Thanh Le-Viet is a bioinformatician at the Quadram Institute in Norwich, working on CLIMB – the platform which stores all of COG-UK’s SARS-CoV-2 genome sequence data. Thanh and his team work around the clock to ensure results are provided as soon as a sequencing run is finished, day or night.
Tell us about your role at COG-UK
I’m a bioinformatician in Andrew Page’s group at the Quadram Institute, a core partner of the COG-UK consortium. I have worked with our team to provide bioinformatics support and infrastructure to the project. We automate bioinformatics analysis for processing SARS-CoV-2 data; ensuring it runs robustly 24/7 on the new CLIMB-BIG-DATA cloud platform at the institute.
What does a typical day of work look like for you?
My work starts when the sequencing team kick off the sequencing instruments. When the run finishes, we need to rapidly deliver sequenced genomes, identify viral lineages and Variants of Concern or Variants of Interest, and report quality metrics to our working group for further assessment, before submitting data to the CLIMB server. If there are any queries from the sequencing team, I provide analysis to further understand what we have for optimising the pipelines.
How has the pandemic affected your work?
I have been working from home for more than a year, which I have never done in my career. I have still provided bioinformatics support to scientists and managed new infrastructure at the institute, though our COVID-19 work has been higher priority.
What’s been the most challenging aspect of your time within the consortium so far?
Providing the results as soon as the sequencing run is finished, at any time. The results must be then quickly reported to the working group who will assess the quality of the genomes and subsequently make decisions.
What is your proudest accomplishment from your time at COG-UK?
I am proud to be part of the hard-working group that has sequenced more than 18,000 SARS-CoV-2 samples over the last year. Our work also rapidly provided information to public health agencies to help prevent the spread of SARS-CoV-2 in the community.
Why did you become a scientist?
When I worked on the Atlas of Human Infectious Diseases project, I became interested in using computational approaches to understand and tackle the transmission of infectious diseases. Inspired and supported by Prof. Heiman Wertheim and Dr. Marc Choisy, I decided to pursue a study on the transmission of dengue virus for my doctorate degree, and now, I’ve had the exciting opportunity to work on SARS-CoV-2.
What do you like most about your job?
There have been many challenges when working on this project, and what I like most is that our team are willing to go the extra mile, learn and manage these challenges together.
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.