The Student
Blue string of DNA
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Cracking the Covid code
by Jude Holden, 25/03/21

Meet an Edinburgh PhD candidate tracking the pandemic’s mutations…

A group of students at the University of Edinburgh are in the vanguard of the microscopic war against Covid-19, trying to head off its myriad mutations and give advance warning if the virus evolves into more contagious forms. It was these students who helped to find the so-called Kent Variant. 

Central to the struggle, as in all wars, are codes and code letters; in this case the four letters, A, C, G and T, used to describe different components of DNA; and for the virus the letters which make up its genetic structures, called RNA. The key technique is something called genome sequencing which works out the order that the letters appear, many thousands of times, in a genetic structure. A genome is the complete set of genetic material in a living thing. 

Edinburgh PhD student Verity Hill explained the science which tracks how the virus changes and moves though the population. It is essential information for the teams developing vaccines and for the government to know what action to take, such as lockdowns. 

“Basically, genome sequencing is just finding out what letters make up an organism’s genome,” She said. The machine used is surprisingly everyday. It’s called a MinION. 

“It’s really small and portable ,and you can plug it into your laptop. You pipette your solution with your RNA or DNA into the machine and it gets pulled through a pore that’s really, really small, and the pore changes shape depending on the electrical charge of the letter of genetic material it’s pulling through and a computer registers that and you get a genome sequence.”

Verity works on the surveillance of mutations in a research group that helped to find the Kent variant, or B.1.1.7. “At the moment everybody is finding another variant every other day.”

The discovery of the more easily transmittable Kent Variant was confirmed, Verity said, when the work her supervisor, in Edinburgh, was doing on the ‘family tree’ of viruses showed up a new cluster of mutations at the same time as Public Health England was looking at unusual infections in Kent. When the findings were compared they realised they had a new variant.  

Verity herself is not involved in using the MinION. 

“My day to day work is coding. Early in the pandemic we were making [digital] tools to help deal with the enormous amount of data. Now we’re slightly more into the analytical end of things so we work out what’s going on. At the moment I’m working on a couple of projects on B.1.1.7, Kent Variant – where it came from and how it spread within the UK and England specifically. I’m also doing some projects on trying to work out what makes corona virus in general spread throughout the UK.”

This work has shoved her into the public forefront of science in a way none of her previous work did. 

“It’s simultaneously exciting and very stressful. Before I was doing this I was working on Ebola in West Africa which is an epidemic which finished a number of years before and was working on things pretty slowly. People were interested in what I was doing but nobody really cared that much.” 

Things changed when the pandemic began. “Suddenly random people on Twitter are saying ‘what are you doing? Why haven’t you done this?’ and journalists from big newspapers call. It is really cool and I do infectious diseases because I want to help people so it is nice that the stuff we’re doing genuinely feels useful. This is very immediate.”

But sometimes the stress outweighs the excitement. “I worked with another PhD student in this lab, to make this piece of software called Civet to do outbreak analysis and every time I find a bug in it I still feel really sick. People actually use that software to monitor outbreaks in populations that they care about to make policy decisions and other things.”

Verity comes from Aylesbury in Buckinghamshire but she loves being in Edinburgh. 

“I love the people that come here. This is my first department ever. I have so much fun here, everyone is really friendly. I’ve heard horror stories about other departments where people do PhDs but it’s great here. There’s much less of that toxic work ethic stuff you hear about in other unis.” 

Image: TheDigitalArtist via Pixabay