£12.2m funding will help Cambridge-led COG-UK expand Covid-19 genomic surveillance
A £12.2million injection of government funding will enable a Cambridge-led consortium to continue mapping the spread and evolution of Covid-19 by expanding whole genome sequencing of virus samples.
The Covid-19 Genomics UK (COG-UK) Consortium has already confirmed a grim milestone this month: it has now sequenced more than 100,000 SARS-CoV-2 genomes, meaning the genetic information of the virus causing Covid-19 infections in 100,000 people has been fully decoded.
The variations found from this extraordinary real-time analysis - unprecedented in its scale and speed - is being used in investigations of outbreaks to reveal patterns between individual cases.
The work can help identify opportunities for intervention and, crucially, enable the monitoring of mutations in the virus that could impact on the effectiveness of treatments or vaccines that target specific components of its structure.
The consortium is spearheaded by the Wellcome Sanger Institute at Hinxton and the University of Cambridge, and also features NHS organisations, the four UK public health agencies and 11 other academic partners.
Consortium director Prof Sharon Peacock, who is 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.”
Hundreds of people have been involved in sequencing the 100,000-plus genomes in the last eight months. The work represents 45 per cent of the entire worldwide sequencing effort for this virus and is on a scale never achieved before for any pathogen.
COG-UK notes: “Prior to SARS-CoV-2, the largest previous dataset for real-time genomic viral epidemiology during an epidemic was about 1,500 genomes from the West African Ebola outbreak, which were sequenced over the course of 2014-2016. By comparison, COG-UK surpassed this total within the first month and has continued to push viral genome surveillance on to an entirely different scale ever since.”
A central database has been built, and cutting-edge analytical methodology and data pipelines developed. The results have been made publicly available and enabled important insights into the spread and evolution of the virus at local, regional, national and international scales.
The consortium has also led the development of analytical software to define viral lineages.
The additional funding follows the £20million awarded when COG-UK was set up in March and will help the consortium grow the genomic surveillance effort amid increasing numbers of Covid-19 cases in the UK.
The genomic data will be integrated within the four UK public health agencies and utilised by NHS Test and Trace to help understand outbreaks and strengthen infection control measures.
Linking the data with epidemiological, clinical and contact tracing records nationally will give us a better understanding of risk factors and help us answer questions about immunity.