Setting up COG-UK

Figure 4.1. Worldwide distribution of COVID-19 cases worldwide, 9 March 2020. Credit: WHO, Distribution of cases 9 March 2020 (COVID-19).

Sharon Peacock gets the ball rolling

In the midst of the rising numbers of COVID-19 cases around the world, one person watching the events was Professor Sharon Peacock at the University of Cambridge. At the start of the pandemic Peacock wore a number of different hats. This placed her in a unique position to see what was happening. Firstly, she was director of the National Infection Service at Public Health England (PHE). As part of this role she was receiving regular reports from the incident management team within PHE that was closely tracking the outbreak in China and beyond. In addition, she became temporarily resident at the Department of Health and Social Care, to facilitate effective communication between the Department and the PHE response. By mid-Feburary Peacock was also regularly attending SAGE meetings (Peacock transcript).

Based on this work, towards the end of February 2020, Peacock began discussing the possibility of leveraging genome sequencing for tracking the SARS-CoV-2 virus with Sir Patrick Vallance, the UK government's Chief Scientific Advisor. The two of them first came into contact through SAGE meetings (Peacock transcript). Looking back at how her discussions started with Vallance, Peacock is 'surprised at how much foresight we had because at the time there were very few diagnosed cases. But we agreed that we needed to establish genomics to start to track the evolution of the virus, as mutations in the genome were inevitable'. She continues, 'If you're a virologist, a microbiologist, or other type of biologist, you appreciate that this is what the virus is going to do. So, I think it was really a combination of the understanding that viruses will evolve over time, and that if it's going to be around for any length of time we needed to set the system up so that we were ready to track that' (Peacock transcript)

The conversation with Vallance helped Peacock crystallise her thinking about where the country had the capabilities to do genomics. That included 'method development, protocol development, developing analysis pipelines for the analysis of the data.' She also knew that it would need 'to reach beyond the public health agencies.' At the time there was never any thought in Peacock's mind that 'COG-UK was going to become a permanent and sustainable long term solution – it was an emergency response.' Instead, what she was aiming to do was 'to bring together academia with the public health agencies to ensure that they had access to and used the best possible minds in the country in relation to genomics expertise' (Peacock transcript).

At the same time as talking to Vallance, Peacock reached out to other pathogen genome experts to gauge their opinion. On 4th March 2020 she sent out a one-line email saying 'can you ring me this afternoon' to five of her close contacts: Professor Julian Parkhill, former head of Pathogen Genomics at the Wellcome Sanger Institute; Professor Judith Breuer, a virologist at University College London; Professor Nick Loman, an expert in rapid genome sequencing for infectious diseases in low-income settings at the University of Birmingham University; Professor David Aanensen, a genomic surveillance specialist at the Big Data Institute at Oxford University; and Dr Richard Myers, head of the bioinformatics unit at PHE. All of them were people that Peacock had collaborated with in the past and whose opinion she trusted. Although not specified in the email, what was in the back of Peacock's mind was she wanted them to answer the question 'do you think that viral evolution is going to be such that we need to set up a sequencing capacity to track it'. Another reason she wanted to talk to them was 'because I was worried that I might be catastrophising the situation and scare mongering…. What I was doing was in a sense checking whether we needed this' (Peacock transcript).

Peacock remembers everyone she contacted were 'overwhelmingly positive and were willing to contribute and help' (Peacock transcript). Parkhil's immediate thought, for example, who immediately phoned Peacock the afternoon he received her email, was 'yes of course we should do this'. He and Peacock had a long history of working together on high throughput bacterial genome sequencing so they were both on the same page. As Parkhill puts it, 'we were already evangelists for doing proactive sequencing to identify transmission, both local transmission and global transmission' (Parkhill transcript) .

Figure 4.2: Drawing by Dr Claire Chewapreecha of Sharon Peacock with her team members behind her. Credit: Anon. The quote 'Toughness doesn't have to come in a pinstripe suit' is from Dianne Feinstein. What helped Peacock in getting COG-UK moving was her strong sense of determination and drive which she puts down to her early years of overcoming the obstacles to train as a doctor after leaving school at the age of 16. This experience she says gave her 'a steely determination to find a way forward even when faced with significant barriers, and an acute sensitivity to the inequalities of opportunity' (Anon).

