Is the UK Losing its World Leading Covid Surveillance Network?
Introduction
The UK‘s Covid-19 Genomics UK Consortium (COG-UK) has been winding down its genomic sequencing network, raising concerns among experts about the loss of a vital tool in pandemic control. COG-UK was established in March 2020 and has been a world leader in producing genomic sequences of Covid-19. The network’s contribution has been significant in identifying new variants of concern throughout the pandemic. However, its funding is being reduced just as the UK government wants to move on from Covid-19. This article discusses the implications of the network’s dissolution on the UK‘s pandemic response.
Background
Genomic sequencing is the process of transcribing genetic instructions that a pathogen requires to develop and maintain itself. While it was slow and expensive when first developed in the 1970s, advances in technology have made it cheaper and faster over the years. When the SARS outbreak occurred in 2002, the genome sequence of the coronavirus responsible took several months to complete and publish. However, in December 2019, Chinese scientists sequenced SARS-CoV-2 from a 42-year-old man in two days, and this was made available to global researchers on the US genetic sequence database GenBank the following month.
COG-UK was funded with £20m from a Covid-19 rapid research response “fighting fund” established by the government’s then chief science officer and its chief medical officer, with support in kind from the Wellcome Sanger Institute. Within five days of its start-up, the network began publishing genomic sequences and sharing data. By the end of the year, it had described the “genomic cluster” of Covid-19 cases in Kent, which were the early signs of the first SARS-CoV-2 variant of concern, alpha. COG-UK contributed one million genomic sequences taken from a quarter of all those collected globally by the Global Initiative on Sharing All Influenza Data, playing a significant role in identifying new variants of concern throughout the pandemic.
The Impact of Funding Cuts
Exactly how the decision to close COG-UK was made will be part of the current Covid-19 inquiry. However, the question remains: what happens to routine sequencing when one emergency is coming to an end and the threat of the next one is unknown but ever-present? As the global community turns its attention to long-term pandemic preparedness, it is essential to consider the role of routine genomic sequencing in pandemic control. Without adequate genomic surveillance, it is impossible to be certain about the infectiousness, pathogenicity, or vaccine immunity of new variants like the Arcturus XBB.1.16 subvariant that caused 66 cases in the UK up to April 11, 2023.
Prof Lawrence Young, a virologist at Warwick University, points out that the scaling back of genomic surveillance “means we are getting an extremely skewed and unrepresentative view of SARS-CoV-2 variants in this country.” The current challenge is, therefore, to establish a range of pandemic response plans and have the ability to establish which one is appropriate for the emergency at hand. Although COG-UK contributed a lot to the UK‘s Covid-19 response, it and other surveillance activities such as the Office of National Statistics (ONS) infection survey, the CoMix behavioral survey, and the Zoe app, were created reactively to fill gaps in the response capability.
Philosophical Discussion and Editorial
The UK‘s current approach to Covid-19 surveillance reflects a broader trend of fragmentation in public health. The pandemic has shown how crucial it is to have a national strategy for pathogen genomics and how future national funding should support and prioritize interdisciplinarity to improve scientific responses in the UK. The pandemic has also highlighted the importance of academic institutions during emergencies and the need for mechanisms to involve them in emergencies.
While the UK has been scaling back its Covid-19 surveillance, African countries have increased their genomic sequencing capabilities. More than 120,000 SARS-CoV-2 genomic sequences have been generated in Africa, a dramatic increase from the 5,000 sequences in early 2020 when the
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