Fighting back against Coronavirus

The Centre for Genomic Pathogen Surveillance (the CGPS) has joined the fight against Coronavirus, working together with experts called up from across the NHS, public health agencies and academic research groups [include links to Cardiff and B’ham] – to form the COVID-19 Genomics UK Consortium (COG-UK). Together, we have a mandate from the UK Government underpinned by a £20m investment, to use whole genome sequencing (WGS) to understand how COVID-19 is spreading through the UK, and to apply this knowledge to ensure that we are better prepared to combat increasing infections in real-time, to understand whether different strains are arising and, to respond to emerging disease pandemics in future. Based across Oxford University’s Big Data Institute and the Wellcome Trust Sanger Institute, here at the CGPS we have been tasked with helping analyse the raw sequence data from COVID-19 patients generated from across a network of sequencing centres (including Belfast, Birmingham, Cambridge, Cardiff, Edinburgh, Exeter, Glasgow, Liverpool, London, Norwich, Nottingham, Oxford and Sheffield), stored and processed by the MRC CLIMB Project.

Our CGPS software platforms are uniquely placed to facilitate rapid data visualisation and analysis – and we are making it easier for hospitals and screening sites across the UK to submit patient metadata (essential clinical data) to CLIMB in real-time using Epicollect, and then to link geographical and temporal views of COVID-19 cases using Microreact, to understand at a glance how the virus is spreading at the local and regional level. We are helping to return weekly actionable reports to the COG-UK consortium – which in turn is helping to inform hospitals, regional NHS centres and the Government to save lives.

Screenshot(s) of a cog-uk m’react

e.g. what David shared in the team meet. if we can show something that isn’t sensitive and can be shared in the public domain right now

omething along the lines of ‘enhancing our understanding of epidemiology and transmission, monitoring interventions and treatments, expanding biological understanding and further research’. How many samples have been analysed/ reported on to date

Professor David Aanensen
Director of the CGPS (

“By tracking the global spread of coronavirus at the genomic level we can see transmission on a local and regional level. This gives us vital insights into how we might stop the spread and look in more detail at the impact of social distancing compared to more extreme policies such as ‘locking’ down, sometimes entire cities and countries”

Dr Catherine Moore,
Consultant clinical scientist at the Wales Specialist Virology Centre
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“This virus is one of the biggest threats our nation has faced in recent times and crucial to helping us fight it is understanding how it is spreading. Harnessing innovative genome technologies will help us tease apart the complex picture of coronavirus spread in the UK, and rapidly evaluate ways to reduce the impact of this disease on our society.”

Professor Sharon Peacock,
Director of the National Infection Service, Public Health England
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