Science

Cardiff Uni computing system for COVID-19 wins major award

COVID-19 genome
Sequencing the genome of the virus has increased understanding of how it replicates and mutates. Source: geralt (via Pixabay)
The team have sequenced the COVID-19 genome and made it available to researchers worlwide to increase knowledge about the virus.

By Holly Giles | Deputy Editor 

The COVID-19 Genomics UK (COG-UK) project at Cardiff University has won a national award this month for its work in processing the COVID-19 genome sequence data and making it available to researchers worldwide. It is commonly overlooked and misses out on the headlines but it is this background work which allows progress to be made in vaccines, medical care and our experience of COVID-19.

The project has been awarded Best High-Performance Computing Collaboration at the HPCwire Readers’ and Editors’ Choice Awards 2020. The award recognises outstanding individuals, organisations, products, and technologies in high-performance computing.

The project has been run by the Cloud Infrastructure for Big Data Microbial Bioinformatics (CLIMB) which is a UK-wide partnership working to sequence COVID-19 genomes and understand the spread of the virus. CLIMB was founded in 2014 to handle the large data sets created from genome sequencing and has so far helped sequence more than 110,000 virus genomes. 

CLIMB is a collaboration between Warwick, Birmingham, Cardiff, Swansea, Bath and Leicester Universities,  the London School of Hygiene and Tropical Medicine and the Quadram Institute. COG-UK is supported by £20 million funding from the UK Department of Health and Social Care (DHSC), UK Research and Innovation (UKRI) and the Wellcome Sanger Institute, administered by UK Research and Innovation.

The project then changed at the start of the pandemic and began focusing on COVID-19 with the aim of sequencing and analysing the genome of COVID-19 in order to increase understanding of the transmission and evolution of the virus. Due to the infrastructure already in place the project was able to quickly adapt to the pandemic, as Professor Mark Pallen, the director of the CLIMB-BIG-DATA project, explained:

It’s been great to see how our infrastructure and our team have been able to respond so quickly and effectively to the national and international challenge of understanding and controlling the spread of COVID-19”. 

The findings are then made available to researchers across the UK and throughout the world through the CLIMB platform, allowing researchers to better understand the virus and to be able to more efficiently manipulate with regards to evolution and vaccination. The CLIMB network includes over 900 users and over 300 research groups in 85 institutions from across the UK. 

The work of the CLIMB project has helped inform national decision-making of the Scientific Advisory Group looking at local public health and monitoring outbreaks in real-time. 

Reflecting on the project Dr Tim Cutts, the Head of Scientific Computing at the Wellcome Sanger Institute, told:

“At the beginning of the pandemic, we were asked to repurpose our cloud infrastructure to handle the large volumes of COVID-19 sequence data that would be coming in. Thanks to the skill and dedication of the team and the high-performance storage solutions provided by DDN, we were able to do this in record time. I’m extremely proud of the contribution that COG-UK has made to the world’s understanding of COVID-19”

This sentiment was continued by Dr Jeff Barrett, the Lead COVID-19 Statistical Geneticist at the Wellcome Sanger Institute:

“The Sanger Institute and its COG-UK partners have sequenced more COVID-19 genomes than anywhere else in the world, which is an incredible achievement. But this would mean nothing without making these data widely available, which has been made possible by our high-performance computing team.”

Professor Tom Connor, from Cardiff University and technical architect of CLIMB, said:

With COVID-19, CLIMB has proved its worth, providing us with the platform to be able to rapidly develop and scale up an analysis infrastructure to support the COVID-19 pandemic response. CLIMB COVID has had a massive impact, from supporting outbreak analysis in our hospitals all the way up to providing analyses that inform government policy. The impact of CLIMB and this award is a testament to both the hard work of the team and the broader vision of the CLIMB and CLIMB-BIG-DATA projects.”

Due to its nature as an information provider, we will never know the full impact of the work at CLIMB but it has directed and shaped the COVID-19 pandemic, and has undoubtedly saved lives through contributions to vaccine developments. The award is a well deserved achievement for the project. 

COG-UK would like to give a special thanks to Dr Sam Nicholls, Radoslaw Poplawski, and Simon Thompson from the University of Birmingham, and Dr Matt Bull and Dr Christine Kitchen from the University of Cardiff for their continued hard work on the CLIMB project and support in hosting the equipment.

Science and Technology

 

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