Despite their faith in the idea, both Parkhill and Peacock were highly aware of the risk involved. According to Parkhill, 'There was a question, certainly early on, as to whether the variation of the virus was sufficient to enable you to do real-time transmission tracking, or whether basically you just get an identical virus everywhere, and therefore you have no information on transmission. So there was a leap of faith to an extent that there would be sufficient variation to pick up.' They also 'knew that in that initial rapid spread, it would probably all be identical, and therefore, that transmission tracking would be of less value immediately.' Nonetheless, they 'knew that as it spread and mutated and started spreading back, and you would get these overlapping waves crossing each other, then you would build up a diversity of the viral population that would allow you to discriminate local transmission from introduction, which proved to be very much the case in a lot of useful ways' (Parkhill transcript) .

Parkhill says they already knew that proactive genome sequencing had proven 'useful in outbreak analysis' so they had the 'confidence' it would be valuable for 'looking at local outbreaks, looking at transmission across the UK, and looking for emerging variants… And crucially, we knew that, to do it effectively, you had to do it proactively'. They realised that if sequencing was not done immediately lots of important information might be lost (Parkhill transcript) .

Both Parkhill and Peacock were more experienced in sequencing bacteria, but knew other people who had successfully deployed rapid reaction sequencing for the Ebola virus in West Africa who could help support the project. Importantly, those researchers had set up genome sequencing 'in the expectation it would be useful, without being able to prove that doing it immediately would have immediate value at the point you were doing it. And yet in those cases, and in others, the information that was gathered from setting it up prospectively was of value, especially in Ebola towards the end of the outbreak' (Parkhill transcript) .

Myers was similarly encouraging of Peacock's idea. He points out that the use of pathogen genomic sequencing for informing public health was not entirely new. Indeed, PHE had been routinely doing pathogen sequencing for diseases like tuberculosis, seasonal flu and some foodborne pathogens like Salmonella and E. Coli, for more than 10 years. What was new for Myers about Peacock's suggestion was the scale and ambition she envisaged for the project. Importantly, she was arguing for the sequencing to be driven by a partnership between public health agencies from England, Scotland, Wales and Northern Ireland together with significant input from academic centres. As he says, 'That idea of a real community public health-academic health-Trust partnership to get this done, to get this data flowing through, and to get this data sequenced, is something that we've probably not delivered or hadn't been delivered as effectively prior to this. It was always pairs of organisations working together or loose alliances of smaller numbers.' Overall the aim was to 'try and generate a picture of the genomic diversity of the virus within the UK as the pandemic unfolded'. This was a bold vision because at that moment in time the number of cases was still very low, and as Myers says, 'I don't think any of us probably fully appreciated how big a thing it would become' (Myers transcript)

What influenced Peacock's thinking was the difficulties she was witnessing among fellow academics trying to get COVID-19 testing set up. As she recalls, 'There were numerous people in academia who wanted to develop diagnostic tests, and roll them out to their local NHS. But creating that linkage between a test that you developed and then having access to patients and their samples and then getting the results back to patient care using a standardised test was complex.' One of the advantages Peacock had was she 'appreciated in broad terms what resources the public health agencies could stand up'. Importantly, she understood that the public health agencies were 'very good at genomics, but they were very busy during the early pandemic and they didn't necessarily have all of the expertise required to develop [analytical] tools' (Peacock transcript).

On Friday 6th of March, Peacock sent an email to a wider number of pathogen genome experts to invite them to a meeting in London to thrash out a plan for the rapid development and roll out of national COVID-19 sequencing in the UK. Her invitation went to a pragmatic list of people whom she thought 'could come to the table and participate in a productive, team-based approach to thinking about how to develop a sequencing capability'. This included representatives from public health agencies as well as academic researchers and clinicians (Peacock transcript).

From the outset Peacock intended the meeting to be a practical discussion 'about the nuts and bolts of sequencing, such as who could do sequencing, and where could we do sequencing, and how we could link it all up.' Essentially the aim was to come up with a 'blueprint for that'. As she says, 'We did have a session in the agenda that was a rapid fire about what science the attendees could bring to the table. But that was it in terms of the science. The rest of it was very much about the logistics of: do we have a centralised model, where we do all the sequencing in one place, or do we have a hub and spoke model with lots of people sequencing all around the country?' (Peacock transcript).

