Cambridge-led SARS-CoV-2 genomic surveillance consortium receives 12.2 million

Transmission electron micrograph of SARS-CoV-2 virus particles, isolated from a

Transmission electron micrograph of SARS-CoV-2 virus particles, isolated from a patient Credit: NIH Image Gallery

The COVID-19 Genomics UK (COG-UK) Consortium has been backed by the Department for Health and Social Care Testing Innovation Fund to expand whole genome sequencing of positive SARS-CoV-2 virus samples to map how COVID-19 spreads and evolves. The 12.2M funding will facilitate the genome sequencing capacity needed to meet the increasing numbers of COVID-19 cases expected in the UK this winter.


To fully understand the spread and evolution of the SARS-CoV-2 virus, we must sequence and analyse the viral genomes

Sharon Peacock


The additional investment will enable COG-UK to grow and strengthen current genomic surveillance efforts spearheaded by the Wellcome Sanger Institute and the University of Cambridge, together with the four UK Public Health Agencies and other COG-UK partners, with the aim of increasing sequencing capacity across the national network and reducing turnaround time from patient sample to genome sequence.

The viral genome sequencing data will be integrated within the four UK Public Health Agencies & NHS Test and Trace to help understand outbreaks and strengthen infection control measures. Integrating real-time viral genomic data into outbreaks investigations identifies patterns linking individual cases and can reveal otherwise unidentifiable opportunities for intervention. Viral genome sequencing also enables monitoring of the evolution of the virus for mutations that may impact on the efficacy of vaccines.

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, represents a major threat to health. The COG-UK Consortium was created to deliver large-scale and rapid whole-genome virus sequencing to local NHS centres, Public Health Agencies and the UK government.

Led by Professor Sharon Peacock of the University of Cambridge & Director Of Science at Public Health England, COG-UK is an innovative partnership of NHS organisations, the four Public Health Agencies of the UK, the Wellcome Sanger Institute and 12 academic institutions from across the UK providing world leading expertise in SARS-CoV-2 genomics and supporting sequencing and analysis capacity nationwide.

Since its launch in March 2020, COG-UK has generated and made publicly available more than 100,000 SARS-CoV-2 genomes, making up over 45 per cent of the global total. This unprecedented effort has not been achieved previously for any pathogen, anywhere in the world.

COG-UK researchers have built a central database and developed cutting-edge analytical methodology and data pipelines for SARS-CoV-2 genomics. COG-UK has led the development of analytical software to define viral lineages and shares methods globally.

Collectively, these data and tools have provided important scientific insights into the spread and evolution of the virus, at local, regional, national and international scales.

However, the steadily rising numbers of cases in the UK requires a prompt increase in the national SARS-CoV-2 genome sequencing capacity, to ensure that the benefits of using genome sequence data can be realised in a rapid and robust manner.

Professor Sharon Peacock, who is the Director of COG-UK, Professor of Public Health and Microbiology at the University of Cambridge and a Director Of Science (Pathogen Genomics) at Public Health England, said: "To fully understand the spread and evolution of the SARS-CoV-2 virus, we must sequence and analyse the viral genomes. The pattern of accumulation of mutations in the genomes enables us to determine the relatedness of virus samples and define viral lineages in order to understand whether local outbreaks are caused by transmission of single or multiple viral lineages. Analysis of viral genome sequences also allow us to monitor the evolution of SARS-CoV-2 and assess whether specific mutations influence transmission, disease severity, or the impact of interventions such as vaccines."

The four UK Public Health Agencies and COG-UK are working to link SARS-CoV-2 genome data with epidemiological, clinical and contact tracing records nationally.

This will help establish a comprehensive national dataset linking viral sequencing with host genomics, immunology, clinical outcomes and risk factors.


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