I’m very pleased to announce the publication of article that several of us have been working on for the past two years that is of particular relevance to this group.
Published in Nature Health, “The value of local use cases for expanding pathogen genomics in resource-limited settings” is a commentary on the importance of scrutinizing the public-health impact of pathogen genomic investments in low- and middle-income countries (LMICs).
The article grew out of a conversation, initially between David Blazes and me, in the aftermath of the expansion of sequencing during the COVID-19 pandemic. A number of relevant review articles and commentaries had already been published by 2024, often focusing on the technical issues around expanding genomics capacity and ways to make progress in this area. But these articles often took for granted the potential benefits of developing this capacity: who was benefitting and how was that benefit manifested? Both of had seen proposals, often technically excellent ones, that were vague about the objectives and about the project merited public or foundation investment.
Other co-authors–Simon Harris, Paul Pronyk, Alan Christoffels, Josefina Campos, Sofonias Tessema and Joseph Bresee–joined us in thinking through these issues and drafting the article, which we link to below. From my point of view as lead author, I think its main messages for those considering pathogen genomics are as follows:
- Consider the objective. It’s surprising how often a proposed project fails to specify a clear objective. What is the potential impact if the project is funded? Research objectives are often relatively easy to define. Public health objectives are less so, particularly for academics with experience applying for research grants. This paper focuses on the public health impact–how to define and evaluate the potential public health impact of a project.
- Consider the potential public health impact. For purely research projects, this may not be relevant. But proposals often allude to a public health benefit, and if that’s the case, the expected impact should be clearly stated. Because defining public health impact is sometimes difficult, we propose a framework (see Box 1 in the article) for doing so. This grew out of a framework we developed while I was at CDC that we used for evaluating proposals the agency’s Advanced Molecular Detection program.
- Consider whom the beneficiaries are. During the pandemic, it was often assumed that countries would benefit from developing SARS-CoV-2 genomic surveillance. Was that benefit universal? Arguably, the main impact of that surveillance (there were others as well) was in informing the development of new vaccines and therapeutics (diagnostics development also benefitted, but in the end, the surveillance effectively showed existing diagnostics to be robust and without need for modification). If LMICs had little access to or use of vaccines and therapeutics, did they benefit from the surveillance they contributed? This isn’t to argue against the development of that surveillance (that novel capacity has other potential benefits for the countries), but rather to make the case that such projects should be clear who benefits and how. And in an example like this, where a benefit may be global in nature rather than local, this argues for global investment in genomic capacity.
The article also puts forward two other potentially useful concepts. The first is a definition of “use case”, which while not unique or original, is hopefully an additional step towards standardizing the term. The second is the economic “break-even proportion”, an indicator that can be useful in evaluating the economics of pathogen genomics investments in the absence of reliable data on impact.
We cannot post a copy of the article on our website because of Nature publication rules, but it is available below, and I can certainly send people a copy on request.
Greg Armstrong, Co-lead, Pathogen Genomics Funders Forum
Gregory L. Armstrong, Simon R. Harris, Paul M. Pronyk, Alan Christoffels, Josefina Campos, Sofonias K. Tessema, Joseph Bresee & David L. Blazes. The value of local use cases for expanding pathogen genomics in resource-limited settings. Nat Health (2026). https://doi.org/10.1038/s44360-026-00084-3