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Virus fundamentals

Virus fundamentals

The UK and global research community has responded quickly to the outbreak of COVID-19, caused by the coronavirus SARS-CoV-2. UKRI supported researchers have been looking at the structure of the COVID-19 virus using a variety of tools and simulating which drug treatments are most likely to act on it, helping advance clinical work.

Synchrotron shines in the search for antiviral treatments

COVID-19 can hold a billion virus molecules on a pinhead, making state-of-the art facilities such as synchrotrons – particle accelerators that can act like giant microscopes – in high demand in the global race to unlock the virus’s secrets.

As part of a transatlantic collaboration, Diamond Light Source, funded by UKRI’s Science and Technology Facilities Council in partnership with the Wellcome Trust and home to the UK’s national synchrotron science facility, has joined forces with structural biologists from the University of Oxford, AI-driven drug discovery company Exscientia and US non-profit biomedical research organisation Calibr to accelerate the development of potential COVID-19 antiviral treatments.

To speed up the process, the team is repurposing existing drug treatments already proven safe for use on humans, and are using the extraordinary power, range and speed of the synchrotron to provide atomic levels of detail to help understand how anti-viral drugs can work against the virus. The synchrotron is also configured for the rapid sample analysis needed to accelerate the path to clinical trials.

To this end, Calibr has made its world-leading collection of over 15,000 drug compounds available for Exscientia to use in the project. Exscientia will screen nearly every known approved and investigational drug against COVID-19 drug targets to search for rapid treatments. Diamond’s research on COVID-19 and its research facilities will help identify chemical compounds of interest and hopefully narrow the search down for a drug to be repurposed.

Scientific computing – key to understanding the structure of SARS-CoV-2

Immediately following the Chinese government’s release of the genetic sequence, in early January 2020, structural biologists around the globe swung into action to determine the three-dimensional structures of the proteins produced by the virus. These will form the basis for efforts to find inhibitor drugs and vaccines.

The Scientific Computing Department of UKRI’s Science & Technology Facilities Council is part of this international response, and is coordinating two international projects, CCP-EM and CCP4, funded by MRC and BBSRC, which are using electron cryo-microscopy and crystallography respectively to provide information about the structure of the virus, including the spike protein that hooks on to the human cell, which is the principle target for vaccine development.

This information will be crucial for virologists, both in the laboratory and for subsequent computational analysis, and is already being used in trials based on synthetic versions of the protein.

Other CCP (Collaborative Computational Project) communities are also providing time, resources and expertise to support the international response.

Read more about how the Scientific Computing Department is supporting research into SARS-CoV-2.

The supercomputer solution

UKRI-supported researchers are using the power of high-performance computers (HPCs) in the fight against the COVID-19 virus. By enabling scientists to develop a molecular-level understanding of the virus through sophisticated models and simulations, HPCs are helping to force COVID-19 to give up its secrets – such as how it can bind to and infect healthy cells. This work will help pave the way for new diagnostics, therapies, antiviral drugs and vaccines.

The EPSRC-supported HECBioSim and CCP-BioSim networks are playing a leading role in promoting the use of HPC resources for biomolecular simulation research into the virus. HECBioSim provides access to the EPSRC-led ARCHER UK National Supercomputing Service, prioritising access for teams working on COVID-19 research. Both networks are working to link with researchers globally, and serve as a global online resource, providing links to open-source software, supporting best practice and fostering knowledge-sharing and data sharing.

STFC's Hartree Centre speeds up search for Coronavirus treatment

Supercomputers at STFC’s Hartree Centre at Daresbury Laboratory are speeding up the search to find the best existing antiviral drugs that are most effective for treating for COVID-19 – and anyone with a personal computer can help!

The Folding@home project, led by the Washington University School of Medicine, is asking people across the globe to lend any unused background capacity from their PCs to power simulations that will give a better understanding of proteins and how they behave.

Seeing a protein in action could be key to identifying drugs already in existence that could potentially treat or disrupt the virus.

STFC’s Hartree Centre is providing its supercomputing capabilities to help design and generate potential drugs at speed, enabling them to be distributed more quickly across the network of thousands of Folding@home users and, most importantly, get results faster.

The team hopes to identify antiviral therapeutics that disrupt one or more of the proteins necessary for the lifecycle of COVID-19, which would help to prevent the further spread of the virus.

Anyone with a personal computer can contribute directly to the project and become a citizen scientist.

See Folding@home information on how to get started and download the software.