20 Apr 2021

What next for COG-UK?

Sharon Peacock

The COVID-19 Genomics UK (COG-UK) consortium entered its second year on 1 April 2021, supported by funding managed by UKRI. Here, we describe our plans for the next 12 months.

COG-UK is just over a year old. Looking back, it has exceeded expectations in terms of the breadth and depth of what has been delivered. A notable success has been defining the case for genomic epidemiology during the pandemic, leading the way internationally. Other achievements include generating >440,000 SARS-CoV-2 genomes for use by public health agencies; national and international collaboration; establishing the administration, legal framework and logistics for a consortium of over 500 members and associates from academia, clinical medicine and public health; and events, seminars, blogs and external reports.

Currently, COG-UK has two tracks of inter-related activity.

The first is research. The consortium has generated a large amount of impactful research on viral transmission and viral variants. Members have also undertaken applied research to improve sequencing efficiency and cost and have developed and released genome interpretation tools. Much of this has influenced public health interventions and policy decisions.

The second activity drives research, but also provides essential data to public health agencies. This is the acquisition of positive samples from people with COVID-19 and the generation of viral genome data of high quality. Initially funded in April 2020 by the COVID-19 rapid-research-response “fighting fund” from Her Majesty’s Treasury (established by Professor Chris Whitty and Sir Patrick Vallance) — and administered by the National Institute for Health Research (NIHR), UK Research and Innovation (UKRI), and the Wellcome Sanger Institute — since December 2020 sequencing has been funded by NHS Test and Trace.

This is a time to look ahead and plan for the future. Following a period of consultation with the COG-UK Steering Group, we have identified three research priorities for the coming 12 months.

Priority one will be to enhance our sequence data. We will create new linkages between viral genome data, human genome data, and detailed clinical datasets including ISARIC, CO-CIN, ONS, OpenSAFELY and data held in SAIL and the Scottish Safe Haven. Additional funds will also be made available to CLIMB, our Cloud Infrastructure for Microbial Bioinformatics.

Priority two will be to disperse residual funding from the UKRI award made in April 2020 through an internal funding scheme for consortium Principal Investigators, for research that addresses one or more of the COG-UK priorities. This will create additional value by capitalising on our wealth of resources and enhanced data linkage.

Priority three will focus on international collaborations. Collectively, COG-UK consortium members are already supporting numerous international collaborations. These include 18 collaborations with low and middle-income countries, and 10 further partner countries. We are developing plans to coordinate our response to international collaborations and requests for expert advice and training.

We are also working closely with public health agencies to work towards a staged handover of routine genome sequencing. These changes were anticipated and were within the original remit of COG-UK from its earliest days, providing the foundation of a lasting and sustainable legacy to the UK. We anticipate a handover by September 2021. During this time, COG-UK sites will be instrumental in providing ongoing knowledge transfer and training.

The start of the second year of the consortium is also a time to reflect on shaping our organisational culture. This will include further development of our Women in COG project. Activities will include a series of monthly lunchtime events, a webpage, and creating opportunities to highlight the role of women in science. We also aim to provide seminars on values and kindness in the workplace for the whole consortium.

At the end of a frantic year, we are gearing up for the next 12 months with plans that maintain our focus on what matters. Making the very best of our data, resources and funding cutting-edge research will provide new insights on the pandemic. Increasing our emphasis on global sequencing will support the international effort. Making careful plans to hand over what has become a world-class sequencing operation and giving a sustainable basis for pathogen sequencing (SARS-CoV-2 and future threats) will mean we have achieved a key founding objective.

And finally, our response to the pandemic has shifted from a sprint to a marathon. Thinking about the wider values to which the consortium aspires, and our ways of working, will help us to take the marathon in our stride.


COVID-19 Genomics UK (COG-UK)

The current COVID-19 pandemic, caused by SARS-CoV-2, represents a major threat to health. The COVID-19 Genomics UK (COG-UK) consortium has been created to deliver large-scale and rapid whole-genome virus sequencing to local NHS centres and the UK government.

Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative partnership of NHS organisations, the four Public Health Agencies of the UK, the Wellcome Sanger Institute and academic partners providing sequencing and analysis capacity. A full list of collaborators can be found here. Professor Peacock is also on a part-time secondment to PHE as Director of Science, where she focuses on the development of pathogen sequencing through COG-UK.

COG-UK was established in April 2020 supported by £20 million funding from the COVID-19 rapid-research-response “fighting fund” from Her Majesty’s Treasury (established by Professor Chris Whitty and Sir Patrick Vallance), and administered by the National Institute for Health Research (NIHR), UK Research and Innovation (UKRI), and the Wellcome Sanger Institute. The consortium was also backed by the Department of Health and Social Care’s Testing Innovation Fund on 16 November 2020 to facilitate the genome sequencing capacity needed to meet the increasing number of COVID-19 cases in the UK over the winter period.