From teacher to SARS-CoV-2 mutation hunter | Dr Alessandro Carabelli
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From teacher to SARS-CoV-2 mutation hunter

A Wall In Naples Thomas Johns

From teacher to SARS-CoV-2 mutation hunter

Blog by Dr Alessandro Carabelli, Research Lead, COG-UK

I joined the Peacock group as a postdoctoral scientist in October 2020, after five fantastic years of research at the University of Nottingham where I gained my PhD. Before that, I taught A level chemistry and biology in Italy for seven years. But life is full of surprises, and it was almost by chance that I found myself directing my entire scientific training at the biggest infectious threat of the last 100 years.  

LIFE-LONG LEARNING

My primary school teacher inspired me to learn about the natural world and how to observe it, and after a science degree I followed in her footsteps and became a science teacher, focused on A level biology and chemistry. I was aware that teachers do more than teach, and their impact extends far beyond the classroom. I wanted to make a difference in the lives of as many students as I could, as well as communicate my passion for science. I was full of questions about my method of teaching. My grandpa used to say “if you are not able to make a child understand something, it means you haven’t understood it yet”. 

This idea of explaining complex ideas simply has served me well throughout my entire scientific career and especially now during the pandemic, when I am often asked to pass on my knowledge and understanding of SARS-CoV-2.

A PHILOSOPHICAL THREAD

Science is rarely a fireworks experience, and my A level students soon recognised that. The experience of awe and surprise is mixed with hard work, laborious procedure, boring definitions, unsuccessful experiments etc. So, what has driven me as a scientist?

The secret is to have faith in the corner of the eye. Sir Ferdinand Mount in an essay on Alan Bennett quotes his words “the faith in the corner of the eyes”, commenting on a painting by Thomas Jones of some towels drying on a balcony in Naples (A wall in Naples, 1782. National Gallery, London). It is an utterly ordinary scene, but in its freshness, its irresistible thereness, that balcony seems to jump off the wall. I think this is a common characteristic in scientists. In the utterly, ordinary, unremarkable scene, a scientist is able to catch with the corner of the eye the detail that to many, would have passed with no attention.

This concept is very apt when it comes to SARS-CoV-2 mutations. Evolution is a fact of nature. We know that the virus is evolving constantly. So many mutations are now present in the genome that spotting the important mutations and variants at pace requires just this idea, backed up with the generation of detailed evidence.

MUTATION DETECTIVE

Months ago, when the COVID-19 pandemic had just started, and everyone was dealing with challenging circumstances including isolation, uncertainty, and the sacrifice of not being able to see their loved ones, I felt a deep desire to contribute.

This forced me to review my contribution to the world and apply for a new role in the COVID-19 Genomics UK (COG-UK) Consortium. I now support the study of the emergence and possible implications of SARS-CoV-2 mutations and variants. I set up and manage a research group focused on mutations where we examine emerging evidence, and I provide numerous analyses to the group.

This Mutational Analysis working group is formed of scientists from many different academic institutions and the Public Health Agencies in the UK. There are clinicians, evolutionary biologists, epidemiologists, microbiologists, virologists, immunologists, structural analysts, bioinformaticians and web-developers. The complex nature of the SARS-CoV-2 pandemic has shown everyone how an interdisciplinary approach is required to ending the pandemic. We need to constantly expand the horizon of what we think we know and share ideas with others. “There are more things in heaven and Earth, Horatio, than are dreamt of in your philosophy” says Shakespeare’s Hamlet.

MUTATIONS AND THE FUTURE

Most of the mutations in SARS-CoV-2 have no effect on the biology of the virus and confer no advantage and get carried quietly in their genetic ‘barcode’. But some changes help the virus spread more quickly among the population, and so become more common. Even more worryingly, mutations may emerge that lead to more serious infection or reduce our immune response to the virus. Observing and tracking these changes allows scientists to uncover how the virus is mutating and spreading.

We have developed bioinformatic tools and pipelines to detect mutations of interest as they are detected in the COG-UK dataset. This information is made openly accessible to others in order to assess community risk implications and to select mutations for further investigations. There are already thousands of different mutations in the SARS-CoV-2 genome and it would be a waste of time to study all of them, so being able to select those that may pose the greatest risk to human health is vital.

The discovery of the variant B.1.1.7 has changed all our lives significantly. But this will not be the last and for the moment, I am aiming to train the corner of my eye at COG-UK.  It is my commitment to self that I will do everything in my power to detect mutations that matter, and bring these to the attention of the world.

To find out more about the work of COG-UK, please visit https://www.cogconsortium.uk

Image credit: Image A Wall in Naples, Thomas Johns https://www.nationalgallery.org.uk/paintings/thomas-jones-a-wall-in-naples courtesy of the National Gallery under a Creative Commons Licence