In recent months – reflecting on lessons learned during the COVID-19 pandemic – the Northern Ireland Public Health Agency (PHA) has been working to understand how the science of pathogen genomics should fit into the work of a public health department. We spoke to Dr Declan Bradley, a Public Health Medicine Consultant and clinical lecturer, who divides his time between the PHA and Queen’s University Belfast, about his work integrating sequencing into the public health decision making process.
Although genomic sequencing had been deployed in public health practice in Northern Ireland, until COVID-19 it was almost always in the context of smaller outbreaks of specific diseases, such as hospital-acquired infections.
“The pandemic led us to have to deal with the question of how to use sequencing on a much bigger scale,” Declan tells us. “And then what decisions can we base on the information that we get from sequencing?”
To facilitate the PHA’s internal processes for integrating pathogen sequencing data into public health practice – and hopefully guide other public health bodies’ activities in this domain in the future – Declan and colleagues in the PHA conducted a qualitative study using the Delphi technique, which is a well-established approach to answering a research question through the identification of a consensus view across subject experts, to explore how the data that comes from sequencing should be applied to decisions that affect day-to-day public health.
“The goal was to set out a framework of how we should use that kind of information, how much we should trust it in different circumstances, how we should judge the technical quality of the data, and how heavily we should weight it compared to other information, such as contact tracing data,” Declan recalls.
Making judgements regarding the reliability of the sequencing data and its role relative to other information necessarily requires storing this information in one place, where it is updated in near real-time. So, in addition to developing a qualitative framework, the PHA pathogen genomics team focused on linking and integrating sequence data, epidemiological data and demographic data to support decision making in an analytics platform.
This meant that “once a positive PCR sample was sequenced, the resulting data could be rapidly analysed in context.” The developmental work on linking genomic data and exploring it using bioinformatics software was made possible through a COG-UK issued grant, Declan tells us. Improving lead time, so that key data are made available as soon as possible, has been one of the hallmarks of effectively addressing the pandemic.
“Over the course of the pandemic the time from the original specimen being taken to the result being available has reduced greatly,” Declan says. “The faster we have information available to us, the faster we can make decisions about what messages the public receive, as well as informing decisions around vaccination programmes and treatment options”
The robustness of the PHA’s systems were tested when the BA.2 Omicron variant arrived in Northern Ireland. Most new variants had previously been identified in other parts of the UK before they reached Northern Ireland. However, the BA.2 variant was prevalent in Northern Ireland earlier than in the rest of the UK. Declan and his team assessed relative vaccine effectiveness and hospitalisation rates and were able to provide a comparison between BA.1 and BA.2, which they shared with policymakers for risk assessment and planning. Having been tried and tested in the pandemic, Declan believes the systems now in place will be useful for all sorts of public health challenges to come.
“Before COG-UK, we had little in-house expertise in genomics or bioinformatics” he says. “But we’ve reached a critical mass now, which means that we will be able to build on our progress and use our resources to work with pathogen genomic data for other diseases.”
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