Last year’s festive period feels like light years ago, such is the impact of COVID-19 where much can change in what feels like the blink of an eye.
One such example is the emergence of SARS-CoV-2 Variants of Concern. In late November and early December 2020, we were busy putting in place plans to scale back our sequencing operations for just a few days to give consortium members (most of whom were volunteers) the chance to rest and recharge their batteries. But as it turned out, very different plans were required. In an email to members on 20th December, I wrote
I had (perhaps unwisely) thought that my Christmas email to you [sent on the 17th of December] was my last for 2020. However, the rapidly unfolding events associated with the spread of the new variant (B.1.1.7 lineage, since named Alpha) has led me to put such thoughts aside and focus on the here and now.
We need to be prepared to generate SARS-CoV-2 sequence data over the holiday period, using a sampling framework that achieves a relatively even spread of data across the country in order to detect spread of the variant, as well as greater data from pillar 1 inpatients so that we can accumulate more data on the variant and disease outcomes. We also need to turn around genome data as rapidly as possible to make this available to Public Health Agencies.
Internally, Alpha was nicknamed the Grinch variant, as it stole Christmas from many of us. However, we were also acutely aware that every sample we sequenced came from an affected person. Alpha was wreaking a heavy toll on individuals and families across the country, and we were determined to maintain our contribution. These sequences supported efforts to examine transmissibility of Alpha (which was higher than for previous variants), disease severity (the proportion of people who required hospital care went up with Alpha), and immunity (no significant reduction).
As the number of people with COVID-19 waned in the UK and our workload became more manageable, we focused from early 2021 on sequencing performance – and in particular, the time it took to perform sequencing and load these data into the computational infrastructure and database (CLIMB-COVID) which holds and analyses genome data. We reduced our median turnaround time from receiving the sample and uploading sequence data to between two and three days from February onwards. Over the same time, we reduced the average cost of each sequence through a range of efficiencies.
This put us in a strong position to sequence Delta when it inevitably arrived in the UK. Once again, the sequence data that we generated was used to inform studies showing that Delta was even more transmissible than Alpha, and was able to partially evade our immune system.
The summer was a period of significant change for COG-UK, as we worked to transition routine sequencing in England into the hands of the relevant public health laboratories. Sequencing of samples from people tested in the community remains unchanged and continues to be generated by the Wellcome Sanger Institute, where output has increased to an industrial scale. By contrast, the end of September has seen sequencing of samples from patients in hospitals (so-called pillar 1) largely transferred from the academic sequencing sites of COG-UK partners in England to the laboratories of Public Health England (now the UK Health Security Agency, UKHSA), as they expanded their capacity and capabilities.
Embedding SARS-CoV-2 sequencing service within the appropriate public health agencies provides notable advantages and drives sustainable and long-term benefits for the UK population. Scientists working in university institutions also become free to return to the important research that was put on hold due to the emergence of SARS-CoV-2. However, numerous COG-UK members will continue to bring their expertise to the ongoing pandemic response, and several laboratories will remain active to provide surge sequencing, and sequencing for the new variant assessment programme (NVAP) established by the UKHSA.
Having handed over routine sequencing, it was time to review how COG-UK could continue to contribute to the COVID-19 response, and pathogen genomic surveillance more generally.
A major development in 2021 was to secure joint funding from the Wellcome and the Foreign Commonwealth and Development Office (FCDO), to support a programme named COG-Train. This collaboration with Wellcome Connecting Science complements a range of activities already being led by consortium members, including the ARTIC network. COG-Train will develop five online courses on SARS-CoV-2 sequencing and analysis using the FutureLearn platform, together with train-the-trainer and virtual classroom training. This aims to complement the many initiatives happening worldwide to increase sequencing capacity and analysis expertise.
An important programme running throughout the year has been Women in COG. We have interviewed a series of women who have made a major contribution to the pandemic, including Dr June Raine (MHRA Chief Executive), Dr Magdalena Skipper (Editor in Chief, Nature), Dr Angela Douglas MBE (Deputy Chief Scientific Officer for NHS England and NHS Improvement). Professor Judy Breuer (Professor of Virology at University College London), and Dr Charlotte Summers (Professor of Intensive Care Medicine at the University of Cambridge and Intensivist at Addenbrooke’s Hospital).
We have continued to hold internal and external science seminars that have been very well attended, with external events available on YouTube. Our most recent COG-UK Science Showcase event on 7th Oct 2021 showcased the role of SARS-CoV-2 genomics in UK national studies and beyond. Recordings are also available on from our one-day COG-UK Together event, a consortium-wide occasion that provided the opportunity to reflect on achievements and impact.
We have also revisited our existing strategic priorities. For March 2021 to March 2022, our three priorities were data linkage and analysis, research on COVID-19 for health impact (14 current funded projects), and global training in SARS-CoV-2 sequencing (COG-Train). A strategy refresh has reaffirmed our commitment to all three priorities.
The importance of data linkage cannot be understated; by bringing diverse datasets together, novel analyses can be performed that may contribute to improvements in clinical care. For example, a combined analysis of viral and human genomes using advanced statistical and machine learning techniques could lead to improved prediction of which patients in hospital with COVID-19 are likely to progress to severe disease. But we also need to make the data available to a wider group of researchers through secure data access agreements and by placing data in Trusted Research Environments. This will be achieved through work with the Open Data Analysis Partnership, supported by the National Core Studies programme, COVID-19 data and connectivity theme. We are also in the process of realigning our research priorities to focus on both the current pandemic and future pandemic threats. In this way, we remain at the interface between cutting edge academic science and public health, leading to discoveries that help prepare us for the future.
The immense challenges faced in 2021, and 2020 before it, have shown that the UK pathogen genomics community is incredibly strong and resilient, and has been able to pull together to achieve notable success and impact on the pandemic response in the UK and globally.
I would like to thank every individual and each partner organisation associated with the work of the consortium during the past year. We can now take the next steps to build on this work, collectively and individually, and apply what we have learned to catalyse change in how we tackle a wider range of infectious diseases.
Sharon Peacock is Executive Director and Chair of COG-UK.
Image Credit: Alex Cagan