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UKHSA Unveils Five-Year Pathogen Genomics Strategy

Image created by Dr. Michael J. Miller

The UK Health Security Agency (UKHSA) has published its
 Pathogen Genomics Strategy, laying out a 5 year plan for the organisation's role in the wider delivery of pathogen genomics to prepare for and respond to infectious disease threats to public health.

The new strategy sets out a programme to improve UKHSA's ability to detect and understand the pathogens that pose the greatest risks to the UK population, which will help to ensure that policy and public health decision making is underpinned by the best possible scientific evidence.

Sequencing pathogen genomes to examine their genetic code can reveal vital information about their identity and ancestry. When combined with other health data and research, it becomes a powerful tool for understanding how a pathogen is behaving in a human population and why.

We can use genomics to detect new threats, to:

  • identify outbreaks and find their source
  • track transmission of disease between people
  • understand whether human immune responses will be protective
  • choose the most effective vaccines for the population
  • detect antimicrobial resistance and determine the optimal treatments for individuals 

The COVID-19 pandemic response showed us that genomics can be fully integrated into public health systems and can inform decision-making locally, nationally and globally. The UK submitted over 3 million SARS-CoV-2 sequences to the international GISAID database over the course of the pandemic, a quarter of the global total and more than any other nation except the USA.

Since then, genomics has continued to show its value - identifying foodborne outbreaks, helping us to assess the risk from emerging pathogens like mpox and influenza and helping to inform the choice of treatment for diseases like tuberculosis.

The UKHSA Pathogen Genomics Strategy recognises that pathogen genomics is a crucial element of modern infectious disease control, and it will ensure that the UK remains at the forefront of genomic research, developing and implementing genomics to benefit public health, protect lives and livelihoods.

By leveraging existing infrastructure, capacity, and scientific capabilities, the strategy outlines UKHSA's vision for pathogen genomics over the next five years through seven strategic aims. These are:

  • using pathogen genomic data to optimise clinical/public health decision-making, from local to global settings;
  • using pathogen genomic data to drive improvements in diagnostics, vaccines and therapeutics;
  • providing a nationally coordinated, scaled-up pathogen genomics service;
  • supporting a pathogen genomics workforce transformation within and beyond UKHSA;
  • committing to pathogen genomic data sharing and global collaboration;
  • driving innovation in pathogen genomics;
  • building high-impact pathogen genomic services that are good value for money

Each of these strategic aims will support and boost UK capability in 3 priority public health areas, directly aligned with UKHSA's priorities:

  • antimicrobial resistance;
  • emerging infections and biosecurity;
  • vaccine preventable diseases and elimination programmes.

Dr Meera Chand, Deputy Director for Emerging Infections and Clinical Lead for the Genomics Programme at UKHSA said:

Pathogen genomics is an essential component of the world's ability to respond quickly to infectious disease threats, whether by increasing the speed at which we can identify emerging pathogens or control outbreaks, or by improving our understanding of what treatments or vaccines might be effective.

The new UKHSA Pathogen Genomics Strategy will provide a framework for us to build on our already substantial capacity in this area, and to implement genomics across all our work to keep the public safe from threats to their health.

Professor Dame Jenny Harries, UKHSA Chief Executive said:

UK experts in the field of pathogen genomics made a vital contribution to the COVID-19 pandemic response and pathogen genomics remains central to the national and international effort to keep the public safe from many other types of infectious disease threats, from tuberculosis to mpox and avian influenza.

We know it will become even more important in the years to come, and our new strategy will ensure that UKHSA continues to be at the forefront of implementing this technology to keep our communities safe, save lives and protect livelihoods."

Minister for Women's Health Strategy, Maria Caulfield said:

Detecting new infectious disease threats, identifying outbreaks and finding their source, and tracking transmission of disease through the community are of critical importance in keeping the country safe from threats to public health.

This new strategy published by UKHSA will help us to identify and analyse the pathogens which pose the greatest threat to the UK population, and to respond to them quickly and effectively.

