Greg Young is a Postgraduate Associate in the Northumbria University Team, who has played a vital role in managing the lab’s logistics of COVID-19 sample transfer and analysis. As an academic lab, his team weren’t ready for the scale of sampling COG-UK demanded, but they managed to overcome the necessary challenges to sequence over 18,000 SARS-CoV-2 genomes throughout the pandemic to date.
Tell us about your role at COG-UK
I worked in the Northumbria University COG-UK regional sequencing hub. We’ve provided genomic surveillance of COVID-19 cases occurring in hospitals spanning the breadth of the country from the borders down to North Yorkshire.
My job in the lab centred around the day-to-day running of the more “hands-on” sample-facing side of genomic surveillance. Specific responsibilities included liaising with clinical colleagues to arrange transfer of samples from local hospitals to the university (sometimes I got to drive the van to collect these!) then performing nucleic acid extraction, reverse transcription (RT), polymerase chain reaction (PCR), library prep and sequencing on all of these. I’m so proud to be able to help in whatever way I can with such a worthwhile cause!
What did a typical day of work within COG-UK look like for you?
Typically a day’s work would start with planning the workload for the team and removing reagents and samples from fridges and freezers. We try to start as early as possible because there are a few long incubation steps which can impact your productivity if you leave them too late.
At the start and middle of the week we often have sample deliveries which need to be aliquoted into 96-well plates before we extract the viral RNA for sequencing. Unfortunately the aliquoting stage can’t be automated because we receive so many different sample tubes from the many hospital trusts providing samples so this is all done by hand in a class II hood. We have a great lab team here at Northumbria, so we take it in turns to do this ever-so-slightly less appealing job and can get through about 500 aliquots and extractions in a day. While one lab member is aliquoting and doing the extractions, another will prepare and aliquot out reagents for the RTs and PCRs so we don’t need to leave RNA overnight.
The fun part of this is the library prep and sequencing. At Northumbria we’ve typically used Illumina sequencing because of the base-call accuracy, but I’ve loved working with the Nanopore technology because you get instant feedback and can track your results in real-time — that’s rare in sequencing technology. We generally try to have at least one person performing these library preps on one or both platforms every day to keep up with the throughput requirements of the project.
Sometimes days can be long. We’ve had plenty of 12-hour shifts and a couple overnighters to turn around urgent samples with suspected Variants of Concern and Variants under Investigation, but generally days are no longer than normal. The adrenaline rush accompanying the potential ID of an exciting variant is enough to get us through!
How has the pandemic affected your work?
I’m a microbial ecologist by training. Despite starting out in a clinical field (the magical world of gut microbiota – meaning thousands upon thousands of poo samples!) I’m currently working in a really exciting new collaborative group between Northumbria and Newcastle universities called the Hub for Biotechnology in the Built Environment (HBBE). COG-UK work does kind-of fit the remit of our role in the HBBE – to identify and characterise microbes associated with built environments – and the group have been super supportive of our involvement which is great!
What’s been the most challenging aspect of your time within the consortium so far?
A big priority has always been making sure we delivered results on sample lineages within a decent turnaround time. Making sure we didn’t run out of consumables when we were at peak throughput in December & January was particularly tough. As an academic lab we weren’t really set up for the scale of sampling COG-UK demanded. With >2000 samples arriving per week we could get through some serious volumes of consumables. If I had my time again I’d have invested in companies producing filter tips back in summer last year!!
What is your proudest accomplishment from your time at COG-UK?
Alongside the rest of the Northumbria team, we’ve managed to sequence over 18,000 SARS-CoV-2 genomes throughout the course of the pandemic so far. I’d say that’s quite some achievement?
What do you like most about your job?
COG-UK has given us the chance to work with so many great colleagues – both experienced and those really early in their careers. I love working with others and I’ve really enjoyed being part of a big lab team. Special mentions to all of the lab members who’ve pitched in throughout the project including: Andrew Nelson, Clare McCann, Matty Bashton, John Henderson, Rui dos Santos, Zack Richards and Will Stanley.
About our Meet the Researcher series
Hundreds of people in the COG-UK consortium have been working tirelessly behind the scenes throughout the pandemic. Many have had to sacrifice their Christmas holidays, put other projects on hold, and work long hours to help ensure the consortium functions as it should. In this blog series, we meet just a few of the countless people whose dedication, commitment and hard work has been essential to the success of COG-UK.
COVID-19 Genomics UK (COG-UK)
The current COVID-19 pandemic, caused by SARS-CoV-2, represents a major threat to health. The COVID-19 Genomics UK (COG-UK) consortium has been created to deliver large-scale and rapid whole-genome virus sequencing to local NHS centres and the UK government.
Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative partnership of NHS organisations, the four Public Health Agencies of the UK, the Wellcome Sanger Institute and academic partners providing sequencing and analysis capacity. A full list of collaborators can be found here. Professor Peacock is also on a part-time secondment to PHE as Director of Science, where she focuses on the development of pathogen sequencing through COG-UK.
COG-UK was established in April 2020 supported by £20 million funding from the COVID-19 rapid-research-response “fighting fund” from Her Majesty’s Treasury (established by Professor Chris Whitty and Sir Patrick Vallance), and administered by the National Institute for Health Research (NIHR), UK Research and Innovation (UKRI), and the Wellcome Sanger Institute. The consortium was also backed by the Department of Health and Social Care’s Testing Innovation Fund on 16 November 2020 to facilitate the genome sequencing capacity needed to meet the increasing number of COVID-19 cases in the UK over the winter period.