March 23, 2020

expert reaction to launch of UK whole genome sequence alliance to map spread of coronavirus

The UK Government announced funding on 23rd March 2020 for a genome sequencing consortium, called COVID-19 Genomics UK Consortium, with the aim of mapping how COVID-19 spreads and behaves by using whole genome sequencing.

Prof Paul Klenerman, Group Head and Consultant Physician, Nuffield Department of Medicine, University of Oxford, who will be involved in the work, said:

“Sequencing virus genomes at scale can give us real insights into how the virus evolves in real time. All viruses accumulate mutations over time – some faster than others –for Covid-19 this has only just begun but this emerging variation can be tracked in detail . The mutations in the sequence can act as the fingerprints of the virus to indicate its identify and where it has come from. To do this scientists can place the viruses on a tree – like a family tree – which gives an idea of how they are related and which their closest relative is. In many cases this can allow tracing of the viruses geographically and identify clusters of connected cases. This would be the idea for COVID-19.

“One other thing the sequences can do is show how the virus is adapting over time to the human population it is in. Viruses will accumulate mutations which allow them for example to evade immune responses – there is lots of information about this for viruses like HIV and hepatitis C and influenza, which are all quite variable. Really it is seeing evolution unfold at great speed – the virus adapts to the forces acting on it. If you can see how the virus is adapting that can give a very strong indication of what the really important immune responses are. Beyond that, if there is variability in key parts of the virus, it would be incredibly important for vaccine design.”

Prof Nick Loman, Professor of Microbial Genomics and Bioinformatics at the University of Birmingham, who will be involved in the work, says:

“Sequencing viral genomes can be thought of as a direct view on evolution. Viruses acquire random mutations which  accumulate over time, leaving scars on their genome. These scars don’t typically alter virus behaviour, but leave useful signposts as to where they have recently been. So if patients share the same patterns of mutations we can infer they are related, which really helps us understand spread. Right now the important questions we can help answer with sequencing are to help understand the role of international importations into the UK versus local spread within and between regions of the UK. As more interventions, both pharmaceutical and otherwise are used, we can see the effect of these on the population of viruses and work out how effective they are. Finally we can start to estimate the true real size of the pandemic bearing in mind there are likely to be large numbers of cases that we are unable to detect.”

Paragraph about Birmingham’s involvement;

COVID-19 Genomics UK Consortium – comprised of the NHS, Public Health Agencies, Wellcome Sanger Institute, and academic institutions – including the University of Birmingham – will deliver large scale, rapid sequencing of the cause of the disease and share intelligence with hospitals, regional NHS centres and the Government.

A team at the University of Birmingham, led by Nick Loman, Professor of Microbial Genomics and Bioinformatics in the Institute of Microbiology and Infection, will employ a real-time genome sequencing facility established at the University to sequence genomes of the virus causing COVID-19 from patients in the West Midlands.

All our previous output on this subject can be seen at this weblink: www.sciencemediacentre.org/tag/covid-19/

Declared interests

Both comments are from experts involved in the COVID-19 Genomics UK Consortium.