First meeting: COG-UK inauguration

Held on Wednesday 11 March 2020, at the Wellcome Trust building in Euston Road, twenty pathogen experts attended the meeting. Peacock invited Sir Jeremy Farrar, the director of the Wellcome Trust to open the meeting. Looking back at the day, what strikes Farrar now is the fact that people attended it in person. As he says, it is important to note that when the meeting happened the 'word lockdown had not been used really. It was still sort of happening elsewhere' (Farrar transcript).

Figure 4.3 Cartoon of first meeting with Peacock in the centre. Credit: Alex Cagan.

But many who attended came with a sense of trepidation. For example, Dr Cordelia Langford, director of scientific operations at the Wellcome Sanger Institutes remembers 'I took a train from Cambridge down to King's Cross, and I was already slightly apprehensive. We hadn't gone into lockdown, but I was already aware of the symptoms that people had. And I was on a train carriage, and it was quite an early one in the morning and there weren't that many other people on the carriage, but I was quite conscious of wanting to keep away from people, even though there hadn't been any of those sorts of public health messages. There had already been the news about a café or a social space, or maybe it was a GP, a health centre or something, that had been closed down and swabbed from ceiling to floor with disinfectant, because a positive case had been found there. And when I was on the train, someone near me coughed, and it was just so strange, because you could literally hear a pin drop afterwards. I think I was also thinking, don't breathe, don't breathe, you're going to catch it, and you're going to die. Yeah, it was strange' (Langford transcript).

When Langford arrived at the Wellcome building she recalls, 'we all met in this one room. So we were all huddled together, but everyone was saying, “Let's not shake hands, let's do the elbow thing.” Again, that was the first time that it really dawned on me that it was ironic that all of these thought leaders had all crammed into this conference room to try and work out how we could tackle this virus that spread really quickly indoors and through proximity. The irony wasn't lost on us.' Another thing that really brought home the seriousness of the situation for Langford was the fact that 'Sharon's mobile phone kept ringing, and it kept ringing, and then, every so often she'd say, “Oh I've got to take this, it's Number Ten”, or something like “it's Sir Patrick”' (Langford transcript). By this point the number of positive COVID-19 cases in the UK had shot up to 456 (Peacock Dec 2020). For those who attended the meeting the threat of catching COVID was very real. This is illustrated by the fact that Myers remembers that Professor Neil Ferguson, who was present from Imperial College, tested positive soon afterwards (Myers transcript) .

What amazed Peacock about the meeting was the fact that 'everybody was willing just to drop everything to come' (Peacock transcript). Farrar also made the same observation. As he comments, getting people to come together at such short notice 'is never easy, and yet essentially everyone turned up'. He was also struck by the 'great enthusiasm and energy' in the room. Similarly, Langford felt there was an enormous 'team spirit'. As she puts it, she sensed 'that everyone realised that they could play a part in making a huge difference. And people genuinely wanted to do that, wanted to offer up. It was just the opposite of competition. I guess normally, when one goes to maybe conferences or whatever, there's sometimes a little bit of a sense of competition. That was one of the most stark, noticeable things of the meeting. I think it was also dawning on people of the great nature of the situation that we were in' (Langford transcript).

Overall, as Parkhill puts it the 'gist' of the meeting was 'we have been asked to set this up and what are the current capabilities in the UK for doing this? How do we pull those capabilities together and stand up a national sequencing consortium? It wasn't a “should we do this” meeting. It was “we must do this”. We're going to do this. How is the best way to do this? How are we going to do this? I don't think anyone at the meeting thought we shouldn't do it. Because Sharon had already selected the people who she knew would be interested in doing this. So there wasn't any discussion about whether we should do it at all. Everyone there had, I think, already bought into the idea that it was an important thing to do' (Parkhill transcript).

