Covid-19 genome sequencing project gets a major upgrade

Supercomputing facilities set up to track the spread and evolution of the Covid-19 pandemic have received £1.2m in government funding to expand globally.

Cardiff University says the new funding will enable the CLIMB COVID-19 project, which it leads with the University of Birmingham, to carry out significant upgrades to computational equipment to process and store genomic data on a global scale.

CLIMB COVID-19 is a big data project supporting the COVID-19 Genomics consortium (COG-UK), which was set up to deliver large scale, rapid sequencing of the causes of Covid-19. It emerged from the CLIMB-BIG-DATA project in March 2020 as a bioinformatics platform providing data analysis pipelines, computing and storage capacity required to analyse large genome datasets produced by COG-UK. The project has so far sequenced more than fifteen thousand genomes in the UK.

Bioinformatics and phylogenetics are key steps to making use of genome data to understand better how the virus spreads, and how it is evolving.

The recent global spread of novel Covid-19 variants has demonstrated the value of genomic surveillance as viruses do not respect borders and can move quickly and easily. It is important to track viruses with different biological properties in order to make informed public health interventions, and to understand better the efficacy of drugs and vaccines.

However, the use of genome sequencing for Covid-19 in many countries has been limited. This new funding will enable global genomic data to be stored and processed. It will also enable researchers to extend research to cover other pathogens with pandemic potential as well as tracking other threats such as anti-microbial resistance.

Professor Thomas Connor, an expert in pathogen genomics from Cardiff University’s School of Biosciences, said “The success of CLIMB-COVID has been built on collaborative endeavour, and we are excited that we will be able to support global collaboration through this new award.

“Within the NHS in the UK we have seen first-hand the considerable benefit of genomics to support the response to COVID-19. This funding will provide a valuable route to share these translational benefits with other public health agencies and healthcare professionals around the world.”

Nick Loman, Professor of Microbial Genomics and Bioinformatics at the University of Birmingham, said “We anticipate being able to help support the sequencing efforts of many countries who may have limited computing resources by offering our cloud-based system which can be accessed from anywhere. Researchers can see how genomes from their local population relate to the hundreds of thousands of others collected around the world easily.

“By allowing a global audience to benefit from the new CLIMB resources we can help facilitate equitable data sharing for fighting COVID-19.”

Thomas Connor said “SARS-CoV-2 provides a great example of the relevance and power of genomics to track and characterise pathogens in real time. There are many other pathogens which are globally significant, and which would benefit from a global collaborative platform – and we are looking forward to being able to support global genomics efforts for other many of these key pathogens.”

Other partners in CLIMB include the Universities of Warwick, Swansea, Bath and Leicester, the London School of Hygiene and Tropical Medicine, and the Quadram Institute Bioscience.

The latest funding is part of the World Class Labs programme, a major £213m investment by UK Research and Innovation to upgrade the UK’s scientific infrastructure.

Announcing the funding, Science Minister Amanda Solloway said the response from UK scientists and researchers to coronavirus had been “nothing short of phenomenal”.

She said “We need to match this excellence by ensuring scientific facilities are truly world class, so scientists can continue carrying out life-changing research for years to come as we build back better from the pandemic.”

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