26  Author’s Notes

Pathogen Genomics is a new and revolutionary field in Public Health and it represents a new direction of infectious disease intelligence and surveillance. What we have accomplished during the COVID-19 pandemic reflects this.

The sequencing of SARS-CoV-2 during the COVID-19 pandemic has transformed surveillance and epidemiologic analyses. This learning experience has ushered us in a new direction of infectious disease intelligence and surveillance, where pathogen genomes can be used for more insightful analyses like phylodynamics, transmission dynamics, variant detection, estimating disease severity, among other things. From this experience, there’s ample opportunity and room to expand sequencing and genomics to other pathogens of notifiable conditions.

In the future, once we are more established in this field, we can begin to build a global warning system for future pandemics of emerging pathogens. In a sense, we do a lot of this kind of work right now with SARS-CoV-2. Therefore, all that we do now and the work that we invest in will serve as a model for the ways in which we can monitor, prevent, and control infectious diseases and it’s looking to be a very optimistic future direction.

This story is meant to help build capacity in Pathogen Genomics, whether you are a laboratorian, epidemiologist, bioinformatician, infectious disease specialist, and the like. Furthermore, this mystery outbreak story is an ode to all of the public health professionals, researchers, scientists, and healthcare workers that worked tirelessly on the frontlines of the COVID-19 pandemic, and for the newcomers who are interested in this area. We seek to revolutionize our surveillance systems and infrastructure, and you too, can be a part of this undertaking.

• Steph M Lunn

Have questions? Feel free to reach out!

Contact WA DOH Molecular Epidemiology Program

This story was inspired by Pokemon, but not affiliated with or sponsored by Pokemon, GameFreaks, or Nintendo.

A Note on Realism

While the scenario itself is fictional, the investigative steps, analytic logic, and genomic results are grounded in reality. Each decision point, from sample prioritization to sequencing method selection, mirrors what practitioners face during actual outbreak investigations. The phylogenetic trees, SNP matrices, and mutation patterns are not arbitrary; instead, they reflect how real-world data might behave under similar circumstances. In that sense, this is more than a story; it’s an example of guided simulation of what genomic epidemiology can look like when applied with clarity, coordination, and purpose.