STFC Daresbury release paper on how to prepare for future Covid-19 variants

Research published in the Biophysical Journal, conducted by a team from the Science and Technology Facilities Council’s (STFC) Hartree Centre in collaboration with IBM at the Hartree National Centre for Digital Innovation (HNCDI), has provided early but crucial insights into the molecular behaviour of viral proteins and the factors driving viral evolution.

Viruses such as SARS-CoV-2, the cause of the Covid pandemic, naturally mutate over time. While many mutations are benign, some can significantly alter the virus's transmission and the severity of the disease, affecting the effectiveness of existing vaccines and diagnostics, and potentially leading to more dominant variants posing increased global health risks.

The ability to detect 'variants-of-concern' at an early stage and quickly assess their public health implications has seen considerable progress. Understanding these mutations at a molecular level and their role in the virus’s evolutionary benefit is just as critical. This knowledge, along with other scientific tools, is essential in the preparation and response to future mutations and variants that are yet to emerge.

At the HNCDI, utilising high-powered supercomputing resources, the team conducted extensive molecular simulations to explore the structure of the SARS-CoV-2 spike protein, crucial for infection, and its interaction with human cell receptors.

The research particularly focused on how genetic alterations in the Omicron variants lead to structural changes at the molecular level in the spike protein compared to the original Wuhan strain and between different Omicron subvariants. It also investigated the role of glycans—molecules on our cells—that could affect the virus's ability to bind to human cells more efficiently, potentially contributing to its swift transmission.

Positioned at STFC’s Daresbury Laboratory in Sci-Tech Daresbury, Liverpool City Region, the Hartree Centre is a hub of UK supercomputing expertise, nestled within thriving Health Tech and Digital Tech industrial clusters in the North West. The Centre's flagship initiative, the HNCDI, a £210 million, five-year collaboration with IBM, is instrumental in driving collaborative research and development endeavours.

David Bray, Team Leader for Chemistry and Materials at the STFC Hartree Centre, stated, “COVID-19 has been exceptionally infectious. Understanding the virus’s binding mechanisms to human receptors is crucial for tackling its infection rates and developing strategies against it and potential future viruses. Collaboration with IBM researchers has provided new insights into the evolutionary dynamics of this critical viral component.”

Ya-Wen Hsiao, a Computational Scientist at the Hartree Centre, commented, “Enhancing our molecular-level understanding aids the broader comprehension of Covid infection and supports vaccine and drug design. Ongoing research partnerships are vital in forming a comprehensive view of the SARS-CoV-2 virus and its interactions with human cells.”

Professor Jason Crain of IBM Research Europe and the University of Oxford remarked, “The pandemic has sharply brought into focus the swift impact of viral evolution. However, the molecular mechanisms conferring advantages to the virus and steering evolutionary paths remain under-investigated. Our collaboration is a promising stride towards better predicting and preparing for future variants.”

The findings are a continuation of previous joint efforts between the team, the University of Oxford, and the Diamond Light Source, applying advanced AI techniques to discover new molecular structures capable of inhibiting Covid viral proteins’ functions.