On Tuesday 18th May, COG-UK chair and director Professor Sharon Peacock participated in a technical briefing co-hosted by the Permanent Missions of the United Kingdom and of Lebanon to the United Nations in New York, and the World Health Organisation.
Titled “COVID-19 genome sequencing: How can we protect the world from new variants of concern?”, the briefing brought together an international panel to discuss how a coordinated and rapid response might best tackle existing and emerging SARS-CoV-2 variants of concern.
Speakers at the briefing included H.E. Ambassador Jonathan Allen (Deputy Permanent Representative of the United Kingdom to the United Nations), Dr Soumya Swaminathan (Chief Scientist, World Health Organisation), Professor Sharon Peacock (Executive Director and Chair, COG-UK), H.E. Ambassador Amal Mudallali (Permanent Representative of Lebanon to the United Nations) and Professor Sima Tokajian (Professor of Microbial Genomics, Lebanese American University).
Below is the script of the speech delivered by Professor Sharon Peacock during this briefing:
Early during the COVID-19 pandemic, we recognised the potential value for rapid and large-scale genome sequencing, for research purposes and to inform public health responses and vaccine development.
We knew that variants of the virus would begin to arise, and as such we sought to establish a system that generated data for public health agencies to use in identifying and monitoring the emergence, introduction and transmission of variants in the UK.
After obtaining swift funding from the UK government’s COVID-19 “fighting fund”, and the Wellcome Sanger Institute, COG-UK was established in March 2020.
COG-UK is an innovative partnership of academic institutions, the four public health agencies of the United Kingdom, together with NHS and high-throughput national testing laboratories.
The consortium established a hub and spoke model for distributed sequencing, with centrally organised logistics operations for moving samples to the appropriate site.
We use the UKs Cloud Infrastructure for Microbial Bioinformatics (or CLIMB), which is funded by the Medical Research Council since 2014, to house a custom data management system.
And we have also adapted or developed the necessary software and analysis tools to support large-scale genomic efforts.
Hundreds of consortium members have contributed to these efforts, many of whom have given up work on other projects to volunteer their time and expertise, often under challenging personal circumstances.
Collectively this has enabled COG-UK to sequence more than 470 thousand SARS-CoV-2 genomes, which represents around 10% of the positive cases in the UK overall.
Underpinning all our activities have been our shared values of transparency, open access data release and collaborative working between public health agencies, academic researchers and the NHS.
The genome sequences and associated metadata have been used to investigate patterns of introductions and transmission at local, regional, national and international levels.
They have also been used to monitor the evolution of the virus and to identify new variants as they emerge.
Our genome data is also being used to enhance the UKs contact tracing and surge testing.
Importantly, the genome sequences of variants with altered biological properties – known as variants of concern, such as the B.1.351 variant first detected in South Africa – are being used to direct the development of vaccine updates to ensure the continued efficacy of our vaccination programme.
With the ongoing emergence of variants of concern, increasing global capacity for rapid sequencing and analysis has become an urgent international priority.
Definition as a variant of concern is based on a virus exhibiting altered properties as compared to the virus first identified in Wuhan.
These properties include increased transmission potential, increased severity or course of clinical infection, or the potential to evade natural or vaccine-induced immunity.
Despite disease rates remaining high at a global level, only four variants of concern have currently been formally designated.
In addition to these four, there are a significant number of other variants are under investigation, and more will emerge over time.
However, with low sequencing coverage for positive cases being the norm in most countries, many potential variants of concern are likely to go entirely unnoticed.
At COG-UK, we believe that understanding the circumstances under which new variants arise, and working to limit emergence and prevent transmission, should be a key priority for the global pandemic response.
As such, rapid genome sequencing should be viewed as a vital public health tool.
But sequencing is not an end goal in itself.
It needs to be aligned with a combination of effective vaccines and non-pharmaceutical interventions.
Sequencing should provide actionable information.
We need to strengthen pathways connecting genomics with modelling and laboratory experiments, to determine whether a variant under investigation should be classified as a variant of concern and prioritised for a suitable response.
At the moment, these pathways are particularly slow, and it can take months to determine if designation as a variant of concern is warranted.
