What next for COG-UK following new funding of £12.2 million?
The news that the COVID-19 Genomics UK (COG-UK) Consortium has been backed by the Department for Health and Social Care Testing Innovation Fund with a substantial award of £12.2M means that change is afoot. Here, I write about how the funds will be used, and what it means for COG-UK.
The new award to the COVID-19 Genomics UK (COG-UK) Consortium of £12.2M from the Department of Health and Social Care Testing Innovation Fund is both timely and welcome and is set to take the work started by the Consortium to the next stage.
COG-UK researchers have already achieved a great deal following an earlier research award. They 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 and data globally. Collectively, these have provided important scientific insights into the spread and evolution of the virus at local, regional, national and international scales.
Our story to date demonstrates that we already straddle the gap between research and service delivery. We develop technologies that help others to sequence and interpret viral genomes. We provide extensive operational ‘glue’ to help the network function effectively, and work with partners such as Lighthouse Laboratories. We provide sequence data at scale to Public Health Agencies. So, what next for the Consortium?
From my perspective, we are entering a period of transition. Our research will stay as strong and important to us as ever, and the original COG-UK remit with continue unabated. The world-leading expertise of the Consortium means that we are ideally placed to bring the best scientific enquiry to one of the largest single bodies of viral sequence data in the world. But we increasingly also inhabit the space between our roots as a research network, and a future in which the delivery of our work becomes fully routine and is delivered by relevant national organisations.
The next few months will see us expanding our operations. Currently, we are sequencing around 8,000–10,000 SARS-CoV-2 genomes every week, but we want to double this in the coming months. We will also strengthen our infrastructure, which includes investing further in our data repository (CLIMB), and the purchase of new equipment so that we can sequence more effectively. For example, we will invest in equipment at PHE Colindale to support higher numbers of viruses to be sequenced with a shorter turnaround time.
More genomes will increase our ability to provide greater sequence data to Public Health Agencies, which can be linked back to people from whom the virus was detected. Genetic changes in the sequence that are accumulating over time as the virus evolves means that increasingly, viruses have differences in their genetic code that tell them apart. Comparison of the sequences of two viruses can then help to unravel whether a cluster of people with COVID-19 were linked (or not). This can lead to changes to decisions over interventions.
We also want to increase our chances of early detection of mutations in the virus that could be important for human health, either because they may be associated with altered ability to cause (for example, cause more severe disease) or be less susceptible to vaccines.
We will put more funding into staff. Our efforts have been carried by a large body of volunteers. Many of our senior scientists are volunteers, and this is not sustainable. Getting the leadership right will also be of upmost importance.
Sequencing can be a major asset to centralised Public Health Agencies that track the pandemic over time. It is also important to have a single unified effort to track mutations as they emerge. This is connected to a wider effort to then pass this information onto experimental scientists who can test whether the mutation changes the behaviour of the virus, and Public Health Agencies to allow tracking and interventions as necessary.
The real power of sequence data generated for outbreak investigations lies in its potential to drive impact at a local and regional level, when placed into the hands of local and regional professionals. For this reason, we are looking at ways of aligning our existing devolved sequencing capabilities with the more effective delivery of information to local professionals who will use the information for ‘boots on the ground’ action. This will necessitate the development of a more formalised regional COG-UK genomic leadership, who are well placed to create vital local links.
This new award also comes with funding to help us develop a vision for the future. What does the United Kingdom want and need in relation to distributed pathogen sequencing? Who will deliver this? What else might it be used for? From my perspective, the ideal outcome would be a future in which pathogen genomic research and public health service delivery are inseparable. The benefits to public health that can result is evident in the Robert Koch Institute in Germany and elsewhere. We have the opportunity to replicate this model for pathogen genomics.
In the meantime, I look forward to the next few months of transition, when we will be working at pace to increase our capabilities, with a network of people that surprise me every day by their dedication, innovation and spirit of cooperation.
COVID-19 Genomics UK (COG-UK)
The current COVID-19 pandemic, caused by the SARS-CoV-2 virus, represents a major threat to health. The COVID-19 Genomics UK (COG-UK) consortium has been created to deliver large-scale and rapid whole-genome virus sequencing to local NHS centres and the UK government.
Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative partnership of NHS organisations, the four Public Health Agencies of the UK, the Wellcome Sanger Institute and twelve academic partners providing sequencing and analysis capacity. A full list of collaborators can be found here: https://www.cogconsortium.uk/about/
COG-UK was established in March 2020 supported by £20 million funding from the UK Department of Health and Social Care (DHSC), UK Research and Innovation (UKRI) and the Wellcome Sanger Institute, administered by UK Research and Innovation. For more information, visit: https://www.cogconsortium.uk
COVID-19 in care homes — what have we learned from genome sequencing?
Read COG-UK partner Quadram Institute’s explainer blog on the latest findings of how the SARS-CoV-2 virus spreads within care homes.
The value of large-scale coordinated sequencing activities to understand a pandemic in real-time
In recent work from COG-UK consortium investigators, Erik Volz and colleagues investigated the D614G mutation in the population by using more than 25,000 viral genomes that have been sequenced in the UK over a period between February and June 2020 in order to understand the pandemic in real-time.
Priority Research Questions for COG-UK
Professor Sharon Peacock, COG-UK Director, and Professor Ravi Gupta, Wellcome Senior Fellow in Clinical Science at the University of Cambridge, discuss COG-UK's research priorities and how advancements in our scientific understanding of COVID-19 have refreshed the Consortium's thinking.