Two hands with a piece of puzzle each joining them


4 Apr 2022

Two years on

Sharon Peacock

On the second anniversary of the inception of COG-UK, we reflect on the collective achievements of the members of our consortium, our experiences along the way, and the enduring impact of the last two years on pathogen genomics and public health.

Second anniversaries are traditionally marked with gifts made out of cotton, for marriages at least. Yet as COG-UK reaches the end of its second year, cotton – as a sturdy yet malleable fabric adapted to meet a range of uses – seems highly appropriate for the consortium as well. Over the past two years of the COVID-19 pandemic, members across the consortium have individually and collectively proven themselves to be incredibly strong, adaptable and resilient. As we moved from emergency mode in the early days of 2020, through delivery, impact and transition in 2021, and now look ahead to what are hopefully calmer times focussed on making the most of the data generated and helping others to learn from our experiences, I am left with a sense of surprise and wonderment. Surprise at how far we have come in such a short space of time – the consortium accomplished in the space of two years what I would previously have imagined taking at least a decade in more normal times. And wonderment, at what so many scientists can achieve when they come together with such focus and dogged determination.

Meeting expectations

Although the experiences of members across the consortium will have varied, I suspect that there are some common threads weaving their way through there too. For example, I shudder to think of the sheer volume of online meetings that the pandemic has required of us. Two years ago, video conferencing was an occasional option rather than the default that we depended upon for our daily duties. Who knew that we would all become expert on Zoom, Teams and Hangouts (and yet still manage to struggle hearing each other on occasion). Reflecting after more than 100 weeks of back to back meetings (more than 4500 in total), a few thoughts occur. I wish that I had bought a treadmill desk before the pandemic began (think of the miles covered since!) and that I had been more mindful of trying to limit meetings and to build in breaks between them. Perhaps most importantly, I realise just how much I have missed being in the company of people and how much of the pleasure of working with colleagues derives from connecting in person. I am certain that I am not alone in feeling joy as we begin to take tentative steps back to a working life that resembles the before COVID-19 era.

On reflection, I was also somewhat surprised that the level of intensity in the day-to-day running of COG-UK diminished little once we transitioned the responsibility for routine sequencing activities entirely to the UK public health agencies. As we became less depended on for providing genomic data, another cycle began in which we sought to develop new research tools and insights within the consortium, to link SARS-CoV-2 genomic data to other useful datasets in partnership with Health Data Research UK (HDR-UK), and to share our experiences to help others develop genomic surveillance capabilities through COG-Train. The pace has barely slackened and there is still much for us to achieve in the coming months, and many zoom calls yet. Maybe still time for that treadmill..!

Combined science

I am firmly of the opinion that both within the consortium and the wider pandemic response, UK scientists have done a genuinely phenomenal job. Whether in genomics, vaccine development, clinical trials, virology, immunology, structural biology, epidemiology, modelling, public health and many more fields besides, researchers and clinicians have come together to create data generation and analysis pipelines that connect different disciplines and which have had incredible impact at national and global scales.

With emergency funding as part of the pandemic response now on the decline, it will be important to ask ourselves how this interconnectedness can be sustained. Maintaining the fluid way in which academia, public health, NHS and the commercial sectors have worked with each other during the pandemic to date will require strategic thinking and a commitment from funders.

It will also be helped along by the breaking down of some of the barriers between these sectors that we are witnessing, as members exposed to different roles through their work with the consortium are moving into new positions in academia, public health and industry. The consortium has always been something of a dynamic caravan, with individuals jumping on and then off at various points on the road. Along the way there have been so many outstanding contributions of individuals and groups, and examples of self-sacrifice and super-human efforts – it is truly humbling to think about this.

To all consortium members that have already moved on to new opportunities, and to those that will begin to plot the next step in their career path in the coming weeks and months, you have my deepest thanks and admiration for the part you played in the COG-UK story so far. I do hope that all members stay in touch with one and other and that one part of the consortium’s legacy in years to come will be a supportive network of COG-UK colleagues that can help each other to push pathogen genomics and public health to ever greater levels of importance and impact.