What was noticeable to Farrar when opening the meeting was the range of expertise of everyone in the room. As he says, 'Sharon had obviously done a lot of work on nosocomial [hospital acquired] infections, and trying to map genomics to find out where the infection came from, and why did this patient get it and that member of staff get it and the rest of them. And other members there at the meeting had a lot of experience in that. But a lot of the expertise there was people like Dominic Kwiatkowski, who was working on artemisinin resistance malaria in Southeast Asia and Africa; Julian Parkhill was there as well, working with colleagues on enteric fevers and typhoid in low- and middle-income countries, trying to map genomics, evolution, population genetics, not purely as a research angle' (Farrar transcript). Another key person present was Professor Nick Loman, who had helped construct a rapid genomic surveillance system, known as the ARTIC network, for responding to emerging infectious diseases which had been used to combat the Ebola virus in West Africa and also the Zika virus in South and Central America. Just how serious the atmosphere in the room was is also highlighted by Professor Emma Thomson, who attended as representative from the Centre for Virus Research at the University of Glasgow. She recalls, ' I had a shiver down my spine watching the potential scenarios that were predicted to emerge by the mathematical modellers [at the meeting]' (Thomson transcript)

Figure 4.4: Agenda drawn up by Peacock for what turned out to be the inaugural meeting of COG-UK.

Farrar argues that the meeting marked a crucial turning point. Importantly, before March 2020 linking pathogen genomic sequencing 'into public health policy making and decision-making was relatively underdeveloped in the UK [and] was certainly not routine.' As he argues, 'Sharon had been doing her very best over many years to put this into the centre of Public Health England, and Public Health UK, and the NHS, but it wasn't there on the 11th of March.' Until then most of the pathogen genomic sequencing had been led by 'people coming from a more academic research background, with less of a link into public health and public health policy making, certainly in the UK'. For Farrar, both COVID and the meeting, which effectively turned out to be the inauguration of COG-UK, was pivotal to moving pathogen genomic sequencing 'from being an academic research question into being mainstream public health. That's a hugely important transition'. He continues, 'I think why that meeting was so important was because what was stressed was this is going to be an academic entity, this is going to be a research tool, this is going to be intellectually interesting, but it's also going to have a massive public health impact, and we need to bring those communities together' (Farrar transcript).

According to Langford, 'the meeting and the day was facilitated incredibly well, really inclusively, and matter of factually, by Sharon. I think she set the scene superbly. And that set such a good tone of collaboration, of everyone's on an equal playing field. We're all here, we all have skills, we all have opinions and contributions to make. Everybody's contribution was welcome' (Langford transcript) The skill with which Peacock managed the meeting was also expressed by Professor Mark Caulfield, then Chief Scientist at Genomics England, who she invited to the meeting to discuss the possibilities 'around human host sequencing'. As he recalled, 'When I attended you had a real sense of camaraderie, people were sharing their experiences, revealing things that they probably wouldn't normally do. Some were even, particularly including their mistakes, “we did this, but it didn't work at all.” Whereas, you know, sometimes you meet colleagues, you don't wash your dirty linen in public. But people were very open. And the success of this was that Sharon was incredibly sensitive to all of the personalities, and led them to a position that, probably, there was no one else who could have done that' (Caulfield transcript).

Adopting a mixed model for sequencing

Ahead of the Wellcome meeting, a number of people had already begun sequencing COVID-19 samples in the UK. But, as Parkhill points out, this was mainly driven by academic interest and 'was not a service or anything like that.' For those attending, two of the significant challenges they had to confront was 'how do we move this from being just something that's being done [ad hoc] at a few specialised hospitals where they have strong academic links, to something that is UK-wide and systematic? And how do we extract the data from those sites that are doing it and collate it, get it together in a usable format over a useful timeframe?' (Parkhill transcript).

Two primary models were discussed at the meeting to scale up the sequencing. The first involved using numerous local or regional centres to do the sequencing and the other was to centralise the sequencing through one large laboratory. Parkhill recalls 'There were plenty of loud voices saying, there are good local academic labs that know how to do sequencing; let them do it and collate the data. And there were other voices saying, it's much more effective and cost-efficient to build two or three mega labs and shuffle everything through those' (Parkhill transcript).