Case studies of the recent impact of UKHSA Genomics 


In April 2022, UKHSA used Whole Genome Sequencing (WGS) to identify and inform the response to contaminated chocolate products. The chocolate was contaminated with a very distinct type of salmonella, from a genetic cluster not seen previously in the UK.

Before the advent of genotyping, we could not always confirm with certainty what organisms were present in contaminated products, hindering decision-making around food recalls. Now, genome sequencing provides the evidence base needed to inform these decisions with a much greater level of confidence.

Early notification of the detection of the outbreak, along with epidemiological investigations and rapid sharing of microbiological sequence information, provided confirmation of the link between the company's products and the outbreak. Routine surveillance using WGS was crucial in detecting the unique genetic cluster.

Following the alert, comparisons of the UK data with national sequences in other countries revealed more cases linked to the outbreak across Europe. A larger multi-country investigation was launched and resulted in the identification of chocolate products from the same business as the source of the outbreak.

SARS-CoV2 variant: Alpha

In March 2020, while investigating an unexplained spike in COVID-19 cases in Kent, scientists from UKHSA's predecessor organisation, Public Health England, sequenced the genomes of samples taken from people with COVID-19.

Their analysis showed that a large number of these sequences were very similar and genomically distinct from other SARS-CoV-2 samples sequenced in the UK up to that point. This was the first identification of the Alpha variant of SARS-CoV-2, a variant with much higher levels of transmissibility than the dominant variants of the time.

Without the use of genomic sequencing, it would have taken far longer for public health officials to understand the significance of the rising cases in Kent, and interventions to slow its spread would have been significantly delayed. In fact, the use of genomic sequencing prevented the hospitalisation, and even deaths, of many more people.

SARS-CoV2 variant: Omicron

In November 2021, the UKHSA's genomic sequencing programme identified the first cases of the Omicron variant of SARS-CoV-2 in the UK, having previously been identified in South Africa, Botswana and Hong Kong.

The speed of this detection - which would not have been possible without Whole Genome Sequencing (WGS) - meant that UK health protection teams were able to take rapid action to slow its onward spread.

Omicron went on to become the dominant SARS-CoV-2 variant around the world, but the delay that the use of WGS bought the UK once again meant that interventions could be put in place before it took over, lessening its potential impact and reducing the number of people in danger of hospitalisation and death.

SARS-CoV2 variant: BA.2.86

Last year scientists used global sequence data to identify a SARS-CoV2 lineage with an unusual mutation. Once recognised as a new variant, we were able to track its appearance in the UK and to quickly identify and control local outbreaks.

Our knowledge of mutations quickly allowed us to establish vaccine and diagnostic test efficacy via a programme of laboratory work to determine that current vaccines and Lateral Flow Devices (LFDs) were effective against BA.2.86.

Tuberculosis (TB) and Antimicrobial resistance (AMR)

In 2017, Public Health England (PHE), one of UKHSA's predecessor organisations, announced its pioneering use of Whole Genome Sequencing (WGS) in diagnosing and managing TB. The UK now uses WGS as a routine tool in TB surveillance - setting it apart from most European neighbours.

Prior to the adoption of WGS in laboratories, our ability to trace the spread of TB between people was far more limited and less precise.

To build up a picture of how the virus could be spreading across populations, scientists first determine whether different cases of TB are related.

Previous methods relied on identifying repeating segments found in the bacteria's genetic code, and then comparing these to those found in bacteria from other samples. By contrast, Whole Genome Sequencing takes the entire genetic code of TB bacteria from different samples, allowing them to be compared at a very detailed level.

Since 2015 there have been a number of improvements in TB diagnostics due to the introduction of Whole Genome Sequencing, including the ability to determine and monitor TB transmission, reduce the diagnosis time of new cases from over a month to just over a week, and make treatment choices which are best suited to each individual - slowing the march of antimicrobial resistance in multidrug-resistant TB.

Where previously it could take up to a month to confirm a diagnosis of TB, confirm the treatment choices and to detect spread between cases, this can now be done in just over a week. This slows the spread of the disease, informs appropriate medication choice and aids in the fight against anti-microbial resistance.

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