Beyond COVID-19

As we cautiously consider life after the pandemic part of COVID-19, we can begin to assess how the infectious disease genomics landscape has changed over the last two years, and where it might go over the next ten. Very few of us will ever have anticipated finding ourselves in a position where the testing for an infectious agent became a common-place event at kitchen tables across the country, or where variants, PCR, LFTs, mRNA vaccines – and yes, genomics – entered the every day vocabulary of the public and its policy makers. It is unfortunate that it took a pandemic for pathogen genomic sequencing to become widely recognised as a fundamental pillar for public health, but now that this realisation has become reality, there is much that needs to be done.

Countries cannot simply revert to pre-pandemic levels of genomic surveillance based on people presenting at their doctor’s surgery and at hospitals. Prospective population-based surveys (such as that undertaken by the UK Office for National Statistics) will be important to better understand and monitor contemporary infection risks circulating in the community, be they viral, bacterial or other categories of pathogens. Sequencing of samples will need to be better integrated into local clinical microbiology laboratories, in addition to long-term investment in national and international genomic data and analysis infrastructures.

I suspect that in the years to come, COG-UK and the work of all of its members will be viewed as a vitally important catalyst. Not just in responding to COVID-19 in the UK, but also in showing how genomics has a vital role in pandemic preparedness and public health resilience. The barriers to utilising genomics in public health settings have never been lower, but we still have some way to go to bring pathogen agnostic sequencing closer to patient samples, to track and then turn the tide on the spread of antimicrobial resistance, and to monitor in real-time the likely interfaces through which future pandemics might emerge.


As I contemplate the last two years, it is difficult not to think of some of the ups and downs along the way. Each consortium member will no doubt have their own. For me, the hardest parts included the long hours and limited time off with friends and family. Furthermore, the consortium never quite reached equilibrium, with different parts of the ecosystem in which we operate changing with regularity. Indeed, against this constant churn of changing demands, adapting to new information, systems, people and partners, the many achievements of consortium members are even more impressive.

On the positive side, there are many individual areas in which I am so proud of the work of all involved in the consortium. But two highlights particularly stick in mind because they reflect the collective effort of our members. The first is the recent report from Rand Europe, which gathered information and input from across the consortium, its partners, and leaders in the pathogen genomics and public health fields, and then analysed our achievements against the backdrop of the first part of the pandemic. The report provided an honest and thorough assessment of our work, the immense motivation and goodwill shown by consortium members in undertaking it, and the impact on advancing genomics as part of the public health landscape in the UK and internationally.

The second highlight for me, and judging by the levels of enthusiasm and emotion on the day probably for many others too, was the COG-UK Together event that saw us gathering across the country and online last October. After an often torrid 18 months, coming together and connecting with other groups doing the same was incredibly cathartic and helped to suitably mark the transition between two very distinct phases of the consortium. I’m very much looking forward to hearing many more COG-UK members’ stories when we meet in the years to come.

Happy second anniversary COG-UK.

COVID-19 Genomics UK (COG-UK)

The COVID-19 Genomics UK (COG-UK) consortium works in partnership to harness the power of SARS-CoV-2 genomics in the fight against COVID-19.

Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative collaboration of NHS organisations, the four public health agencies of the UK, the Wellcome Sanger Institute and sixteen academic partners. A full list of collaborators can be found here.

The COVID-19 pandemic, caused by SARS-CoV-2, represents a major threat to health. The COG-UK consortium was formed in March 2020 to deliver SARS-CoV-2 genome sequencing and analysis to inform public health policy and to support the establishment of a national pathogen sequencing service, with sequence data now predominantly generated by the Wellcome Sanger Institute and the Public Health Agencies.

SARS-CoV-2 genome sequencing and analysis plays a key role in the COVID-19 public health response by enabling the identification, tracking and analysis of variants of concern, and by informing the design of vaccines and therapeutics. COG-UK works collaboratively to deliver world-class research on pathogen sequencing and analysis, maximise the value of genomic data by ensuring fair access and data linkage, and provide a training programme to enable equity in global sequencing.