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13 Oct 2022

How the COVID-19 pandemic and viral genomic sequencing could change the UK’s approach to infection control

Throughout the pandemic, genome sequencing has identified SARS-COV-2 Variants of Concern that can evade our immune system. We spoke to Professor Emma Thomson, Clinical Professor of Infectious Diseases at the MRC-University of Glasgow Centre for Virus Research about how genomic sequencing is catalysing a change in the way we monitor viral evolution and immune escape during vaccine roll-out.

To investigate the impact of the evolution of the SARS-CoV-2 virus on vaccine efficacy in Scotland, Emma and her colleagues used viral genomic data alongside epidemiological, public health, and clinical data. Historically, pathogen genome sequencing has not been embedded as standard in the UK’s public health or NHS response strategies, and so this approach required new infrastructure to be developed and put in place as part of the study design.

“Bringing together and analysing these data sources was an interdisciplinary effort. The collaboration seen between scientists, the NHS, and public health specialists was incredibly rewarding,” Emma tells us.

The study used robust and multifaceted approaches to demonstrate that the Omicron variant and its sub-lineages (sub-divisions that arise during further mutational change) can evade the vaccine-induced immune response. “Two doses of the vaccine were not very effective in preventing people from becoming infected,” Emma tells us, “However, three doses of vaccine were much more protective.”

Genomic sequencing was central to the finding that the Omicron variant is more easily able to bypass our vaccine-induced immune response. These insights reinforced the idea that variant-specific vaccines may be needed to tackle strains of SARS-CoV-2 that appear in the future. In fact, the UK has already taken a step in this direction, becoming the first country to approve a bivalent vaccine – providing protection against the original SARS-CoV-2 strain and the Omicron variant.

However, in the past, sequencing was not a central element of health protection and infectious disease control. The COVID-19 pandemic changed this. “Public health experts now see the value of sequencing in a way that they hadn’t previously, because we hadn’t really done it at this scale before,” says Emma.

Although viral sequencing had never been seen on such a large scale, the UK’s capabilities were internationally recognised before the COVID-19 pandemic began. For example, UK-based scientists supported the tracing of other outbreaks – such as Ebola in 2013, and Zika Virus in 2015.

This heritage in sequencing meant that at the beginning of the COVID-19 pandemic, the UK were able to play a significant role in leading the change. “We were able to support research institutions across the devolved nations to track how many times the virus entered the UK through international travel,” says Emma.

Viral genomic sequencing can be used to answer a range of questions. Of all its uses, though, Emma thinks that it is most valuable for monitoring vaccine effectiveness, and the possibility of re-infections occurring in vulnerable populations.

While Emma recognises that we don’t have the resources to spend vast amounts of money on sequencing everything, Emma believes that we should exploit the infrastructure developed for SARS-CoV-2 to monitor patterns of other pathogens. “One of the first things we should do is to understand how best to sample people who have been in hospital, and in the community, so that we can keep an eye on how a given virus is evolving. This is important for SARS-CoV-2 and for any other viruses that we decide to monitor.”

To enable useful insights to be gleaned from sequencing in the future, Emma reiterated the importance of collaboration, and tying genomic, clinical and epidemiological data together more readily. “COG-UK changed the culture for us,” Emma says, “Rather than working in isolated laboratories around the UK, we are now working in teams. I think that this collaborative working is the future of science.”


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.