COG-UK consortium members have made major contributions to the pandemic response through the generation of SARS-CoV-2 genomes, the development of sequencing methods and tools that interpret the genomes, and data linkage and analysis. But there is a wealth of research and development still to do before the benefits from these data are fully realised. Here, we describe a new initiative that begins to address this need.

COG-UK is enhancing its research portfolio by awarding up to £40,000 to 12 of its consortium partners. This funding comes from the original award that created COG-UK on 1st April 2020, and is now available because of cost-savings we made through improvements in logistics and sequencing methods pioneered by consortium members during the pandemic. The 12 institutions include 10 universities across the UK and two Public Health Agencies. Research is focused on variants, data linkage and quality, and planning for future pandemics.

SARS-CoV-2 genomic surveillance depends on high quality sequence data that has been through stringent quality-control steps. This is relatively straightforward to achieve in established sequencing laboratories. But in laboratories that are just beginning to establish SARS-CoV-2 genome sequencing, tools to support this could have considerable utility. This is recognised in a project from the Quadram Institute, which will develop an online resource for SARS-CoV-2 genome Quality Control, improving data quality over and above standard QC processes. The tool can be repurposed for other pathogens which is a great future benefit.

The emergence of SARS-CoV-2 variants with the potential to transmit more readily and/or circumvent immunity represents a substantial challenge to on-going pandemic control efforts. Five complementary projects focus on this area. The MRC-University of Glasgow Centre for Virus Research aims to conduct an observational study to monitor vaccine response in the Scottish population following exposure to SARS-CoV-2 variants. Northumbria University will develop new computational methods for Variant of Concern detection and Variant of Interest classification. University College London will use a genomic approach to identify potential reservoirs for the emergence of SARS-CoV-2 variants of concern. The University of Sheffield will examine the impact of SARS-CoV-2 mutations on recognition by a specific type of immune cell (T-cells). Queen’s University Belfast will focus on SARS-CoV-2 genomic variation within individuals, whether owing to mutations within a single infecting viral lineage or co-infection with multiple lineages.

SARS-CoV-2 genomic surveillance depends on high quality sequence data that has been through stringent quality-control steps. This is relatively straightforward to achieve in established sequencing laboratories. But in laboratories that are just beginning to establish SARS-CoV-2 genome sequencing, tools to support this could have considerable utility.

This is recognised in a project from the Quadram Institute, which will develop an online resource for SARS-CoV-2 genome Quality Control, improving data quality over and above standard QC processes. The tool can be repurposed for other pathogens which is a great future benefit.

Several projects will improve linkage and integration of genomes with metadata to enhance the pandemic response. Public Health Scotland aims to further improve data linkage and data flows, and Northern Ireland will further improve the integration of genomes and contract tracing data for outbreak control. The University of Liverpool aims to link data from COG-UK and Cheshire and Merseyside’s Combined Intelligence for Public Health Action (CIPHA) dashboard. The University of Exeter plans to implement models to infer transmission directionality during hospital-associated infection.

Several projects will link complex datasets with a view to future therapeutics for SARS-CoV-2 or the next pandemic. The University of Cambridge will link SARS-CoV-2 sequence data with human genomes generated by our collaborators, GenOMICC. This could shed new insights on the basis of disease and how to treat it. A project from the University of Oxford recognises the need to move from pandemic response to pandemic preparedness through the integration of diagnostics, rapid genotyping and whole genome sequencing of SARS-CoV-2 and other respiratory pathogens.

This broad range of applied research will help COG-UK’s genome data yield even greater benefits to the COVID-19 response in the UK and beyond.

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 like the Quadram Institute 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.