The UK’s Department for Health and Social Care Testing Innovation Fund has backed the Wellcome Sanger Institute and the COVID-19 Genomics UK (COG-UK) Consortium in expanding whole genome sequencing of positive SARS-CoV-2 virus samples to map how COVID-19 spreads and evolves. The £12.2M funding will allow the Sanger Institute to contribution to building a national real-time genomic surveillance system of COVID-19 to help tackle the pandemic.
As part of the genomic surveillance system, researchers at the Wellcome Sanger Institute are creating surveillance software to help public health authorities detect and respond to local outbreaks faster, monitor for viral mutations associated with escape from vaccines once they are deployed, and support the diverse science and public health aims of the COG-UK Consortium.
Viral genome sequencing data generated across the COG-UK network, including the Wellcome Sanger Institute, is integrated with data from the four UK Public Health Agencies and NHS Test and Trace to help understand outbreaks and strengthen infection control measures.
Since March 2020, COG-UK has generated and made publicly available more than 100,000 SARS-CoV-2 genomes, making up over 45% of the global total. This unprecedented effort has not been achieved previously for any pathogen, anywhere in the world.
The Sanger Institute has been using its funding from Wellcome for its SARS-CoV-2 sequencing and is the largest genome sequencing hub within the COG-UK consortium. As part of the effort, the Institute rapidly established new high-throughput sequencing pipelines and developed supporting software to sequence and analyse positive SARS-CoV-2 virus samples.
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 current second wave of COVID-19 cases in the UK and throughout Europe means that it is more important than ever that genomic tracking of the virus is supported for the long term. The genomic data will be used in genomic surveillance of the virus as new vaccines are deployed, to determine whether the virus evolves to escape them.
Professor Sir Mike Stratton, Director of the Wellcome Sanger Institute, said: “Our mission is to build a national real-time genomic surveillance system for COVID-19. Using genomics to track the SARS-CoV-2 virus in real time will help public health authorities detect and respond to local outbreaks faster and show us how the virus responds when new vaccines are introduced. This new genomic surveillance system will only be possible through sequencing viral genomes at huge scale, thanks to the monumental efforts of scientists at the Wellcome Sanger Institute and across the whole COG-UK network.”
Professor Sharon Peacock, who is the Director of the COVID-19 Genomics UK (COG-UK) Consortium, 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 Wellcome Sanger Institute, with COG-UK, the four UK Public Health Agencies and other academic partners 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.