COVID-19 Genomics UK Consortium
Cardiff University is an Academic Partner of the COVID-19 Genomics UK Consortium. We support their work with bioinformatics and genetic sequencing, as well as through computational resources, analysis, data storage, and penetration testing.
Background
First observed in Wuhan City, China in December 2019, the SARS-CoV-2 virus is the cause of the ongoing COVID-19 pandemic. The COVID-19 Genomics UK Consortium (COG-UK) collects, sequences, and analyses UK samples of SARSCoV-2 genomes, allowing for a detailed study of the transmission and evolution of the virus in the UK. This work informs vaccine development, policy decisions, and public health responses.
As an Academic Partner, the University’s Advanced Research Computing at Cardiff (ARCCA) team and our computing infrastructure support the consortium, which has sequenced over a million viruses to date.
Response
We work with COG-UK in two areas: the bioinformatics and genetic sequence work undertaken by the School of Biosciences, and through the computational resources and team at ARCCA.
Before releasing clinical COVID-19 sample data for sequencing, NHS Digital required assurance that the data could be stored securely. The ARCCA team completed penetration testing on the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) system, which is hosted here at Cardiff University and at Birmingham University. After demonstrating our robust system security, our computational resources provided capacity for analysis, sequencing, and data storage.
We continue to provide data centre hosting support for genetic sequencing work, facilitating futher expansion of the CLIMB system.
The team at ARCCA has enabled work to be undertaken for COVID-19 using Hawk which has included penetration testing for NHS Digital to gain approval to hold English NHS data.
Outputs and impact
The sequencing of SARS-CoV-2 genomes is crucial to identifying mutations of the disease. This work, in conjunction with examination of patient metadata, allows analysis of the impact of the virus’ mutations on COVID-19’s severity. In addition, it informs on effective disease control measures and interventions, guiding UK public health policy. The information provided by COG-UK also supports the development of novel treatments and vaccines, and provides the ability to monitor the effectiveness of these treatments as they are introduced.
COG-UK has had a major impact – more samples have been sequenced in the UK than in the rest of the world. The publicly available dataset that COG-UK provides allows for a comprehensive analysis on a wider scale than what is achievable using the datasets provided by other organisations.
Key Academics and collaborators
Prof. Thomas Connor,
Reader, School of Biosciences,
Cardiff University and Consultant
Bioinformatician/Pathogen Bioinformatics Lead,
Public Health Wales NHS Trust
Dr. Anna Price,
Research Software Engineer
(Supercomputing Wales and CLIMB-BIG-DATA)
Joel Southgate,
Research Student, School of Biosciences