Sharon Peacock and the COVID-19 Genomics UK Consortium (COG-UK)

Six guest lecturers will be joining Jonathn Van-Tam for this year's lectures. Lab News interviewed both Sharon Peacock and Catherine Noakes. The other four British experts are pictured above.

Professor Sharon Peacock spent lockdown researching ways to use sequencing technologies to provide actionable information for public health and patient care relating to SARS-COV-2. Her work fed into the COVID-19 Genomics UK Consortium (COG-UK) which delivered large-scale and rapid whole-genome virus sequencing to local NHS centres and the UK government. The virus genome data is combined with clinical and epidemiological datasets to inform UK public health interventions and policies.

“I am the director of COK-UK, which was formed in March 2020 in response to the pandemic,” said Sharon. “COG-UK is a pioneer in the use of large-scale, rapid whole-genome sequencing of SARS-CoV-2, the virus causing the COVID-19 pandemic, to understand viral transmission and evolution, and to inform public health responses and vaccine development. Throughout lockdown, many people in the consortium were working in the lab, generating essential genomes. Generating SARS-CoV-2 genomes has been instrumental in vaccine design, tracking variants of concern, tracking the emergence of variants with greater transmissibility and /or immune evasion.”

In a blog post published in December 2020, ‘A short history of the COVID-19 Genomics UK (COG-UK) Consortium’, Sharon describes the early days when rapidly rising COVID-19 case numbers prompting a series of hurried phone calls and emails led to a meeting between 20 pathogen genome experts. By the end of that first meeting, held on 11 March 2020 one week later, most of the objectives and framework for COG-UK had already been negotiated. Potential models capable of sequencing the COVID-19 genome were discussed and debated, a single model selected, pathway, workflow and governance described, and the outline of a funding proposal agreed.

The consortium was driven by the knowledge that the provision of genome data, associated sequencing methods and analysis tools would be a critical contribution in the national response to the exploding threat posed by COVID-19. Despite their expertise being in constant demand, the research consortium delivered a scientific proposal by Sunday 15 March. On 1 April 2020, the group was awarded a £20M award to develop a major research consortium.

“What happened next has been likened to assembling an aeroplane from its component parts while already in the process of taking off,” Sharon writes in her blog.

Within eight months, COG-UK had grown into a consortium of many hundreds of people, supporting 16 sequencing hubs distributed across the country. These hubs included the four Public Health Agencies (PHAs) and researchers from academic partners across the UK. Many other institutions also became essential to the COG-UK effort and hundreds of laboratory and business professionals across the country sacrificed time with loved ones to get the work done, most of whom worked on a voluntary basis.

While some funding was used to purchase equipment and remunerate staff, the vast majority ws used to meet the cost of sequencing (more than 137,000 SARS-CoV-2 genomes by December 2020 when Sharon wrote her blog). World-class expertise from within the consortium helped develop the bioinformatics infrastructure and tools necessary to meet the excessive volume of sequencing needed to provide a dataset large enough to provide the resolution needed to make genome surveillance a useful investigative tool, able to compare viral transmission, reveal patterns in cases, and spot potential intervention opportunities.

Sharon wrote, “Prior to SARS-CoV-2, the largest previous dataset for real-time genomic viral epidemiology during an epidemic was ~1500 genomes from the West African Ebola outbreak, which were sequenced over the course of 2014–2016. By comparison, COG-UK surpassed this total within the first month and has continued to push viral genome surveillance on to an entirely different scale ever since.”

Many analytical tools and sequencing methods were designed by COG-UK specifically for COVID-19 and will remain open access for the benefit of future research. COK-UK’s data is used by PHAs and researchers who provide interpretations based on phylogeny, modelling and other approaches that inform policy decisions. All data generated is rapidly accessible via MRC-CLIMB (the Cloud Infrastructure for Microbial Bioinformatics — funded by the UK’s Medical Research Council). COG-UK is now developing on-line courses, virtual classrooms and train the trainer courses on SARS-CoV-2 sequencing to support sequencing efforts elsewhere.

Sharon Peacock is Professor of Public Health and Microbiology in the Department of Medicine at the University of Cambridge, Chair of the COVID-19 Genomics UK (COG-UK) Consortium, and Non-Executive Director on the Board of Cambridge University Hospitals NHS Foundation trust cogconsortium.uk

Read our coverage on this year's Christmas lectures with Jonathan Van-Tam

Read our companion interview with Catherine Noakes and the Scientific Advisory Group for Emergencies (SAGE)