The COVID-19 Genomics UK Consortium (COG-UK) brings together experts from across the NHS, academia and public health agencies for large scale, rapid sequencing and analysis of the disease.

This information can then be quickly shared with hospitals, the NHS and the government to help inform their response to the pandemic.

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Cardiff University reports the £20m funding will create Wales’ only Covid-19 sequencing centre, comprised of a team of Cardiff University and Public Health Wales (PHW) scientists.

Dr Tom Connor, who will lead the Cardiff sequencing centre, said “Genomic sequencing will help us to understand coronavirus and its spread.

“By analysing samples from people who have had confirmed cases of COVID-19, scientists can monitor changes in the virus at a national scale to understand how the virus is spreading and whether different strains are emerging.

“Having this information available will help in the clinical care of patients – and ultimately help to save lives. The Cardiff centre means that we will be able to help in the UK’s national effort against the virus.”

The team has already sequenced more than fifty Covid-19 virus genomes from Wales, through funding from the Welsh Government and Public Health Wales.

The service has the potential to sequence Welsh samples within twenty four hours to enable real time response to the results.

Dr Catherine Moore, consultant clinical scientist at the Wales Specialist Virology Centre, said the data being generated already was giving scientists “incredible” insights into the transmission and dynamics of a new virus into a population with no immunity.

She said “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.

“Within Wales, we have been able to monitor not only the introduction of the virus into the country but also determine when local transmission events have occurred, and then when we started to see more sustained community transmission.

“Over the coming months, by freely sharing our data globally, researchers and modellers in public health will be able to determine the effect of preventative interventions and policies adopted by different countries governments. Most importantly once a vaccine has been developed, we will be able to monitor how that will impact further on reducing transmission.”

Tom Connor, a reader in Cardiff University School of Biosciences and bioinformatics lead for pathogen genomics at Public Health Wales, said “This consortium is unprecedented in both the speed it has come together and the ambition to sequence so many samples in real-time. By using the expertise and capacity across the whole of the UK, COG-UK will bring benefits to the NHS across the UK, delivering an equitable service and providing insight at both local and national levels.

“By analysing COVID-19 genomes from Welsh patients we will be able to more accurately track the evolution of the outbreak in Wales, providing valuable information to inform the public health response both here and on a UK-wide level.”

Wales is well placed to contribute to COG-UK, thanks to substantial funding by Welsh Government since 2017, associated with the Genomics for Precision Medicine Strategy. This funding has seen the foundation of a Pathogen Genomics Unit within the Welsh NHS to examine the genomes of pathogens of interest, including viruses such as HIV and Influenza. This capacity, developed as part of Genomics Partnership Wales, and in which Tom Connor is a core team member, has enabled the Welsh team to get sequencing rapidly.

Tom Connor said “This is a great example of how the work that has been going on within the NHS in Wales to build genomics capacity can pay dividends when unexpected issues arise. It is also a great example of how integrated working between the NHS and academia can deliver real benefits to the NHS. With the support from Welsh Government and Public Health Wales, the sequencing approaches we have developed within the NHS have been designed to be modular and expandable, which has enabled us to rapidly repurposed for the sequencing of COVID-19.”

In addition to building on strong, longstanding, collaborations between the NHS and Cardiff University in Wales, COG-UK also benefits from another project where Cardiff has played a key role; the MRC CLIMB project, which was recently refunded by the MRC. CLIMB, led in Cardiff by Tom Connor and supported by Supercomputing Wales, is providing COG-UK with the computational resources to share and analyse the large volumes of Covid-19 genomics data that is now being generated across the UK.

As well as Cardiff, other sequencing centres will be based in Belfast, Birmingham, Cambridge, Edinburgh, Exeter, Glasgow, Liverpool, London, Norwich, Nottingham, Oxford and Sheffield.

The UK Consortium, supported by the UK Government, including the NHS, Public Health England, UK Research and Innovation (UKRI), and Wellcome, enables clinicians and public health teams to rapidly investigate clusters of cases in hospitals, care homes and the community, to understand how the virus is spread and implement appropriate infection control measures.