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Whole genome sequencing to identify transmission clusters and variants of concern

The COVID-19 Genomics UK Consortium conducted large-scale, rapid whole-genome sequencing of SARS-CoV-2, the virus causing COVID-19. The data generated provided critical information on transmission clusters occurring in the workplace, pubs, clubs and schools. The work is estimated to have saved thousands of lives.

Joint working across the eight organisations that make up our Academic Health Science Centre has been central to delivering a more effective response to the challenges of the pandemic. Here we show how collaboration among our member organisations, building on relationships and networks fostered by the AHSC, has enabled the rapid translation of health research into practice as part of the COVID response.

Challenge

With COVID-19 spreading rapidly across the UK in March 2020, it was important to understand how the virus was being transmitted and identify new variants. This knowledge could then be used to inform public health planning and healthcare activities.

A rapid response

The COVID-19 Genomics UK Consortium (COG-UK) received funding from UKRI, the Wellcome Sanger Institute and the Department of Health and Social Care to conduct large-scale, rapid whole-genome sequencing of SARS-CoV-2, the virus causing COVID-19, to understand viral transmission and evolution, and inform public health responses and vaccine development.

The sequencing carried out by COG-UK was run by the Pathogens Genomics Unit (PGU) at UCL, who provided support to the Royal Free London NHS Foundation Trust and Barts Health NHS Trust as well as others around London. The relationships and networks supported and fostered by UCLPartners Academic Health Science Centre were essential to enable these working relationships.

COG-UK sequenced up to 50,000 samples per week.

Impact

The data generated provided critical information on transmission clusters occurring in the workplace, pubs, clubs and schools. Through sequence surveillance it also identified potential variants of concern. Both the discovery of the Alpha variant and the realisation that the Delta variant was present and rapidly growing directly influenced UK policy in terms of lockdown restrictions and accelerated vaccinations. The results are estimated to have saved thousands of lives.