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The University of Cambridge’s Prof Sharon Peacock: ‘Another pandemic is inevitable - here’s what we must learn from Covid-19’

In this opinion piece, Sharon Peacock, professor of public health and microbiology in the Department of Medicine at the University of Cambridge and chair of the Covid-19 UK Genomics (COG-UK) Consortium, discusses its work, the lessons learned from the Covid response and how scientists and public health agencies should build upon this knowledge to prepare for the next pandemic.

Prof Sharon Peacock
Prof Sharon Peacock

In March 2020, we saw the world come to a grinding halt and governments rushing to cope with the emerging Covid-19 outbreak.

That year was a time of extraordinary collaboration between the scientific community and the United Kingdom’s public health agencies.

Recognising the need to provide large scale genomic sequencing to public health agencies, I worked with a team of dedicated scientists to establish the Covid-19 Genomics UK Consortium (or COG-UK) in April 2020.

Enabling the identification and monitoring of SARS-CoV-2 variants as they emerged and spread, the outputs of the consortium have been used to inform public health policies, border control and outbreak management, as well as gain an understanding of variant transmissibility, immune evasion and disease severity throughout the pandemic.

The response to viral genomics seen in the UK exemplifies how robust scientific processes and discoveries are essential to the appropriate and timely response to emerging viral outbreaks. Now, we need to look to extend our understanding of emerging infectious diseases and build upon the learnings of the Covid-19 response to prepare for the next pandemic, an inevitable event.

Lessons learned

At a time of urgency, one can only work with the tools and information that is currently available to you. Therefore, preparedness is the single most important aspect of responding to infectious disease outbreaks.

Over the last 10 years, multiple research groups and institutions across the UK have been working on how to apply pathogen genomics to public health interventions, which formed the foundation of our country’s viral genomics response to Covid-19.

The established and sophisticated network of scientists, equipment and tools in the UK enabled us to rapidly mobilise it into action and bring these pieces of the puzzle together to create a joined-up response.

The ARTIC network, which rapidly develops and releases sequencing methods for pathogens associated with viral outbreaks, was already thriving. This provided methods to sequencing the SARS-CoV-2 virus from the outset.

The pre-existing infrastructure known as ‘CLIMB’ (Cloud Infrastructure for Microbial Bioinformatics), allowed us to store and analyse the genomic data and combine this with the anonymised patient identifier, after which this could be accessed by the four Public Health Agencies of England, Scotland, Wales, and Northern Ireland. It was incredible to provide a mechanism for the public health agencies to work closely together on genomics, the scale of which was unprecedented.

Phylogenetic tree of SARS-CoV-2 genomes from the COG-UK data in 2020. Image: COG-UK
Phylogenetic tree of SARS-CoV-2 genomes from the COG-UK data in 2020. Image: COG-UK

With so many elements in place and with funding made available to us, we were able to kick-start our work early, allowing us to be prepared for when variants emerged, the first being the Alpha variant. But this was still no easy feat. We needed to connect the laboratories that were performing the PCR tests for Covid-19 with our sequencing hubs, which was a logistical challenge.

We also needed to connect the genome data we generated with anonymised patient information. Data connectivity proved to be one of our biggest challenges but was essential if the genome data was to have real-world applications on public health interventions.

A combination of CLIMB and our collaborative approach helped to mitigate barriers to data sharing.

I witnessed the best in team efforts through the remarkable nature of people and their ability to work together. United by the common goal to tackle the virus, it was incredibly humbling to see such high levels of collaboration throughout the pandemic.

To ensure we produced tangible results, we adopted an “outcomes over processes” ethos, which essentially means that we prioritised thinking about what we were trying to achieve over the processes required to achieve them. Traditionally, you can spend many months developing a proposal for a scientific project but in this case, rapid action and leadership was needed and within weeks COG-UK was up and running.

The rapid pace at which we were able to begin our work would not have been possible had the funding not been made readily available by Sir Patrick Vallance and Sir Chris Whitty through the Covid-19 Emergency Response funds.

What the pandemic has shown us is that in a time of crisis, the scientific community has the capability to elevate their work to respond effectively. Moving forward, we need to ensure that these channels remain responsive, when needed.

As infection levels decrease and other pressing issues take centre stage, we are seeing the funding for Covid-19 research declining and many of the initiatives, including COG-UK, are going to be dissolved.

Additionally, several of the collaborations developed during the emergency response will start to diminish, as scientists return to their own work. This is not to say that we are regressing in our efforts to tackle infectious diseases. What we have generated is proof of principle and learnings to apply for future responses.

What comes next

What the outcomes of COG-UK have shown us is how important pathogen sequencing is to informing public health interventions.

Whilst government priorities and funding shift, I hope to see the level of funding and capacity building for genomic sequencing sustained over time, so that we can truly build on our understanding of infectious disease outbreaks.

Crucially, we need to have strong public health capabilities for sequencing to ensure that emerging pathogens are identified in a timely manner.

During the peak of the pandemic, researchers worked very closely with infection prevention and control teams in local hospitals to understand what viral variants were circulating at the time.

Unfortunately, we are now seeing a decline in this localised sequencing capability, which could slow our progress in introducing innovative technologies into outbreak detection and prevention protocols that tackle challenges beyond the pandemic. Local sequencing at hospitals can be used to track multidrug resistant gram-negative bacteria, methicillin-resistant Staphylococcus aureus (MRSA), and many other pathogens that may emerge and spread in healthcare settings.

A Covid-19 vaccine
A Covid-19 vaccine

Since the start of the Covid-19 pandemic, pathogen sequencing has been used to investigate other infectious diseases – including the spike in acute hepatitis infections in children during 2022.

Similarly, sequencing is being used in the investigation of the recent increase in invasive Group A streptococcal infection. Under these circumstances, sequencing is used to better understand whether this is associated at least in part with the emergence of a new strain, although current indications suggest that this is not the explanation.

Going beyond sequencing at the local and national level, we need to align our capabilities and outputs to global efforts, so that we continue to contribute our data and expertise to the wider understanding of infectious diseases and the global response to infectious disease control.

From what we have achieved over the last three years, it is clear that the role sequencing plays in outbreak detection and intervention should not be underestimated. We must now set out plans to consolidate and further build our pathogen sequencing capabilities at a local and national level, and boost global collaboration. Both actions will be required for an effective respond to the next pandemic and will make a meaningful contribution to public health and disease control in the meantime.

Closing remarks

Because it is impossible to predict when the next pandemic will occur, we should not run the risk of reducing the scientific capabilities that were implemented in response to Covid-19, given how essential they proved to our understanding of the SARS-CoV-2 virus and how it evolved over time.

We are seeing a pattern of emerging infectious diseases with epidemic and pandemic potential, and the pace at which these outbreaks are occurring is gathering pace.

What we can say with certainty is that another pandemic threat is inevitable.

I would anticipate that the next pandemic is likely to be caused by another virus, likely to have come from an animal reservoir. Because we cannot say whether this will happen – it could be this week, next month, next year, or longer still - we must equip ourselves now with the tools and capabilities required to prepare for another outbreak.

To learn more about our response to the pandemic please join me at the Association of Physician’s Annual Meeting in April 2023, where I will be delving deeper into what worked and the challenges we faced in COG-UK, and how we build on these learnings for the future.

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