20 Nov 2020

Priority research questions for COG-UK

Sharon Peacock and Ravi Gupta

Priority Research Questions for COG-UK

The rapid expansion in our scientific understanding of COVID-19 makes it essential to revisit our research priorities in COG-UK on a regular basis. A recent exercise has provided an impetus to refresh our thinking.

The COVID-19 Genomics UK (COG-UK) Consortium is just eight months old. In this short space of time, COG-UK has grown into a substantial network of people across the UK who are committed to working as a team to understand how we can derive the greatest benefit from large scale SARS-CoV-2 sequencing.

Our understanding of COVID-19 infection in people and the causative virus has grown exponentially in the last few months and maintaining an up-to-date view on research questions that COG-UK should prioritise is challenging. But a recent exercise has given us the opportunity to do just that.

Along with other sub-groups reporting into the Scientific Advisory Group for Emergencies (SAGE), we were recently asked by the Government Office for Science (GO Science) to provide a list of research questions that we as a Consortium considered to be important.

To address this, we used a Google survey to gather information from Consortium members, who were asked about priority research questions in three areas: those that improved our understanding of SARS-CoV-2 evolution, biology and disease pathogenesis; priority questions for surveillance, epidemiology and infection management; and questions that did not fall neatly into these two categories.

We received 67 questions/statements, which we grouped into seven categories (see right). The full list can be downloaded here.

Perhaps predictably, many of the questions that were proposed are already being addressed by the Consortium.

Topics of questions included the genomic evaluation of SARS-CoV-2 transmission in particular settings. We have just completed a rapid review of all the internationally available studies on genomics applied to COVID-19 in residents and staff of long-term care facilities. This has included a synthesis of key findings and recommendations for the use of future genome sequencing. We are taking the same approach to draw together data on all genomic studies on infections acquired in hospitals, and in universities.

Our survey highlighted genetic mutations in SARS-CoV-2 as a major area for research. This is because these can result in changes in the way that the virus can behave. For example, they could alter how much the virus transmits within the population, or the severity of disease in people who develop COVID-19. But perhaps of most concern in the longer term, genetic mutations may emerge that make vaccines less effective. We are developing the technology and capabilities to track and report mutations as they arise, predict their biological importance, and link this information to clinical/epidemiological data. We also have mechanisms in place to rapidly pass on this knowledge to laboratory scientists who can test the biological importance of mutations of hypothetical concern.

After sequencing more than 110,000 SARS-CoV-2 viruses, COG-UK is well-placed to undertake in-depth genetic analyses on a wide range of questions, providing an unparalleled level of insight that is unlikely to be realised through short-term observations at the coal face of the COVID-19 response.

But we recognise two issues. First, we must prioritise our efforts so that they focus on the most important questions for public health in the short, medium and longer term. Second, we must not rest in our efforts to integrate our sequencing capabilities, data architecture, and analytical capabilities into the public health response, providing maximum support to the four UK Public Health Agencies.

The data that we generate will be of vital importance as we plan ahead for the possibility of third and subsequent COVID-19 waves. Throughout, we will maintain a commitment to generate and analyse genomic data for Public Health Agencies, so that we can influence practice and policy, and support interventions to limit the impact of COVID-19 on people’s lives.


COVID-19 Genomics UK (COG-UK)

The current COVID-19 pandemic, caused by the SARS-CoV-2 virus, 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 twelve academic partners providing sequencing and analysis capacity. A full list of collaborators can be found here:

COG-UK was established in March 2020 supported by £20 million funding from the UK Department of Health and Social Care (DHSC), UK Research and Innovation (UKRI) and the Wellcome Sanger Institute, administered by UK Research and Innovation. For more information, visit:

Ravi Gupta is Professor of Clinical Microbiology and a Wellcome Senior Fellow in Clinical Science at the University of Cambridge. He has a special interest in viral evolution and drug resistance.

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.