2 Welcome to the Mystery Outbreak Workshop!

Warm greetings! Traditionally, epidemics and outbreaks tend to feel like a good mystery waiting to be solved – and that will be our approach for our Viral Genomics Fundamentals Workshop! For this workshop, you will be reading through a short mystery story centered on a hypothetical outbreak scenario in the fictional city of Fuchsia City.

2.1 Intended Audience

This module is designed for public health professionals, laboratorians, bioinformaticians, and epidemiologists who are interested in the real-world applications of viral genomics and genomic epidemiology. Whether you work in a public health lab, manage outbreak response, analyze sequencing data, or coordinate epidemiological investigations, this workshop will provide practical, scenario-based learning relevant to your work.

2.2 Workshop Format

You will explore a fictional scenario that unfolds like a detective story. It is set in an idealized world – a world where the value of genomics has already been realized, and the infrastructure is firmly in place. The toolsexists, the workforce is trained, and the systems function as intended. The only task left is to respond.

The deliberate design choice allows us to focus on how to investigate outbreaks using sequencing and genomics, not whether we can. In this setting, we bypass the real-world limitations of funding, staffing, politics, and bureaucracy so that we can map out the ideal progress from sample collection to genomic analysis to public health response. This clarity is essential for understanding the logic, reasoning, and decisions that underpin effectie outbreak response.

As you progress, you will encounter:

    - Multiple choice questions to test your understanding of key concepts.
    - Discussion prompts designed to be open-ended, mirroring real-world ambiguity and complexity.
    - Opportunities for creative thinking — often, there is no single “right” answer in genomic epidemiology, only more or less appropriate approaches depending on circumstances.

Points and feedback in this workshop emphasize thoughtful reasoning and creative problem-solving rather than strict accuracy. In practice, effective outbreak response is about adapting to uncertainty and making the best possible decisions with incomplete information.

2.3 Learning Objectives

By the end of this workshop, participants will be able to:

    - Interpret genomic data to identify and characterize viral pathogens involved in an outbreak scenario.
    - Apply bioinformatics concepts to analyze sequencing data, including genome assembly and variant identification.
    - Integrate epidemiological information with genomic findings to trace transmission pathways and outbreak sources.
    - Evaluate the effectiveness of different public health interventions based on genomic and epidemiological evidence.
    - Communicate findings effectively to stakeholders, considering the uncertainties and limitations inherent in outbreak investigations.

2.4 How to Get the Most Out of This Workshop

Engage with the material as if you are part of the outbreak investigation team. There are no trick questions; your insights, creativity, and logic are what matter most. Don’t hesitate to propose alternative solutions or discuss real-world limitations you’ve experienced in your own work. We encourage discussion and debate, as these are the hallmarks of strong outbreak response teams.

2.5 Lecture Resources

This mystery outbreak story focuses on practical applications of viral genomics during an outbreak investigation. If you would like to learn more about the technical and theoretical foundations of viral genomics before digging into the story, feel free to check out these lectures:

Lecture I: Molecular Biology of Viral Genomics Introduce why molecule biology concepts are relevant to understanding viral genomics and review the processes of replication, transcription, and translation. Prerequisite for the Viral Genomics Fundamental Lectures Recording Slides

Lecture II: Viral Genomics Fundamentals I: Genome Overview Viral genome overview and assumptions underlying viral genomes; what do viral genomes look like, what are viral replication strategies, and what information is encoded in a viral genome? Recording Slides

Lecture III: Viral Genomics Fundamentals II: Genome Evolution Viral genome evolution: assumptions of viral genomes, reassortment, recombination, mutation, selection, and evolution Recording Slides

Lecture IV: Viral Genomics Fundamentals III: Genome Diversity Viral genome diversity: the diversity of viral genomes, sense of viral genomes, and the reproductive life cycle of a virus and how it can impact the genomic epidemiology, surveillance, and sequencing Recording Slides

Note: these lectures assume the audience has a basic background in biology, and understands at the bare minimum, the structure and function of DNA.

Let’s begin the investigation!

- Steph M. Lunn