This two-half-day training course introduces the participants to the use of genomic data analysis to gain a deeper understanding of the epidemiology of mpox, an emerging viral pathogen. We will introduce the current state-of-the-art in mpox ecology and epidemiology and explain the application of whole genome sequencing for surveillance and outbreak response. Using a realistic scenario, we will explore which methods and analysis tools can be used, and how to interpret the results. The exercise will allow the participants to get hands-on experience in how to construct and interpret phylogenetic trees and how to perform outbreak investigations in real world settings.

 Dates: 5 and 12 October 2026. 

 Duration: Two half-days 09:00-12:30 CEST. 

Location: Online - Find the link after enrolment. 

Audience: This training is primarily designed for bioinformaticians involved in infectious disease surveillance and outbreak response. It is also intended for epidemiologists, microbiologists/virologists, and public health professionals with bioinformatics expertise, who are seeking to incorporate genomic data into outbreak investigations.

Learning Objectives  

Upon completion of this workshop, participants will be able to:

1. Explain the principles of genomic epidemiology and their role in infectious disease surveillance and outbreak response.
2. Describe the ecology, epidemiology, and transmission dynamics of zoonotic and sustained human-to-human transmissible mpox lineages.
3. Access and utilize appropriate reference genomic datasets and analytical approaches for investigating mpox outbreaks.
4. Perform basic quality assessment and interpretation of mpox genome sequence data including the use of masking strategies to exclude potential misguiding parts in the alignment.
5. Use bioinformatics tools to perform basic genomic and phylogenetic analyses.
6. Apply phylogenetic methods to investigate the evolution and spread of mpox viruses.
7. Interpret phylogenetic trees to infer genetic relatedness, transmission patterns, and outbreak clusters.
8. Identify APOBEC-3 specific mutations and thereby discriminate between zoonotic infections and ongoing human-to-human transmission.
9. Evaluate the strengths, limitations, and uncertainties of phylogenetic analyses in public health decision-making.
10. Formulate evidence-based conclusions from genomic epidemiology investigations.

Participation: This course is open for public enrolment. It's made available for free, thanks to EU funding.