The COVID-19 Genomics UK Consortium and genomic surveillance
Aligned with our mission to advance the understanding and impact of microbiology, the Society reached out to our community of microbiologists to share their experiences in responding to SARS-CoV-2. We aim to showcase the perspective of scientists during the COVID-19 pandemic and the variety of roles adopted to mitigate the global crisis.
This case study comes from Andrew Page, Head of Bioinformatics at the Quadram Institute in Norwich. He shares with us his experience of helping to establish one of the founding sequencing centres for the COVID-19 Genomics UK (COG-UK) Consortium, and how his work there aided the government and impacted on the wider society.
How did you respond to the SARS-CoV-2 during the COVID-19 pandemic?
In March 2020, the UK Government announced an initiative to map the spread and behaviour of COVID-19 in the UK using genome sequencing, called the COVID-19 Genomics UK (COG-UK) consortium. The Quadram Institute was one of the founding COG-UK sequencing centres.
As a team of microbiologists and bioinformaticians we had to hit the ground running to deliver genomic surveillance at pace and at scale. Over that time, we’ve sequenced more than 70,000 genomes and helped the National Health Service (NHS) and Public Health England deal with successive waves of the virus.
Our work has helped NHS hospitals understand whether they were dealing with nosocomial (originating from within a hospital) or community COVID-19 outbreaks; we reported to the Scientific Advisory Group for Emergencies (SAGE) on care home outbreaks in the first wave; and we helped directors of public health bodies understand how an industrial workplace outbreak was seeded and spread, as well as where the virus originated.
Was this response related to your work prior to the outbreak?
Yes, as part of the Quadram Institute’s normal work we undertake whole genome sequencing of pathogens in the food chain and work closely with government agencies such as the Food Standards Agency and the UK Heath Security Agency.
We had the skills, knowledge and facilities to pivot towards doing similar work (but on a whole other scale) for COG-UK and the Department of Health.
What were some of the challenges that you faced during this time?
Scaling up, consumables, logistics and working from home for informaticians have all been challenges (as they have for many other people).
How did your experience throughout the response aid in your development?
We value scientific outputs differently now. The rapidly evolving nature of the pandemic meant that getting information out to the people who needed it as fast as possible was more important than getting a beautiful, polished, published paper. We had to multitask and look at different avenues such as podcasting, preprints and slack channels.
What can we learn about the importance of microbiology from the COVID-19 pandemic?
Microbiology has become central to the everyday functioning of our society in a way it wasn’t before. The pandemic has underscored the importance of microbiology in our understanding of pathogenic threats and the role we can play in addressing those threats.
How did the Microbiology Society play a role in your response?
The Microbiology Society published a paper from our group looking at the first wave (and summer) of the pandemic in our local region. The Society waived the publishing fees and got the paper through review and out the door in quick time.
References
Page, A. J., Mather, A. E., Le-Viet, T., Meader, E. J., Alikhan, N. F., Kay, G. L., de Oliveira Martins, L., Aydin, A., Baker, D. J., Trotter, A. J., Rudder, S., Tedim, A. P., Kolyva, A., Stanley, R., Yasir, M., Diaz, M., Potter, W., Stuart, C., Meadows, L., Bell, A., Gutierrez, A. V., Thomson, N. M., Adriaenssens, E. M., Swingler, T., Gilroy, R. A. J., Griffith, L., Sethi, D. K., Aggarwal, D., Brown, C. S., Davidson, R. K., Kingsley, R. A., Bedford, L., Coupland, L. J., Charles, I. G., Elumogo, N., Wain, J., Prakash, R., Webber, M. A., Smith, S. J. L., Chand, M., Dervisevic, S., O'Grady, J., The Covid-Genomics UK Consortium. Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management. Microb Genom. 2021; 7(6):000589.
About the author
Andrew Page is Head of Informatics at the Quadram Institute, Norwich. His main interest is in high performance computing and high throughput bioinformatics sequence analysis pipelines. Find out more about his work on the Quadram Institute’s website.