By Emily May, Research Analyst, Deloitte Centre for Health Solutions
In March 2020, the UK government established the COVID-19 Genomics UK Consortium (COG-UK) with an initial remit to contribute to the UK’s response to the COVID-19 pandemic by sequencing the SARS-CoV-2 genomes, identifying new variants of the virus, and combining this with clinical information to inform public health actions and policy decisions.1 To mark its first anniversary we explore some of the critical breakthroughs arising from COG-UK’s genomics research and how this is paving the way for a future in which genomics applications are fully integrated into public health.
The importance of genomics in responding to the COVID-19 pandemic
This discovery and monitoring of virus variants enables prompt responses to the changing pandemic, informs vaccine development, and helps to assess the impact of interventions like social distancing and lockdowns. Furthermore, knowledge of a virus’ genome can enable clinicians to trial the use of medications that have been successful in treating other, similar viruses and provide crucial information in the race to develop a vaccine – for example, the novel mRNA based vaccines apply the SARS-CoV-2 knowledge in combination with existing genomic research on SARS and MERS.2 Continuous real-time surveillance of a pandemic can provides the necessary information to inform interventions along with potential vaccination modifications as new variants are discovered that are more infectious or resistant.
COG-UK’s partnership approach and the role played by genomic sequencing
COG-UK is a partnership organisation comprising NHS organisations, public health agencies, a number of key academic institutions and other institutions, supported by £20 million funding from the UK Department of Health and Social Care, UK Research and Innovation, and the Wellcome Sanger Institute. GOG-UK was also given rapid access to MRC CLIMB (Cloud Infrastructure for Microbial Bioinformatics), an established and readily accessible cloud bioinformatic infrastructure capable of handling large volumes of data and tools.3
One year on, COG-UK has led the development of novel analytical software, sharing methods and data globally, as well as providing expertise and evidence to the Medicines and Healthcare products Regulatory Agency (MHRA) and Scientific Advisory Group for Emergencies (SAGE). It has also published scores of scientific papers and as a result is recognised as a prominent voice on SARS-CoV-2 genomics worldwide4.
Currently COG-UK are sequencing some 8,000-10,000 SARS-CoV-2 genomes every week and aim to double this over the coming months. Prior to SARS-CoV-2, the largest previous dataset for real-time genomic viral epidemiology during an epidemic was ~1500 genomes from the West African Ebola outbreak, which were sequenced over the course of 2014–2016. COG-UK surpassed this within the first month and continues to push viral genome surveillance to an entirely different scale.5 GOG-UK considers its success is due in part to having an open science culture with willing partners having the shared values of transparency, open access data release, robust surveillance methods and a collaborative approach to working between public health, academic research and the NHS. But also, the fact is it acted quickly within a strong governance framework.6
Globally, between January 2020 and January 2021, more than 360,000 SARS-CoV-2 genomes have been sequenced and stored on the GISAID platform, a non-profit online database which plays a vital role in sharing viral genomes. The UK is among some 140 countries across a wide geographic distribution deriving sequences of SARS-COV-2. However, most countries have uploaded only a small number of sequences, the two exceptions being the UK and Denmark, which respectively account for 45 per cent and seven per cent of SARS-CoV-2 genomes on the GISAID database.7
Lessons to be learned from COVID-19 surveillance
Some of the traditional boundaries to data sharing and joint working have been removed during the pandemic enabling an unprecedented breadth and quality of collaborations to develop. For example, the swift access granted to COG-UK to access CLIMB (Cloud Infrastructure for Microbial Bioinformatics) enabled the Consortium to use this established bioinformatic infrastructure and render it capable of handling the volume of data and tools necessary.8
However, one of the issues we have raised in our Intelligent biopharma series of reports and The future unmasked: Predicting the future of healthcare and life sciences in 2025, is that access to the right skills and talent is a crucial challenge that needs to be addressed if the industry is to realise the benefits of our increased knowledge of science and the massive amounts of data, including genomics, and also real-world data, available today.9 The extent and scale of collaboration and cross fertilisation of experience that has been seen during the pandemic has helped address some of these skills challenges. Nevertheless, building on the experience of COG-UK, and the increase in collaborations more generally, developing a more diverse and digitally literate workforce, and embracing new ways of working, will be crucial in maintaining the progress seen from scientific advances.
Incorporating genomics capabilities into the future of public health
While the importance of having a strong genomics infrastructure in tackling the global pandemic is now firmly acknowledged, the role of genomics in medicine has been growing exponentially over the past few years. In particular, as highlighted in our report, The future unmasked: Predicting the future of healthcare and life sciences in 2025, genomic sequencing is well placed to play a crucial role in driving more predicative, preventative, personalised and participatory (4P) medicine. It is also important in empowering clinicians through new diagnostic and treatment paradigms.10
Moreover, if the NHS Long Term Plan’s vision for a more preventative, sustainable and affordable public health system is to be realised, genomics will continue to be important in helping to identify health risks and improve their health outcomes. Indeed, the application of genomic technologies to meet the commitments outlined in the NHS Long Term Plan has the potential to transform patients’ lives by, for example:
- enabling quicker diagnosis for patients with a rare disease (around 72 per cent of rare diseases are genetic11)
- reducing the likelihood of an adverse drug reaction through medication and intervention matching
- increasing the number of people surviving cancer each year due to accurate, early diagnosis and effective use of therapies.12
The availability of a strong genomic science base across the UK healthcare system and having the right expertise, tools and techniques developed through organisations such as Genomics England, the NHS Genomic Medicine Service and Matt Hancock’s bold aspiration to sequence five million genomes has been central to the success to date of genomics in the UK. We have now seen first-hand the benefits of COG-UK in informing the public health response to COVID-19 and the advantages of being able to bring together the different skills and talent from relevant organisations across the UK. Together, these developments which, in turn, have led to an improved understanding of science, individual’s susceptibility to disease, as well as vaccine discovery and development, should serve to consolidate the UK’s position as a leader in genomic healthcare.
2 How genomics is changing vaccines - Genomics Education Programme (hee.nhs.uk)
4 COG-UK Publications | COVID-19 Genomics UK Consortium (cogconsortium.uk)
7 d41586-021-00065-4.pdf (nature.com)
8 CLIMB project receives honours for supporting COG-UK alongside other computing teams | COVID-19 Genomics UK 9 Consortium (cogconsortium.uk)
9 Intelligent biopharma series
10 The future unmasked: Predicting the future of healthcare and life sciences in 2025
12 NHS Long Term Plan