In the end the consensus was to go for a mixed model. Among those who strongly advocated for the mixed model was Professor Judith Breuer from University College London. Asked by Peacock to present at the meeting on different set-ups, she went through the advantages and disadvantages of local and centralised sequencing. She concluded her presentation by saying a 'Mixed model will give us the data we need to inform public health planning AND future-proofing data on the utility of local sequencing plus centralised data collection for combining patient management and public health utility' (Figure 4.5). By going for a mixed model Breuer believed they could empower communities to build up sequencing capacity locally and have a central hub to do the heavy sequencing which was needed to help inform public health decisions. Breuer recalls there was really no question in the room that this was the way to go forward because it helped satisfy what everybody was aiming to do. Together with Nick Loman and Andrew Rambaut, Breuer had already begun planning a mixed model before the arrival of the pandemic for dealing with norovirus (Breuer transcript). Some idea of the capacity local centres could provide was captured in another presentation given by Thomson to the meeting (Figure 4.6).

Figure 4.5: Slides Breuer presented to the Wellcome Trust meeting on 11 March 2020 to set up national sequencing for COVID-19. Credit: Professor Judith Breuer.

Figure 4.6: Slides Thomson presented to the Wellcome Trust meeting on 11 March 2020 to set up national sequencing for COVID-19. Credit: Professor Emma Thomson.

Getting funding and support

Most of the objectives, governance framework and sequencing pipeline for COG-UK had been fleshed out by the end of the meeting, setting the stage for putting together a funding proposal. The primary task of putting this together fell on Peacock, who 'worked every hour' she 'possibly could'. Fortunately her family were very supportive, which enabled her to stay in London hotels all the time but, as she says, 'they were potentially quite worried about my health because it was difficult to eat properly and sleep properly.' As she recalls 'it was like being a junior doctor all over again where you're on call constantly. I guess I got the bit between my teeth and decided that I was going to lead it and get it done'. (Peacock transcript). She describes the days that followed as 'frantic and frazzled' as she and her colleagues 'assembled our thoughts into a coherent written argument for the development of COG-UK, supported by a scientific proposal. The backdrop to this was a working life when many of us were receiving as many as 250 emails a day, together with a meetings schedule that spanned from dawn to dusk.' Throughout this process, they were clear that they wanted to build 'a research consortium … to contribute to the UK response by providing genome data, associated sequencing methods and analysis tools that could be used to inform public health actions and policy decisions' (Peacock, Dec 2020).

Against this, they had to contend with a number of sceptics who made it clear that they believed the exercise would be a waste of time. Even Peacock and others who attended the first meeting were very nervous about this possibility. The main challenge was 'whether there would be enough genetic variation generated in the viral population for sequencing to be worthwhile for outbreak detection and other purposes.' Some took the view that there was no point 'getting ahead of the curve'. However, Peacock and her collaborators took the 'view that waiting until the worst happens, only to realise that one is totally unprepared' was not where they collectively wanted to find themselves. At the end of the day they 'reasoned that under such circumstances, it would be better to be wrong and to have generated new tools and a great deal of data that, if not of direct relevance to the national COVID-19 response, would at least be of immense value to the scientific community and for innovation more generally' (Peacock, Dec 2020).

The first draft of the proposal was ready for rapid internal critical review by senior UK government and funding body advisors just four days after the Wellcome meeting took place. A lot of this work was done over the course of the weekend (Harrison Jermy transcript). Submitted at the close of Sunday March 15th, the proposal provided a rationale for why the development of COG-UK was important and gave a structural framework to achieve its objectives. Reading the proposal now (below), with the benefit of hindsight, it is remarkable to see how much foresight its authors had and how well they had worked out how to deliver 'large scale and rapid SARS-CoV-2 sequencing capacity to local NHS centres and the UK government at pace.' It is even more striking when we consider how fast the document was prepared and the emergency circumstances in which it was created. Furthermore, at that point nobody knew quite what lay ahead or the vital role genome sequencing would play in detecting troubling new variants. As Peacock puts it, 'at the time, of course, we didn't have the perfect forward vision' (Peacock transcript).

Figure 4.7: COG-UK's full financial request (names redacted), March 2020. Credit: Professor Sharon Peacock.