Only through the international generation of large-scale sequencing data, will we be able to comprehensively monitor for variants whose increasing prevalence suggest cause for concern.
One of the most important lessons learned through our experience with COG-UK to date has been the benefits of acting with urgency.
COG-UK focussed on pace over perfection.
We began sequencing before the ink was dry on our consortium agreement.
Despite many challenges, our various partners and members learned how to interact productively with each other as we went along.
Pipelines for handling samples and data were rapidly established and then adapted as we sought to increase sample volume and speed from swab to sequence over time.
Importantly, our focus on sequencing at pace and scale meant that when B.1.1.7 – the variant of concern first detected in Kent – began spreading rapidly in the UK in late 2020, we were already generating the data that could be used to identify and track it.
In short, the emergence of the B.1.1.7 variant validated our approach.
Without the genome sequence data generated by COG-UK, it would not have been possible to observe and track this and other variants of concern.
Moving forward, the lesson of pace over perfection can be equally applicable at an international level.
We suggest that COG-UK could be used as a paradigm for how rapid action can provide vital public health information in a timeframe relevant to informing worldwide pandemic responses.
We identify two distinct needs.
For the long term, there is a need for a fully-integrated, trusted international system, whereby member states can work with WHO and regional health organisations to generate and analyse genomic data for microbial pathogens causing future pandemics.
However, we cannot delay our efforts while such a system is established.
With the rate of infection and fatality remaining high at the global level, getting any sequence information is an urgent priority and can help us to understand where variants are emerging, what they are and how we need to respond.
Unfortunately, globally we have sequenced less that 0.5% of reported positive cases over the past 30 days, with the vast majority of these sequences coming from just a handful of countries.
We therefore lack an understanding of the variants responsible for the over-whelming majority of infections worldwide.
Increased co-operation between countries is needed to establish a globally distributed model for SARS-CoV-2 sequencing, to utilise available capacity more effectively, and to share genome data in a rapid and open manner.
Large-scale sequencing of a high percentage of positive cases in most countries with ongoing pandemic waves is not going to be feasible in the short term.
However, through international cooperation, it should be possible to undertake unbiased random sampling in most countries.
This will provide a good sense of the variants that are prevalent in a given country and enable us to monitor for the emergence of new variants of concern.
Discussions on precisely how to mobilize the international community to establish such a distributed sequencing capability should be given high priority.
Attention should be given to where capacity currently exists, where it could be expanded, and how best to support countries with little or no genomics infrastructure.
Importantly, any mechanisms put in place will need to ensure equitable data use and appropriate recognition for those gathering samples and generating data in all countries.
Helping to lead the way towards this goal, COG-UK members have been supporting sequencing efforts in 28 countries, including 18 low- and middle-income countries.
We are also establishing freely available online training modules and developing a train-the-trainer approach to make our support for international genome sequencing efforts more sustainable.
This work, and that of many others in the global pathogen genomics community, can provide a springboard from which to accelerate genome sequencing of SARS-COV-2 at the global level.
We urge the international community to consider adopting the COG-UK mindset of rapid action – to move now, and move at pace.
To undertake the short-term rapid action needed to identify variants as they arise around the world that will keep our vaccines working.
And at the same time begin planning for a long-term global pathogen genomic observatory, that can serve the world in flagging new and urgent threats going forward.
Thank you for your time.
COVID-19 Genomics UK (COG-UK)
The current COVID-19 pandemic, caused by SARS-CoV-2, 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 academic partners providing sequencing and analysis capacity. A full list of collaborators can be found here. Professor Peacock is also on a part-time secondment to PHE as Director of Science, where she focuses on the development of pathogen sequencing through COG-UK.
COG-UK was established in April 2020 supported by £20 million funding from the COVID-19 rapid-research-response “fighting fund” from Her Majesty’s Treasury (established by Professor Chris Whitty and Sir Patrick Vallance), and administered by the National Institute for Health Research (NIHR), UK Research and Innovation (UKRI), and the Wellcome Sanger Institute. The consortium was also backed by the Department of Health and Social Care’s Testing Innovation Fund on 16 November 2020 to facilitate the genome sequencing capacity needed to meet the increasing number of COVID-19 cases in the UK over the winter period.