A UK research consortium to look into breaking the chain of infection

The COVID-19 Genomics UK Consortium or COG-UK has received government funding of about £20 million to deliver large-scale, rapid sequencing of the cause of the global pandemic to fuel the UK’s overall response towards the virus. 

COG-UK is a widescale partnership comprised of the National Health Service (NHS), Public Health Agencies, and academic institution which includes the University of Birmingham among other leading research universities. 

The research results produced by the consortium will be shared across the board with hospitals, regional NHS centres and the government to help curb the pandemic and ultimately save lives. 

Samples from patients who have tested positive for COVID-19 will be collected and sent to a network of sequencing centres which include the Birmingham, Belfast, Cambridge, Cardiff, Edinburgh, Exeter, Glasgow, Liverpool, London, Norwich, Nottingham, Oxford, and Sheffield. 

For the University of Birmingham, a research team led by Professor of Microbial Genomics and Bioinformatics in the Institute of Microbiology and Infection Nick Loman will deploy a real-time genome sequencing facility that has the capability to sequence the virus genomes from patients in the West Midlands in less than 24 hours. 

In addition, a premier genomic research facility the Wellcome Trust Sanger Institute will also provide large-scale sequencing capacity and additional support. 

“This is a remarkable collaboration which brings together Birmingham and the UK’s incredible depth of expertise and knowledge in viral sequencing and genomics. An open and distributed model of sequencing involving both academia, the NHS and our public health bodies is the right way to ensure results are delivered quickly to decision-makers. We are now well-positioned to return deep insights into understanding the rapidly-accelerating pandemic of COVID-19, easily the most pressing infectious disease emergency we have faced in two generations in the UK,” said Professor Loman.

“The government’s investment is well-timed to accelerate the pace of viral genome sequence production and ensure this information is openly available to epidemiologists and virologists worldwide. This will provide an unprecedented real-time view of COVID-19 virus evolution.”

Genomic sequencing will aid the research alliance and overall health systems in the country to further understand how the COVID-19 pandemic evolves and spreads across local, national and international settings. 

It will provide an avenue for further research regarding what must be done to break the chains of transmission in order to curb the spread of the virus. 

It will also be possible to examine how the virus adapts and possibly change within a human host over time and how drug treatment interventions, and eventually vaccines may affect the virus. 

Two key research initiatives, which the University of Birmingham has played an important role in will contribute greatly to the expected outcomes from the consortium’s efforts. 

The first initiative is the CLIMB project, which recently secured funding for an additional five years with the CLIMB BIG DATA project. CLIMB provides the data analysis pipelines as well as the computing and storage capacity required to analyse the large genome datasets. 

The second initiative is the ARTIC project which received funds from the Wellcome Trust Collaborative Award. It is a collaborative project to put genomics at the heart of outbreak response. 

From this initiative, a method to sequence the coronavirus which was built upon previous successful methods for the Ebola and Zika viruses was released back in January which is currently widely used by researchers across the globe. 

The ARTIC project, funded by a Wellcome Trust Collaborative Award, is a collaborative project to put genomics at the heart of outbreak response. Dr Josh Quick, a UKRI Future Leaders Fellow in the Institute of Microbiology and Infection rapidly developed a method for sequencing coronavirus, released to researchers back in January, and which has already been widely adopted across the world. This method builds on work previously successfully used to trace epidemics of Ebola virus and Zika virus. 

“Based on previous experiences with Ebola and Zika virus we were able to rapidly develop an approach to sequencing the COVID-19 virus rapidly using a targeted method. The importance of this method is that it works well even when only minuscule amounts of virus are present in the sample, something we commonly see,” said UKRI Future Leaders Fellow in the Institute of Microbiology and Infection Dr Josh Quick. 

“It has been used to generate the first genomes from countries including Brazil, Scotland, Wales and Northern Ireland with nanopore sequencing and we have helped over 50 groups in over 20 countries establish genome sequencing capabilities in their own labs.”