The top line of the financial request was to get support for a consortium to see whether they could generate data that 'could be fed back into the public health system in such a way that it altered decisions' (Peacock transcript). At the outset the proposal made it clear that the low evolutionary rate of SARS-CoV-2 meant that 'large-scale genome sequencing' would be 'more powerful when applied to certain questions than others'. It identified five public health applications where it could help. This included enhancing the understanding of the epidemiology and transmission of the virus as well as its biology and providing a means to monitor how it would respond to interventions and treatment. At this early juncture the proposal flagged up the possibility of the emergence of mutations in response to the introduction of new treatments and vaccines. It also highlighted how it might help in the identification of virus genetic markers associated with clinical severity.

Eight deliverables were outlined in the proposal (figure 4.8). Notably these envisaged COG-UK not only as a tool to understand the evolution and spread of SARS-COV-2 and the impact of interventions and treatment, but also a means to help build out UK wide capacity for future pandemic preparedness. At the heart of the vision was also the importance of open sharing of UK data to 'facilitate international collaboration on COVID-19'.

Figure 4.8: Eight deliverables outlined in the COG-UK financial proposal compiled in March 2020. Credit: Professor Sharon Peacock.

The proposal anticipated three phases for the roll out of the national SARS-CoV-2 sequencing. Phases 1 and 2 were expected to start immediately and run in parallel, following which phase 3 would be launched. In phase 1 the focus was to be on the expansion and standardisation of sequencing in academic and public health centres that were already undertaking sequencing of clinical samples and ensuring their data was collated into a single central repository. The aim of this work was to get a rapid sequencing turnaround time of 24 hours. By this point eight academic sites had been identified to do the work in addition to three public health agencies (England, Wales and Scotland). Phase 2 envisaged the launch of large-scale centralised sample processing and sequencing undertaking by the 'Wellcome Sanger Institute, based in Cambridge, to run alongside and support existing centres where necessary'. In this case the aim was to get the sequencing completed within 72 hours of receiving the sample. Figure 4.9 highlights the location of the different sites already pinpointed to take part in phase 1 and 2. The aim of phase 3 was to build further sequencing capacity in places around the country which did not yet have the means to do so. Such work was seen as particularly important for overcoming 'inequalities in access to sequencing'.

Figure 4.9: Location of COG-UK sequencing sites identified in COG-UK's first Financial proposal, figure 1. Credit: Professor Sharon Peacock.

Overall, the plan was to engage as many places as possible to get maximum coverage around the country. The sequencing model advocated in the proposal allowed for maximum flexibility so that as many centres could take part as possible based on their available assets and methods of working. Each place was given the freedom to choose what the best process was for them. Figure 4.10 provides an overview of the way samples were expected to flow between different sites for sequencing.

Figure 4:10 Diagram showing how COG-UK envisaged samples flowing between different sites for sequencing with different turnaround times. Source: figure 2 COG-UK financial request. Credit: Sharon Peacock.

Figure 4.11: Data pipeline envisaged for COG-UK. Diagram sourced from COG-UK financial request. Credit: Professor Sharon Peacock.

The financial application also outlined a data pipeline for the project. Critically, this was to be constructed to allow groups to perform local analysis to inform and respond to local needs. It also intended to take advantage of CLIMB. Set up to provide a free open source computational and bioinformatics infrastructure for microbiologists to share large genome datasets, CLIMB was important in that it provided a place to both store the sequenced data and house an analytical pipeline (ConnorPeacock transcript). Having access to CLIMB meant COG-UK would be able to do large-bulk analysis to get a sense of what was happening at the national level. Data from this would then be fed into international databases to help contextualise UK data. Figure 4.11 provides an overview of the data flow mechanism within COG-UK.

The proposal indicated that a key output of COG-UK would be the delivery of weekly analytical reports of the national picture of SARS-CoV-2 to both the UK government and public health agencies of the devolved four nations. It also stipulated the setting up of a working group to determine how samples should be handled, the chain of custody and storage retention or destruction.

Figure 4.12 Timeline of key events surrounding the setting up of COG-UK.

Funding awarded

On April 1st 2020 the COG-UK initiative gained its first tranche of £14.5 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.' It was to be administered by the UK Research and Innovation (UKRI). (Peacock, Dec 2020; Peacock transcript). At the same time, Professor Sir Michael Stratton, the director of the Wellcome Sanger Institute agreed to provide an additional £6.3 million from its existing Wellcome core grant to the project (Marjanovic Final Report; Peacock transcript; Kwiatkowski transcript transcript; Farrar transcript).

