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UKHSA release 5-year Pathogen Genomics Strategy

By January 31, 2024No Comments

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.

BIVDA wholeheartedly believes in UKHSA’s mission to incorporate genomics into all aspects of infection control and public health decision making, which will aid the global fight against antimicrobial resistance (AMR). We will work with UKHSA to achieve their strategic aims, namely to drive improvements in diagnostics through the use of genomic data.

The COVID-19 pandemic response showed 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 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.

Case studies of the recent impact of UKHSA Genomics 

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.