Using mutations to track the pandemic coronavirus

Research Lives: Áine O’Toole, PhD student at University of Edinburgh

What are you working on at the moment?

I’m working with the Covid-19 Genomics UK Consortium, to find out more about how the Covid-19 virus – SARS-CoV-2 – is circulating.

How does that work?

Around the UK, labs are sequencing the genomic material of the SARS-CoV-2 in the samples they receive, and they send us the virus sequences for analysis. We use computational tools to look for changes, or mutations, in the virus and feed back the information to the government and the researchers working across the country.

What do you mean by mutations?

Viruses can evolve very quickly, they can develop small changes or mutations in their genomes. A lot of people think mutations are automatically bad news, but they are just random changes, they are not necessarily good or bad.

By finding these small changes, we can build up a picture of the diversity of Covid-19 viruses that are circulating and help to provide an extra level of information to track its spread.

I have written software called pangolin that assigns lineages to SARS-CoV-2 virus genome sequences, and I am working on another piece of software for use in hospitals to assess local outbreaks that can rule out transmission if sequences aren’t closely related.

How did you get into this line of work?

I was in my final year of a PhD with Andrew Rambaut at the University of Edinburgh when the pandemic locked everything down. For my PhD, I have been developing computer-based tools to allow people to easily analyse virus genomes, and I was just back from a trip to the polio reference lab in Pakistan, where I was helping set up a new sequencing system for poliovirus surveillance.

Then SARS-CoV-2 arrived, and everyone in the lab started working on that. Before coming to Edinburgh, I studied genetics at Trinity College Dublin, and I did a master's degree with Prof Aoife McLysaght, where I was working on molecular evolution in primates.

What do you like most about the research?

I like its application. I decided to take up this PhD in Edinburgh because I wanted to use skills I’d developed in Aoife’s lab and apply them to global health. Viruses can change so quickly, so by building tools to track the changes in the virus over time, you can provide information about outbreaks that we wouldn’t otherwise know.

And what has been the biggest challenge?

I came into this field through genetics and biology, and I think the steepest learning curve was learning to write computer code and develop software. But I have had great mentors in Aoife and Andrew – and the people I work with.

How has lockdown been for you?

I've been busy with work, which is welcome, but I miss my family and partner back in Donabate, where I am from, so video calls have been good. I have recently caught up online with my old lab in Trinity too, which was fun.

Also the yoga class I was doing on a weekly basis went online, so I could do that during my lunch hour, and that has helped me to keep calm.”