Figure 4.13: Tweet put out by Professor Nick Loman announcing the successful funding of COG-UK.

Under normal circumstances it would have taken at least 12 months of detailed planning and preparation to secure such a large sum. But Peacock and her COG-UK colleagues managed to do it in just one month. The fact that they succeeded is not only a testament to their hard work but also reflects the extreme emergency that everyone faced. For Peacock, securing the funds was just the start of the process and 'led to a paradigm shift in what I did'. As she says, 'Having got the money, it then became my responsibility to actually put the operations in place and all of the legal agreements and so on' (Peacock transcript).

Peacock points out that the sum awarded 'was not a trivial amount of money to organise'. But fortunately she had some experience to fall back on. She reflects that what helped her was 'I'd been a non-exec director on the board of Addenbrooke's Hospital for four or five years by then.' For this role she had done 'a course with the Financial Times to learn the skills of a non-exec director, including financials.' That meant she 'had a lot of understanding of governance, management, finances, etc' which meant she could 'bring to the table an approach to running something quite large.' She also points out that 'Being a researcher, you're used to running a small business because effectively that's what researchers do' (Peacock transcript).

Peacock and her team subsequently worked together with Piers Rickets and Neil Bentley to secure further funding for COG-UK from the Department of Health and Social Care's testing Innovation Fund. It was awarded £16 million and £5 million, respectively in January 2021 and August 2021, to augment its genome sequencing capacity to meet the anticipated increasing number of COVID-19 cases (Ricketts transcript).

Figure 4.14: Cartoon entitled 'COG-UK meets Olympus' to depict the hard work that went into building the consortium. Credit: Alex Cagan.


Anon (n.d.) 'About Sharon Peacock', Sharon Peacock Blog.Back

Connor, TR, Loman, NJ, Thompson, S, et al (26 July 2016) 'CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community', Microbial Genomics.Back

Marjanovic, S, Romanelli, R, Claire-Ali, et al (2022) 'Evaluation of the COVID-19 Genomics Uk (COG-UK) Consortium, Final Report, RAND Europe.Back

Peacock, S (17 Dec 2020), 'A short history of the COVID-19 Genomics UK (COG-UK) Consortium', COG-UK blog.Back

Interview transcripts

Note: The position listed by the people below is the one that they held when interviewed and may have subsequently changed.

Breuer, Judith, Professor of Virology, University College of London (interviewed 24 Nov 2022, unpublished transcript).Back

Interview with Sir Professor Mark Caulfield, Vice Principal for Health, Queen Mary University’s Faculty of Medicine and Dentistry, COG-UK contributor, former Chief Scientists at Genomics England.Back

Interview with Dr Ewan Harrison (Deputy Director COG-UK and UKRI Innovation Fellow, Wellcome Sanger Institute, Senior Research Associate, Department of Medicine, University of Cambridge) and Dr Andrew Jermy (External Communications Advisor COG-UK).Back

Interview with Professor Dominic Kwiatkowski, Head of Parasites and Microbes Programme at the Wellcome Sanger Institute in Cambridge and Professor of Genomics at University of Oxford.Back

Interview with Sir Jeremy Farrar, Director of the Wellcome Trust.Back

Interview with Dr Sharon Glaysher, Specialist Biomedical Scientist who manages Portsmouth Hospitals University NHS Trust's Research Laboratory.Back

Interview with Dr Cordelia Langford, Director of Scientific Operations, Wellcome Sanger Institute.Back

Interview with Dr Richard Myers, Head of the Bioinformatics Unit at Public Health England (now UKHSA), Principal Investigator COG-UK.Back

Professor Julian Parkhill, Department of Veterinary Medicine, University of Cambridge.Back

Interview with Sharon Peacock, Professor of Public Health and Microbiology in the Department of Medicine, Cambridge University and Executive Director of the COVID-19 Genomics UK (COG-UK) Consortium.Back

Interview with Piers Ricketts, Chief Executive, Eastern Academic Health Science.Back

Interview with Professor Emma Thomson, Clinical Professor in Infectious Diseases, Centre for Virus Research, University of Glasgow.Back

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