How should public health authorities use pathogen genomics in practice?

Posted on February 6, 2023   by Dr Declan Bradley

Dr Declan Bradley takes us behind the scenes of his latest research 'How public health authorities can use pathogen genomics in health protection practice: a consensus-building Delphi study conducted in the United Kingdom' published in Microbial Genomics.

From the first detection of SARS-CoV-2 infection in humans, genomics was central to defining and understanding the threat posed by this emerging infectious disease. Pathogen genomics services grew to operate at a scale that was orders of magnitude greater than before the COVID-19 pandemic. Health protection services in public health authorities are responsible for surveillance and prevention of communicable diseases. 

What should health protection teams do with SARS-CoV-2 genomic data?

The COG-UK SARS-CoV-2 sequencing programme provided genomic data to researchers and public health authorities. This posed questions for the health protection teams about how to use these new data, as there were no guidelines or protocols for this new situation. Was the information ‘nice to know’ or a necessity? Was it for surveillance, for outbreak management or for clinical care? What specialist knowledge and skills were required to interpret the data correctly? Producing and processing the information also had financial and opportunity costs with practical consequences: should staff be redeployed away from other important activities in favour of strengthening pathogen genomics services? What activities does a high-quality pathogen genomics service undertake, and how should quality be judged?

What was the goal of the work?

I work in Northern Ireland’s Public Health Agency, Queen’s University Belfast, and during the course of this project, I also worked in Northern Ireland’s Department of Health. This meant that I had the opportunity to view the development of SARS-CoV-2 sequencing services from research, practice and policy perspectives. The in-house pathogen genomic epidemiology functions in the Public Health Agency were very limited prior to the COVID-19 pandemic, when we partnered with COG-UK. We received funding from COG-UK to develop our capability and capacity to use pathogen genomics in practice. We wanted a clear picture of the service we should aim to create and how it should operate, so we undertook a Delphi study of UK-based experts to gather recommendations about how public health authorities should use pathogen genomics in practice. A Delphi study is a way of proposing statements based on literature or surveyed opinion, and surveying experts to indicate their agreement with statements, and refining them through several rounds of a survey.

What did the experts recommend?

Through the study, the experts recommended that public health authorities should use pathogen genomics: to monitor the emergence of new diseases or variants, and their spread over time and place; to monitor the characteristics of people who were affected by the infection, understanding the connections between individuals and the contexts in which transmission occurred; to manage outbreaks, by identifying whether or not transmission occurred, monitoring the impact of measures to prevent spread, and monitoring severity, vaccine effectiveness and therapeutics effectiveness; to direct sequencing services to specific purposes, such as unbiased sampling, detection of immune escape in high-risk contexts, or the import of new variants; and lastly, to monitor and improve the quality of sequencing services through measuring timeliness and completeness, and facilitating access to training to increase capability.

How do the recommendations help public health authorities use pathogen genomics?

The recommendations by our expert participants form a framework that we have already applied in our own service and which we will use for the future development and evaluation of how our health protection service uses pathogen genomics. The challenge of the SARS-CoV-2 pandemic has resulted in a step change in the availability of pathogen genomic data, with other pathogen data increasingly available. This requires public health authorities and health protection services to increase the maturity and sophistication of their genomic epidemiology and practice functions. We hope that this framework will be useful for other public health authorities and pathogen genomics services on this journey.

You can read Dr Bradley and his team's work in Microbial Genomics.