Sarion Bowers, Head of Policy at the Wellcome Sanger Institute, on the Institute’s role in tackling the Covid pandemic and what we can learn for the future.

On the 23rd March 2020 as everyone was grappling with the new reality of lockdown, the Wellcome Sanger Institute was thinking about a different problem: how could we utilise our massive-scale, high-throughput genomics pipelines to help tackle the pandemic?

The Sanger Institute was established in 1992 as part of the Human Genome Project and since then has built up an extensive program of genomic research. Genomics looks at structure, function and evolution of an organism’s complete set of DNA, including all of its genes. Since the Human Genome Project, the Sanger Institute has used genomics to tackle some of the world’s most intractable problems.

The Sanger Institute’s work is done at scale, sequencing thousands of genomes of humans and other species every month, and rapidly releasing our data in to archives and databases for researchers and clinicians to access. This work is primarily funded by Wellcome, but we receive additional funds from medical research charities, UK Research and Innovation (UKRI) and Horizon 2020 amongst others. Horizon 2020 has a particular strategic importance to the Sanger Institute as it funds the kind of large collaborations and consortia we use to drive our science. We work in collaboration with organisations around the world, leading large global consortia to deliver science beyond the ability of any one organisation and even any one country.   

With this background, the Sanger Institute was well placed to support UK efforts to tackle the pandemic. Discussions on what to do started at the beginning of March and on April 1 funding for the launch of COG-UK, led by Sharon Peacock, was awarded, with money coming from The Department of Health and Social Care, UKRI and the Sanger Institute. COG-UK is a collaboration between academic partners, public health agencies, NHS organisations, the Lighthouse laboratories, with the Sanger Institute acting as the central sequencing hub. The purpose was to provide genome data, sequencing methods and analysis tools that could be used to inform public health and policy making. Using genomic surveillance we aimed to track the spread of COVID, and identify new variants that might affect the transmission of COVID or its ability to evade treatment or vaccines once they were developed.

Although never tried before at this scale, the Sanger Institute already had previous experiences of using genomics in infectious outbreaks having used it in a proof of principle study looking at MRSA in a neonatal unit, and at larger scale in the West African Ebola outbreak of 2014. The pandemic posed new challenges though, with the first being how to get hold of samples from COVID19 patients. The solution was to take the waste from the PCR test plates from the Lighthouse laboratories that had been used for testing and cherry pick the positive samples from amongst thousands of negatives. Using robotics, we have handled nearly 20 million samples since the start of the pandemic.

The next challenge was to scale up our pipelines so that we could reliably sequence thousands of SARS-CoV-2 genomes every week. As a result, the Sanger Institute alone has generated 25% of the world’s SARS-CoV-2 genome sequences and approximately 65% of the data produced by the UK, making the UK the global leader in genomic surveillance. The Sanger Institute is now sequencing 20,000 SARS-CoV-2 genomes a week and we have plans to scale up further.  

The benefit of COG-UK was exemplified at the end of 2020 with the early discovery of the B.1.1.7 lineage, also known as the “Kent variant”, which was found to be more transmissible, and prompted the Government to implement a new lockdown. The investment by Government and medical research charities into COG-UK has established the UK as the global leader in genomic surveillance, and as the vaccination program rolls out across the UK will play a critical role in the early detection and characterisation of SARS-CoV-2 variants which can escape the vaccine.

The UK has much to be proud of in its scientific response to the pandemic. It has played a well-recognised globally significant role in vaccine development and also in identifying drugs to treat COVID19.  The UK’s pioneering use of genomic surveillance has established us as the world leader and lays out the template for a completely new way that infectious disease may be managed in future.  

COG-UK was able to enact this revolution because of the Sanger Institute’s phenomenal sequencing power, and the strong academic and health partners in the UK who were able to rapidly come together to mount this powerful genomic surveillance response. The Sanger Institute operates within a UK and global ecosystem of public and private scientific organisations, funded from the public purse, through charities and by commercial organisations. We use our connections to establish and deliver transformative scientific projects and leverage them to improve human health.  The strong scientific ecosystem of the UK demonstrated enormous fire power when called upon in this crisis and demonstrates that investment in science over many years in the UK has paid off.

Recent cuts to UKRI’s funding, notably the Official Development Assistance (ODA) budget, threatens UK science and the global ecosystem in which we operate. Alongside, our work on COVID we have long worked on infectious disease in Low and Middle Income Countries (LMICS). The ODA funding cuts have resulted in us curtailing a major project on Malaria, a disease which kills a child every 45 seconds, but has also damaged our standing with collaborators on other projects. Start-up costs of projects are often offset against future payments of the grant. Informing collaborators that promised funding potentially would not materialise was distressing for our researchers, potentially devastating for collaborators in Low and Middle Income countries and felt like a significant breach of trust.

COVID has hit science hard. With medical research charities suffering and making funding cuts of up to 40%, it is more important than ever that the Government invests in research, not only with budget, but through maximising the UK’s participation in Horizon Europe, the replacement to Horizon 2020, and by building relationships globally through and for science. 

The scientific success of genomic surveillance offers us opportunities to mitigate some of the economic damage caused by the pandemic and by future outbreaks of infectious disease, and gives us new ways to tackle infectious outbreaks, saving lives. There are also commercial opportunities for the UK, building another pillar in our already strong genomics sector. These opportunities are waiting to be realised and it is important now more than ever that we challenge cuts to science budgets and the investment in science continues for the benefit of the UK and the world.