discovery World

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