An Interview with a COVID Researcher
Online Science Editors Vincent Plant and Issy Murray interviewed Dr Michell about his experience of research during the pandemic
The COVID-19 pandemic has undoubtedly affected everyone’s lives. But what about researchers? We spoke to Dr Michell, a researcher at the University of Exeter, about his experience of research during the pandemic.
Dr Michell’s involvement with COVID-19 research began when the pandemic began in the UK, with a phone call from Ray Sheridan- a consultant at the Royal Devon and Exeter hospital with whom he had previously collaborated working on the bacterium Clostridium difficile. Dr Sheridan asked whether a project could be set up surrounding the sequencing of the virus. Around the same time, another researcher at the university- Dr Ben Temperton- had been approached by a group from Birmingham led by Nick Loman- a molecular geneticist interested in the application of Next Generation Sequencing techniques when applied to clinical microbiology. Both Dr Michell and Dr Temperton then agreed to join the COVID-19 Genomics UK Consortium (COG UK) and establish Exeter as the South West sequencing hub for COVID-19.
COG UK – then still in its infancy – is a project which aims to draw together UK-wide expertise in genomics in order to better understand how the Coronavirus evolves and is transmitted. As of early December 2020, the organisation has scanned close to 120,000 individual virus genomes. At Exeter, there are over a dozen individuals in the team working on this project, from both the Royal Devon and Exeter NHS Trust and the University of Exeter.
When a patient is COVID-positive, RNA extracts are prepared. The viral genome is amplified using polymerase chain reaction (PCR) and sequenced on MinION platforms- small and cheap genetic sequencers which allow researchers to obtain sequence information in rapid time. Sequenced genomes are then uploaded to a high-performance computing cluster and analysed to provide information on local and national prevalence of particular viral strains. Sequences are shared with the GISAID and NextStrain resources which incorporate this information into global genomic surveillance tools to better understand the pandemic.
Such information can provide valuable insight into the spread of the virus. As an example, genomic studies of the virus have demonstrated that the virus entered the UK on over 1300 different occasions – 80 per cent of which arrived between late February and late March, when the nation was debating whether or not to enter a period of lockdown. The majority came from Spain and France, with only 0.1 per cent of infections coming from China.
Such information can provide valuable insight into the spread of the virus
This genomic data may also help in both diagnostics and therapy. When it comes to therapy, genomics can allow researchers to identify conserved regions of DNA- stretches of genetic code which are similar across viral genomes. If these regions code for a protein expressed on the surface of the virus, this can be a suitable target site for a vaccine – as demonstrated by the more recent success of vaccines targeting the spike proteins of the Coronavirus. High-throughput sequencing with real-time results will be invaluable to measure how the virus responds to evolutionary pressure applied by vaccines and to monitor their long-term efficacy.
Coronavirus is similar to many disease outbreaks, both recent and historical, in that it ultimately stems from an animal host. The Black Death, for example, started out in rats and was transmitted to humans via fleas. Human encroachment on previously untouched lands exacerbates the situation, as the proximity of humans to potential disease reservoirs increases. If you apply the notion that animal and ecosystem health is tied to human health – known as the One Health concept – the pandemic doesn’t seem as unexpected anymore to some.
If you apply… the One Health concept, the pandemic doesn’t seem as unexpected anymore
The pandemic has clearly had an enormous impact on the world we live in. However, collaborative research projects have allowed us to better understand the virus and ultimately develop a vaccine.