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23 Jul 2021

How SARS-CoV-2 sequencing is becoming a national service

Formed at the start of the pandemic in March 2020, the COVID-19 Genomics UK (COG-UK) consortium contributed to the UK’s COVID-19 response through genome sequencing. As a research consortium, COG-UK has focused on providing genome data that informs public health actions and supports policy decisions.

Moreover, through the tireless sequencing efforts across the COG-UK network in the last 16 months, our unique dataset will help us to explore a deeper understanding of why some people develop severe disease – through the combined analysis of viral and human genomes and detailed patient information. Our ambition is that this will lead to improvements in patient care.

Having developed a world-class sequencing network with its associated methods and analysis tools, COG-UK has now initiated the handover of routine sequencing to a national sequencing service run by the four UK public health authorities to provide a sustainable, long-term framework.

Here, we depict our transition journey and celebrate the lasting legacy of COG-UK sequencing efforts.

 

1 Apr 2021

Transition initiated

After 13 months of being the UK’s SARS-CoV-2 genome sequencing body, COG-UK began developing a plan for transition of routine sequencing to Public Health England (PHE) on 1 April 2021. COG-UK sites in Northern Ireland, Scotland and Wales (Glasgow, Edinburgh, Cardiff and Belfast) are supporting the transition of Pillar 1 (NHS samples) and Pillar 2 (samples from testing in the community) to their respective public health authorities. In addition to sequencing and knowledge transfer, COG-UK handed over the responsibility for shaping the sampling strategy (how sequencing capacity is used and prioritised) to NHS Test & Trace. While we no longer determine what is sequenced, COG central operations continue to provide feedback on the prioritisation model.

26 May 2021

COG-UK as a safety net

With all English Pillar 1 samples migrating for sequencing to PHE Laboratories, COG-UK academic partners stepped in to support the Wellcome Sanger Institute by distributing and sequencing high volumes of Pillar 2 samples (a minimum of 5,000 a week). During this time, the COG-UK network has repeatedly exhibited its proficiency and flexibility as the sites stood ready to take the strain to maintain continuity throughout the transition. Importantly, COG-UK ensured a seamless transition of sequencing and project management of several core national studies (including The Office of National Statistics {ONS} COVID-19 Infection Survey and the ‘Investigating a vaccine’ study).

2 Aug 2021

Successful completion

From 2 August 2021, two COG-UK sites in England remain on standby for surge sequencing, while the Quadram Institute in Norwich will continue to support the Real-time Assessment of Community Transmission (REACT) study until its transition to PHE in September.

With our role in national sequencing successfully handed over to public health agencies, COG-UK will continue its focus on research, data linkage and global training.

1 Oct 2021

Research ahead

Throughout the pandemic COG-UK has provided open access data and protocols to the global science community, and remain committed to research and improving the linkage of sequencing and public health data. CLIMB continues to provide essential infrastructure as a trusted environment for sharing of genomic data for public health surveillance between the four nations and collaboration with academic researchers. Our work with Health Data Research UK (HDR UK), the four UK Public Health Agencies and other data custodians is crucial to enhancing our understanding of COVID-19. This work focuses on progressing linkages between important COVID-19-specific datasets with viral genomic data from COG-UK, including human genome sequence data and detailed patient information.

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.