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The Covid detectives helping to track the spread of the virus

The Delta and now Omicron variants of Covid-19 show the frightening speed that the virus can spread through the population. At Nottingham, by sequencing the DNA of many thousands of samples of Covid-19 and its variants, we are helping to track the virus and raise understanding of how it behaves.

To help supply the data to provide a picture of what is happening for health officials and government is very rewarding. At times, at the height of the spread of the Delta variant when we were processing so many DNA samples, it also felt close to overwhelming.

DNA sequencing of viruses is nothing new for us here at the DeepSeq facility – we’ve been involved in studying things like the Zika virus in the past – so when I heard that a national consortium was being put together to study the Covid-19 genome I was very keen to be a part of it.

In March 2020 we joined the Covid-19 Genomics UK Consortium (COG-UK), a Government-funded partnership of public health agencies, academic institutions and the NHS.

It was a fantastic collaboration and demonstrated just how valuable and important the work we do is at a national level.

By the time the project ended in August 2021, we’d sequenced over 10,000 samples and provided vital insights into the virus’s behaviour to public health experts, as well as hospitals across the country. We still contribute to sequencing but this is now being led the Department of Health and Social Care, which I think reflects the national importance of this work.

We’re now working with another national consortium looking for Covid-19 in sewage samples. Very quickly and from a relatively small number of samples you can survey a wide area, using samples routinely collected by water companies. It allows you to go down to a granular level, looking at what’s happening in a particular street or in a school or hospitals, and also build a picture in a particular town or city.

Wastewater acts as a sentinel system for our health, at hyperlocal and national level. We can spot variances in samples at a moment in time, right across the UK. For example, in late March, April and May 2021 we could track the spread of the Delta variant and now wastewater sampling is being used to monitor the spread of Omicron as the prevalent variant.

Wastewater sampling has the potential for showing you things that you can't see by sampling the population. It’s a technique that has been used in the past for other infections like polio, but never on this scale. By screening every wastewater site in the UK we will ultimately have a coverage across the country.

Ultimately, it has been an amazing thing to be able to contribute to understanding of the pandemic and how it unfolded.

Every virus sequence we generated was analysed and uploaded to a central database for reporting to Public Health England, along with the correct supporting data. A viral genome sequence on its own is interesting but because you’re looking at how a virus changes over time, you really you need to know information on the patient it's come from, when was it collected and what date was the test was done.

When the Alpha variant spread through the community it behaved very differently. Our findings enabled us to give hospitals a ward-by-ward analysis of what was happening and ensure they were able to respond in the correct way, as well as feeding into the national response and helping to shape wider public health policies.

"Our findings enabled us to give hospitals a ward-by-ward analysis of what was happening and ensure they were able to respond in the correct way."
Professor Matt Loose

The speed of Delta’s spread was astonishing. Watching those sweeps of different viruses move through the population was interesting academically, but deeply worrying. It’s been extremely challenging at times, especially when we were seeing such a relentless rise in cases. There were times where we would have between 300 and 400 samples sequencing at any one time but we still couldn’t get through everything on our lists, which was hard for everyone.

"Watching sweeps of different viruses move through the population was interesting academically, but deeply worrying."
Professor Matt Loose

We know we’re going to be looking at this virus for years and months to come, and it’s great to be part of a team developing new, more efficient ways to fight it.

Making better connections with hospitals and their staff has reinforced the collaboration we have between the university and the health service and as a consequence of the work that we've done, new collaborations have been built and new projects are forming.

We’re also involved with work to look at Covid and the human genome, and I’m involved with a project led by the veterinary school in Sutton Bonington to look at Covid within wild animal populations in the UK.

Professor Matt Loose

Professor Matt Loose is Professor of Developmental and Computational Biology in the School of Life Sciences, Faculty of Medicine & Health Sciences 

Further reading

Journal of Infectious Diseases September 2021, Rodric V Francis, Matthew Loose et al. The impact of real-time whole genome sequencing in controlling healthcare-associated SARS-CoV-2 outbreaks

The Lancet Infectious Diseases August 2021, COVID-19 Genomics UK (COG-UK) consortium et al. Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study

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