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Dr Samantha Lycett on tracking outbreaks

Understanding evolution and spread of viruses and bacteria, and contributing to tackle the pandemic.

Dr Samantha Lycett in the office
Dr Samantha Lycett in her office looking at sequence data.

Dr Samantha Lycett is a Group Leader at the Roslin Institute, where she analyses data from the genetic code of viruses and bacteria to understand their spread and evolution. In this interview, she talks to MSc Science Communication student Cheir Lu about her work and how she is applying it during the Covid-19 pandemic.

Could you describe your career path?

I did my undergraduate degree at the University of Cambridge and my PhD at Imperial College London, both in physics. I spent several years working in signal processing before moving to biosciences. I did a Master’s in Bioinformatics at Newcastle University and came to Edinburgh, firstly with the Institute of Evolutionary Biology in 2007, and then at Roslin since 2014.

Why did you decide to become a scientist?

My interest in science has been from a very young age, around six years old. I cannot really say that I ever at some point decided to become a scientist. I think I just did science all my life.

What made you turn to biological research?

In the first few years of the 21st century, there was a big explosion in gene sequencing technologies, which meant that there was lots of really interesting data to look at all of a sudden. I wanted to move to biology to look at all the interesting data.

Was it a big change in your career?

It sounds like a big change, but actually physics and biology are not so different. The ultimate outcome of these two disciplines is perhaps different, but the underlying methods can be quite similar.

In biology there's more complexity, which is very interesting for a physicist. In fact, there are quite a few physicists who now work in biology. For example, several group members and collaborators are also former physicists.

Why did you decide to work at the Roslin Institute?

I came to Roslin because I received a Chancellor's Fellowship and this is an excellent opportunity to work with people who are interested in the same biological problems as me.

Could you tell me about your work in a nutshell?

I work on pathogen phylodynamics, analysing the genetic code of harmful viruses and bacteria through computational work. The data shows how they can adapt from infecting one organism type to another, their patterns of spread, and the underlying factors that drive these processes. Viruses and bacteria evolve quickly and accumulate changes in their genetic code over time. The information I analyse can be used to track where they have been, both in space and in which species.

What do you like the most about working at Roslin?

I like a lot of things about working at Roslin. I really like interacting with my colleagues. I also like working in the research division of Infection and Immunity, where I work on infection and particularly on the diversity of harmful organisms. These are my core interests and at Roslin I get to speak to other experts about my favourite science topics.

Could you tell me about a real-world application of your work?

Generally, the application of my work is related to outbreaks, such as where they are coming from and what we think might happen. When there is already infection among people or farms, I can trace the infection to particular places and suggest good strategies to eliminate or eradicate a harmful virus or bacteria, given the data and the patterns of infection transmission.

I heard that you did research connected to the coronavirus pandemic. Do you have anything to share with us about that?

I have been working on coronavirus sequences with groups from universities around Scotland and other parts of the UK, Public Health Scotland and the UK’s National Health Service. This consortium has sequenced approximately 20 per cent of the cases which had a positive test in Scotland. Our outcomes can be used to see where and when different cases have been imported into Scotland and to analyse how quickly the number of cases is increasing or decreasing. Most recently, our research found that the new wave in October mostly originated from people coming back from places outside Scotland.

Can you describe your work with the Scottish Government?

For the coronavirus research, we have written a report, and it has been sent to some committees in the Scottish Government. Apart from the work connected to Covid-19, I work in advising the Scottish Government on animal disease outbreaks. I’m currently working on the bird flu outbreaks. This 2020 autumn season has brought highly pathogenic avian influenza back into Europe and the UK.

What are the challenges you experience as a scientist?

I really like challenges and scientific problems. To have a problem and work out how it can be solved, how it can be made better, or how it can be understood is my favourite thing.

If I have to mention other challenges, I think there are three that scientists would meet: understanding how to relate experimental results to what is happening in a population; predicting what might happen among all the possibilities; and processing enough data quickly so that the results can be used in a meaningful way.

How do you overcome such difficult challenges?

Sometimes I use techniques from other disciplines and adapt them into the current one, sometimes I just try to invent new approaches myself or with my colleagues. For the Covid-19 related research, our team have had to come up with new ways to adapt the techniques, in order to be able to manage the big datasets.

What was the most unusual thing you have done as a scientist?

Before I came to biology, I designed a signal processing system that used radar to help detect small objects on runways. This system was sold to several airports and I was in the team that installed the first one.

Do you think the importance of science communication has been increasing?

Absolutely, especially during the pandemic. It is necessary for scientists to communicate with the government and the public in a way that is understandable, to inform them about scientific results and how these help with decisions. My colleagues and I are currently doing this.

Do you have any advice for students who want to go into this field of research or are starting a career as a scientist?

My general advice is that there are lots of very interesting, very relevant questions worth trying to understand. Learning the latest techniques is helpful to answer these questions.

Particularly on the computational side, even in experimental science, a lot of data will be generated. Being able to handle, process, analyse, or model and predict the data is very important. It would be very useful if you could code or script in an appropriate language.

What would you be doing if you hadn’t become a scientist?

If you had asked me this when I was a PhD student, I would have said I would become a dancer, as it was a big passion of mine at the time.

Related links

Scottish funding supports Roslin Covid-19 work

Prediction tool could help control bird flu

EPIC: Centre of Expertise in Animal Disease Outbreaks