The Quadram Institute’s key role providing world-leading pathogen genomics expertise as part of the COVID-19 Genomics UK (COG-UK) consortium has been cited in a new report.

An independent evaluation by the not-for-profit institute RAND Europe concludes that COG-UK made a significant and valuable contribution to the United Kingdom’s public health genomics landscape.

The new report concludes the COVID-19 Genomics UK (COG-UK) Consortium helped to:

• advance scientific knowledge about different variants of the SARS-CoV-2 virus
• inform key policy and public health decisions related to the COVID-19 pandemic
• inform medical innovation efforts

Researchers found that the consortium’s efforts to sequence and understand the diverse variants of the SARS-CoV-2 virus, which causes COVID-19, have been key to informing public health decision-making and efforts to control its spread.

The study evaluated the progress, evolution and impacts of COG-UK, a collaboration of experts in pathogen genomics established soon after the UK went into its first lockdown in March 2020. It includes 16 academic institutions, including the Quadram Institute, the four public health agencies of the UK, the Wellcome Sanger Institute, National Health Service (NHS) Trusts and Lighthouse Labs.

COG-UK received funding from the National Institute for Health Research, the Medical Research Council part of United Kingdom Research and Innovation (UKRI), Genome Research Limited (operating as the Wellcome Sanger Institute), the Testing Innovation Fund, and NHS Test and Trace.

The report highlights the key role Cloud Infrastructure for Microbial Bioinformatics (CLIMB) data and computing infrastructure held by public health partners was leveraged for COG-UK activities and has played a vital role in these efforts.

Funded by the MRC, CLIMB launched in 2016 as a shared computing infrastructure for the medical microbiology community. It is a collaboration between Warwick, Birmingham, Cardiff, Swansea, Bath and Leicester Universities, the MRC Unit the Gambia at the London School of Hygiene and Tropical Medicine, and the Quadram Institute on the Norwich Research Park.

During the evaluation period, COG-UK sequenced more than 800,000 SARS-CoV-2 genomes across the UK. The total is now nearing 2 million. Such sequencing data and associated research and analyses have helped identify variants of concern and increased knowledge about viral behaviour, transmissibility and spread, as well as the impact of diverse public health measures.

Dr Andrew Page, COG-UK principal investigator and CLIMB co-investigator at the Quadram Institute, said: “At the Quadram we were well placed with extensive genomics expertise with pathogens, excellent bioinformatics, and the cloud computing infrastructure (CLIMB) to respond in March 2020 when the COVID-19 pandemic hit.

“We are very proud of the role the Quadram Institute plays in tracking and understanding the spread of the SARS-CoV-2 virus in our hospitals and communities. The collective COG-UK experience and expertise should ideally stand us in good stead to maintain a genomic surveillance system that can act as an early warning system to protect public health from future threats.”

“The work of experts in the field of pathogen genomics that are part of COG-UK has underpinned key sequencing and research efforts,” said Sonja Marjanovic, lead author and director of healthcare innovation at RAND Europe. “This helped policymakers understand SARS-CoV-2 behaviour better, such as links between new variants and disease severity, and also informed policies related to border control, travel, lockdown and social distancing across the four nations of the UK.”

The study further found that COG-UK has provided important inputs into medical innovation in response to the pandemic through its data and analytics. For example, the consortium’s open sharing of data and insights have helped in efforts to understand and evaluate how well vaccines work against specific variants. The collaboration is also working with various groups to identify and characterise variants of concern in a way that could inform the development of the next generation of vaccines.

The report also concludes that efforts should be made to ensure that the expertise, experiences, and relationships that have developed are not lost. A public health genomics ecosystem should be built with pathogen-sequencing networks at its core. Achieving this would depend on the abilities of decision makers in the public health system to transition from an emergency response operation to a legacy of sustained impact.

Professor Sharon Peacock, executive director and chair of COG-UK, said: “Commissioning an independent evaluation of COG-UK was vital both in terms of accountability for the public money invested in the consortium and also in ensuring that we learn from what worked, and what could have been improved, to maximise the legacy of the endeavour and achievement of all involved.”