This course develops pathogen genomic epidemiology end to end: from sequencing and phylogenetics through phylodynamic inference to transmission-cluster detection and genomic surveillance. It is deliberately applied and surveillance-oriented, going beyond generic bioinformatics to connect genomes to the epidemiologic questions they can answer.
The course syllabus is shown below.
Draft syllabus. This is a scaffold for the concentration. Course number, credit hours, dates, and specific assignments are placeholders and will be finalized before the course is offered.
Course title and instructors
Title: Applied Genomic and Phylodynamic Epidemiology
Course Number: BIO 6xx (proposed; cross-listed undergraduate, confirm with the Department of Biology)
Semester: TBD
Credit Hours: 3
Meeting Time: TBD
Course Director: Michael E. DeWitt, MS
Email: medewitt@wakehealth.edu or dewime23@wfu.edu
Course description
Pathogen genome sequences, linked to metadata such as date, place, and host, have become a routine part of outbreak response and disease surveillance. Turning that data into epidemiologic insight requires a specific chain of skills that a general bioinformatics course does not assemble in one place. This course follows the pathogen-genomics workflow from sample to decision: sequencing technologies and their trade-offs, quality control and consensus calling, alignment and phylogenetics, molecular-clock and coalescent reasoning, phylodynamic inference of transmission and epidemiologic parameters, and the detection of transmission clusters from genetic distance. Students situate these methods inside real surveillance systems, learn to predict antimicrobial resistance from genotype, and work throughout with the metadata standards, data governance, and equitable data-sharing practices that make genomic surveillance trustworthy. The intended contrast with the existing genomics and bioinformatics electives is deliberate: this course is about pathogen surveillance and epidemiology, not generic sequence analysis.
Learning outcomes
Upon successful completion of this course, students will be able to:
- Describe the end-to-end genomic-surveillance workflow from sample to actionable output
- Choose appropriately among sequencing platforms and quality-control steps
- Build and interpret phylogenies and reason about molecular-clock and coalescent models
- Apply phylodynamic thinking to reconstruct transmission and estimate epidemiologic parameters
- Detect transmission clusters from genetic distance and integrate genomes with epidemiologic metadata
- Apply metadata standards, data governance, and equitable data-sharing practices to genomic surveillance
Textbook and other resources
There is no single required textbook. Recommended references include:
- Black A, Dudas G. Applied Genomic Epidemiology Handbook. An applied, practical guide to genomic epidemiology. https://alliblk.github.io/genepi-book/
- Hill V, et al. Progress and challenges in virus genomic epidemiology. Trends Parasitol 2021. https://doi.org/10.1016/j.pt.2021.08.007
- Selected primary literature on phylodynamics, genomic surveillance, and pathogen bioinformatics
- Public tooling and documentation (e.g. Nextstrain, PulseNet, GenomeTrakr) as assigned
Additional readings will be assigned throughout the course.
Site resources
This course draws on IDEEEP content pages as assigned readings:
- Genomic surveillance
- Phylodynamics
- The molecular clock
- Coalescent theory
- dN/dS and selection on sequences
- Quasispecies
- Research and data ethics, governance, and responsible sharing
- HPC clusters and Slurm
- Diagnostics and surveillance
Course structure and schedule
This course meets over 15 weeks and combines lecture with computer labs on real pathogen-genomic datasets. The schedule below is a draft outline of topics.
| Week | Topic |
|---|---|
| 1 | Why genomic epidemiology: from retrospective genomics to actionable surveillance |
| 2 | Sequencing technologies and their trade-offs |
| 3 | Quality control, assembly, and consensus calling |
| 4 | Alignment and building phylogenies |
| 5 | Reading trees: what a phylogeny does and does not show |
| 6 | The molecular clock and time-scaled trees |
| 7 | Coalescent theory and effective population size |
| 8 | Phylodynamics I: linking trees to epidemic dynamics |
| 9 | Phylodynamics II: estimating transmission and parameters |
| 10 | Transmission clusters and genetic-distance thresholds |
| 11 | Genotype-to-phenotype: antimicrobial resistance |
| 12 | Genomic surveillance systems and tooling |
| 13 | Metadata standards and integration with epidemiologic data |
| 14 | Data governance, equity, and responsible sharing |
| 15 | Project presentations and wrap-up |
Note: Specific dates will be provided at the beginning of the semester. Topics may be adjusted based on class progress and student interests.
Grades and assignments
| Activity | Weight |
|---|---|
| Participation and literature discussion | 20% |
| Computer labs and assignments | 30% |
| Exam(s) | 20% |
| Final project | 30% |
Final project: Students will analyze a real or realistic pathogen-genomic dataset, reconstruct transmission or estimate an epidemiologic quantity, and present the result with attention to metadata quality and data-sharing practice.
Course policies
Attendance: Regular attendance is expected, particularly for discussion sessions. Please alert the instructor if you are unable to attend for any reason.
Late/Makeup work: Assignments are due on the dates provided. We recognize that extenuating circumstances arise, and assignments may be submitted up to 2 days late without penalty. If you need an extension, contact the instructor as soon as possible and before the due date.
Artificial intelligence: Artificial intelligence tools and large language models such as ChatGPT, Claude, and Gemini are now part of the academic and professional landscape and we encourage you to find ways to use them to enhance your learning. However, if you use these tools, you must cite your sources and provide a detailed description of the tools you used to complete the assignment. In no way can these tools take the place of your own work and understanding of the material. They should be used to supplement your learning, not replace it. You are ultimately responsible for your work including content and the use of valid citations and references. Using these tools without proper attribution is plagiarism and will be treated as such.
Department/School/University policies
Academic Integrity: Wake Forest University is committed to a culture of academic integrity. As a part of this community, you share the responsibility for creating a place of honesty, intellectual curiosity, and individual accountability. As you committed to with your honor pledge signature, you agree “not to deceive any member of the community; not to steal, cheat, or plagiarize on academic work; and not to engage in any other form of academic misconduct.” If you have questions about documenting your work, working with external sources, or working with peers on assigned work, consult with me as soon as possible. Instances of academic dishonesty will be referred to the Honor and Ethics Council.
Accessibility: Wake Forest University provides reasonable accommodations to students with disabilities. If you are in need of an accommodation, please contact me privately as early in the term as possible. Retroactive accommodations will not be provided. Students requiring accommodations must also consult the Center for Learning, Access, and Student Success (118 Reynolda Hall, 336-758-5929, class.wfu.edu).
Accommodations for Religious or Spiritual Practices: Wake Forest University benefits from the multitude of faiths and spiritual identities held by members of our learning community. Should you need accommodations this semester, email me as soon as possible to ensure we have time to develop equitable alternatives.
Class recordings: In case any class recordings are provided, they are reserved only for students in this class for educational purposes and are protected under FERPA. The recordings should not be shared outside the class in any form.
Syllabus change notice
This syllabus and the dates herein are subject to change.