Updated: May 22
Life is full of initially hidden and unintended impacts and consequences; for something as huge and pervasive as COVID, no doubt they will be many and varied: some good, some bad, some just resulting in different. The global infrastructural leadership of the UK in the area of genomics, underpinned by the public and charitable contributions of the UK Research Councils and the Wellcome Trust, has been critical in surveillance, variant detection, and now screening. By February 2020, strains being sequenced were ramped from 10,000 to 20,000 per week, around 10% of isolates were being characterised, and an entirely new high-throughput pipeline had been established to achieve this. The only place with comparable capabilities and expertise, the US, had obstacles of State-based organisation and other things to address and could not (or at least did not) leverage its substantial commercial / private genomics infrastructure to the COVID challenge. The achievements in viral sequencing, centred in Cambridge, but with a COG network which extended more widely, are substantial; one should not forget the patient-focussed genomics of groups like the GenOMICC led by the team at Edinburgh University. Then there are the existing Genomics Centres around the UK supported by the NHS, the Biomedical Research Centres, and others, and of course, Genomics England.
You can mistake this achievement for one empowered by good strategic planning, leveraging a particular national strength and infrastructure, good prioritisation and wise investment, and the application of hands where they were needed. All of these were necessary, but none of these describe the most critical resources that were used, because the most essential resource was the expertise and the heads of those involved, not their hands or their lab toys. This is where an important cost lies: the opportunity cost of what these people were working on before – but now aren’t.
It doesn’t take much to realise that the best talents, robots and sequencers of our experts in Genomics have been recruited in an effort to reflect the national emergency response to COVID. But this has included some of our world leaders in bacterial pathogens, most obviously Professor Sharon Peacock in Cambridge, who now holds substantial funding for the COG project and who is its head. What they have achieved is outstanding, world-leading, and commendable, but a quick scan of their research group web pages will show that not only Sharon but her whole team (or at least most of it) have been diverted and seconded to the COVID effort. The same is true of critical staff and resources at the Sanger Institute and presumably more widely. This means that the research effort and progress in the application of genomics to AMR and nosocomial infection control has to have been impacted as not only the sequencing resources but also the people are diverted away from it.
I cannot and should not speak for Professor Peacock, but it must be frustrating and challenging to put aside your main work in such circumstances because that work is itself important; every researcher cares deeply for the problems they have chosen to address and attempt to solve. The work that has had to be put aside is also urgent! Nosocomial infections (infections acquired in hospital and as a result of health care interventions) already kill tens of thousands in the UK alone each year, and while some progress has been made in the control of some of them, the challenge has not gone away and combined with AMR and increasing adaptations of bacteria to hospital environments, and ageing and compromised patient groups this is only going to get worse without a step-change in our knowledge and capabilities to intervene. Given the urgency and trajectories of the nosocomial and AMR challenges, to lose impetus in the quest to address them at this time – in the equivalent of an early stage of the emergence of new epidemics – may have long-term consequences, ultimately ones that have a greater impact than COVID-19 itself.
Dr Nigel Saunders, Chief Scientific Officer