Using supercomputing for SARS-CoV-2 genome sequencing

Supercomputing Wales provides access to powerful computing facilities to high-profile science and innovation projects across Wales, with the aim of capturing more research funding, increasing scientific partnerships, creating highly-skilled research jobs and supporting collaborations with industrial and other partners.

Supercomputing Wales (SCW) has taken part in crucial work that has been undertaken at Cardiff University to support the UK pandemic response. This has included supporting the COVID-19 Genomics (COG-UK) consortium, which received in excess of £30M of government funding to establish SARS-CoV-2 genome sequencing in the UK (with a grant of over £1M for Cardiff University).

The University hosts one of the two computational sites that provide platforms for data aggregation and analysis of SARS-CoV-2 data in real time. The SCW team has supported the setup of these systems, contributing expertise in a range of areas – from completing work to provide assurance around the security of the system through to supporting the on-lining of new capacity to enable the processing and storage of more than 500,000 SARS-CoV-2 genomes in the last 15 months. This support is now transitioning to providing analysis capability directly to the UK Public Health agencies, as well as continuing to support the research mission of COG-UK. The University’s contribution also includes bioinformatics and sequencing work undertaken by members of the School of Biosciences.  

This work has impacts at multiple levels. At a local level, work undertaken in partnership with Public Health Wales (PHW) has contributed to multiple outbreak investigations in Wales, at a regional level, the data being generated underpins the COVID-19 genomic surveillance efforts in Wales. At a national level, the team at Cardiff and PHW has generated analyses for the Welsh Government’s Technical Advisory Group and has directly contributed to multiple COG-UK reports presented to UK Government SAGE.   

“I’ve been working on using patient metadata datasets to investigate the geographic spread of lineages of SARS-CoV-2 within Wales, and the impact of the importation of lineages into Wales,” says Dr. Anna Price (Research Software Engineer, Supercomputing Wales and CLIMB-BIG-DATA). “This work feeds into the COVID-19 genomic surveillance efforts in Wales and would not be possible without the infrastructure at Cardiff and the datasets that COG-UK provides, as well as the skillset I bring as a RSE in being able to generate analyses of these datasets.”  

Supercomputing Wales has provided essential support to this work through hardware provision and the expertise of the SCW team. Key contributors at Cardiff University include: Prof. Tom Connor (Professor, Cardiff University; Bioinformatics Lead, Public Health Wales), Dr. Anna Price (Research Software Engineer, Supercomputing Wales and CLIMB-BIG-DATA), Alex Southgate (Systems Engineer, CLIMB-BIG-DATA), Drew Mack (PhD student, CDTAIMLAC), Dr Christine Kitchen (Supercomputing Wales), Professor Martyn Guest (Supercomputing Wales), Steffan Adams (Supercomputing Wales) and Robert Munn (Supercomputing Wales). The group also recognises the support of the datacentre team who have facilitated datacentre works required to support the pandemic response activities.