9 May 2023

Acknowledging the exceptional contribution made to COG-UK by Professor Dominic Kwiatkowski

By Professor Sharon Peacock

I was deeply saddened to hear news of the death of Dominic Kwiatkowski, who was the founder and chair of the MalariaGEN network, an honorary faculty member at the Wellcome Sanger Institute, and Emeritus Professor of Genomics and Global Health at the University of Oxford.

I want to record my deep debt of gratitude for Dominic’s contributions towards the development and success of COG-UK.

Dominic was present at the very first planning meeting for COG-UK, held at the Wellcome Trust building in Euston Road on 11th March 2020. He and Cordelia Langford (Director of Scientific Operations at Sanger) shaped the conversation around how the Wellcome Sanger Institute could become the national COG-UK hub for sequencing the SARS-CoV-2 virus. Dominic co-chaired a session on how we could describe and agree the individual components of an end-to-end pipeline for COVID-19 sequencing, from sample processing to use of data.

These discussions underpinned our ideas in our first funding proposal, written over the next few days and submitted to Sir Patrick Vallance and Sir Chris Whitty (A proposal from the COVID-19 Genomics UK (COG-UK) consortium for rapid development of a national capability for COVID-19 sequencing for public health benefit). This proposal was the gateway to the development of a national sequencing consortium. Our proposal referred to the significant capacity for large scale SARS-CoV-2 sequencing at the Sanger, which could be rapidly ramped up to fill the gap in sequencing capacity and expand the nationwide coverage of sequencing.

The funding proposal noted that critically, the Sanger had 25 years of experience in producing and handling genomic data at world-leading scales that would be crucial to the delivery of COG-UK. The work that Dominic had led through MalariaGEN predated and fundamentally underpinned this. He had been immersed in thinking about how the Sanger not only had the sequencing technology (which many other labs had), but how to scale operational pipelines that drove pathogen sequencing at a very different scale. This was not just in terms of the process of the sequencing – it was the whole information flow, from samples coming in to producing data that was usable for public health purposes.

The Sanger were already discussing sequencing scale up for the pandemic before COG-UK came together, but after the meeting in London, one of the first things that the Sanger did was to assemble teams to work on the project for COG-UK. The Institute named these efforts Project HERON. Dominic played a leading role throughout the life of the HERON project.

MalariaGEN and Dominic’s forward vision was a strong influence on data curation and analysis at Sanger. Developing the capability to integrate large-scale patient, sample and genome information during the pandemic required software development and a data pipeline. This work included numerous members of the MalariaGEN programme.

Sanger went on to generate more than two million SARS-CoV-2 genomes over the pandemic. These were vital for the national mapping of the emergence and spread of variants, for which they developed intuitive and open-access visualisation tools. These genomes were also important for studies that examined whether variants were more transmissible or had altered immune evasion properties.

Dominic advocated for, and supported SARS-CoV-2 sequencing at every stage. He provided thoughtful support and advice each day to the teams at Sanger and COG. Dominic was a member of the COG Steering Committee (our main decision-making body), which also reviewed scientific publications as part of our publication policy. The latter was an important part of ensuring that everyone in COG-UK was given authorship on papers that used our data. He was unstintingly generous with his scientific experience and wisdom.

It’s clear that Dominic played an instrumental part in the success of COG-UK, which created a vital capability to the UK pandemic response. I will always carry the memory of this exceptional contribution. I will miss him greatly for the generous and wise colleague that he was.

COVID-19 Genomics UK (COG-UK)

The COVID-19 Genomics UK (COG-UK) consortium works in partnership to harness the power of SARS-CoV-2 genomics in the fight against COVID-19.

Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative collaboration of NHS organisations, the four public health agencies of the UK, the Wellcome Sanger Institute and sixteen academic partners. A full list of collaborators can be found here.

The COVID-19 pandemic, caused by SARS-CoV-2, represents a major threat to health. The COG-UK consortium was formed in March 2020 to deliver SARS-CoV-2 genome sequencing and analysis to inform public health policy and to support the establishment of a national pathogen sequencing service, with sequence data now predominantly generated by the Wellcome Sanger Institute and the Public Health Agencies.

SARS-CoV-2 genome sequencing and analysis plays a key role in the COVID-19 public health response by enabling the identification, tracking and analysis of variants of concern, and by informing the design of vaccines and therapeutics. COG-UK works collaboratively to deliver world-class research on pathogen sequencing and analysis, maximise the value of genomic data by ensuring fair access and data linkage, and provide a training programme to enable equity in global sequencing.