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13 Apr 2022

“An unprecedented collaborative effort”: How COG-UK and our partners came together to do something extraordinary

At home and internationally, COG-UK established itself as one of the leaders in genomic sequencing during the pandemic. Professor Sharon Peacock and Dr Katerina Galai reflect on their journey so far, from collaboration to training, and look to the future for the consortium at this year’s Cambridge Festival event, in partnership with the Cambridge Infectious Diseases Interdisciplinary Research Centre.

“There are very few opportunities in life where you can set up something that makes such a difference to the public health of a country”, says Sharon at the opening of the In conversation with SARS-CoV-2 variant hunters session.

 The use of pathogen genomics and using sequencing tools to improve public health is not a new concept. Scientists have been evaluating its utility for about a decade. In the early stages of the COVID-19 pandemic, Sharon and a group of scientists realised that the UK was in need of national sequencing capability as part of the response. “It wasn’t a matter of if the virus was going to mutate, it was a matter of when”, says Sharon. The UK needed to be prepared.

One of the biggest challenges of making national sequencing a reality was the scaling up of existing sequencing capabilities in the UK. “To give you an idea, in the year before the pandemic, Public Health England sequenced around 50,000 genomes in a year to track infectious disease outbreaks, such as tuberculosis and foodborne outbreaks”, says Sharon. “Last week (April 2022), around 70,000 SARS-CoV-2 genomes were generated across the UK.”

Alongside the scaling of existing sequencing structures, COG-UK needed to build a network. “Samples had to flow from hundreds of NHS testing sites and the Lighthouse labs into the sequencing labs”, says Sharon. “The whole process would look like a spider diagram; it was extremely complex.”

Map of UK with the logos of the alliance members

Moving away from practicalities, it was also important for COG-UK to reinforce a culture of collaboration and data sharing, which was key for success. This included partnering with the four public health agencies of the UK and academic institutions. The value of the data was amplified after public health agencies accessed, reviewed and acted on the findings. “The impact of COG-UK was to bring everyone together and be the glue between organisations to facilitate this approach – this really does sit at the heart of our success.”

The model that COG-UK developed didn’t go unnoticed. Across the globe, people were reaching out to see if it was something that they could replicate in their own countries. Although it may not have been suitable for all countries depending on their circumstance or their size, COG-UK ensured that the data generated was available to everyone. “This gave countries the opportunity to see what was circulating and think about their own public health response”, says Sharon.

But COG-UK isn’t just about the execution of genomic sequencing. When the sequencing was fully transitioned across to the public health agencies, “there was still so much to do”, Katerina points out.

Sharon, Katerina and the team were aware that not everyone had the same expertise, capabilities or funding to match the sequencing efforts of the UK. “We could have taken a small number of samples from other countries and sequenced them,” says Sharon, “but actually, we decided to focus on training and education as a way to contribute and provide support to other nations”. And so, COG-Train was born.

The World Health Organization have recently published their Global genomic surveillance strategy which reported that by January 2022 over two thirds of countries had genomic sequencing capacity. “We shouldn’t underestimate what is already happening, and that many countries have been able to do their own sequencing. But the ability to maintain these systems will come down to training together with a range of other factors,” says Sharon.

When it comes to how we can support countries in learning to live with COVID-19, Sharon’s feelings are clear. “Our legacy as COG-UK is that we know how to sequence at scale in times of emergency. We mustn’t allow this capability to decay.” Building on what we have and being able to dial up or dial down sequencing depending on a country’s specific needs will be key in learning to live with COVID-19.

Sharon believes that we should also consider how sequencing can help with other health challenges, such as antibiotic resistance. “Sequencing could be a huge help, for example, in detecting known or emerging antimicrobial resistance. The potential of what we have built is vast, and we should continue to explore how it should be used to advance our understanding of pathogens, and how we respond to them to protect public health worldwide”.

Watch the full recording from the session here.

COVID-19 Genomics UK (COG-UK)

The COVID-19 Genomics UK (COG-UK) consortium works in partnership to harness the power of SARS-CoV-2 genomics in the fight against COVID-19.

Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative collaboration of NHS organisations, the four public health agencies of the UK, the Wellcome Sanger Institute and sixteen academic partners. A full list of collaborators can be found here.

The COVID-19 pandemic, caused by SARS-CoV-2, represents a major threat to health. The COG-UK consortium was formed in March 2020 to deliver SARS-CoV-2 genome sequencing and analysis to inform public health policy and to support the establishment of a national pathogen sequencing service, with sequence data now predominantly generated by the Wellcome Sanger Institute and the Public Health Agencies.

SARS-CoV-2 genome sequencing and analysis plays a key role in the COVID-19 public health response by enabling the identification, tracking and analysis of variants of concern, and by informing the design of vaccines and therapeutics. COG-UK works collaboratively to deliver world-class research on pathogen sequencing and analysis, maximise the value of genomic data by ensuring fair access and data linkage, and provide a training programme to enable equity in global sequencing.