Topic outline

  • Pathogen evolution, genomic epidemiology, & phylodynamics (June 26-28)

    This course page is not finalized: more information will appear later


    Course Instructors

    Erik Volz, Imperial College London

    Nicola de Maio, EMBL-EBI

    Course contents:

    # Summary

    This course provides and in-depth introduction to pathogen genomics and evolution with a focus on applications of genomics to understanding epidemiological dynamics. At the end of this course, students will have a practical understanding of how to analyse pathogen genetic data to address a variety of public health questions, such as investigations of epidemic origins, identifying emerging variants, evolution of antimicrobial resistance, epidemic growth rates, and transmission patterns.

    We will review
    - Population genetics of evolving pathogens, including how epidemiological and immunological dynamics influence pathogen genetic diversity.
    - Evolution of antimicrobial resistance, including mechanisms of resistance, how natural selection leads to development of resistance and how to detect and quantify natural selection in genomic data.
    - Phylogenetic methods and approaches to understanding how pathogen genetic diversity changes over time. This will include tutorials on software used to estimate pathogen phylogenies, including BEAST.
    - Epidemiological modelling and phylodynamics. This will include applications of phylogenomics to epidemiological surveillance, such as monitoring for emerging variants and estimating transmission patterns over space and time.

    # Software

    IMPORTANT: All participants are expected to bring a laptop.
    Students should install R:
        - Optionally use R Studio: https://posit.co/products/open-source/rstudio/
        - Students should be able to install the `ape` R package.
    Students should install BEAST >1.10: https://beast.community/

    Time and Place

     All lectures take place at Stockholm University in Campus Albano, house 1, level 2, room ??. See Registration and Venue for further details.

    Lecture times (includes also problem solving, tutorials, computer sessions, ...): 

    Wednesday June 26: 14.00-15.30, 16.00-17.30

    Thursday June 27: 9.00-10.30, 11.00-12.30, 14.00-15.30, 16.00-17.30

    Friday June 28: 9.00-10.30, 11.00-12.30, 14.00-15.30, 16.00-17.30

    General prerequisites

    It is expected that course participants have basic knowledge of statistics and mathematics and rudimentary knowledge of infectious disease epidemiology. It is also expected that participants have basic computer software knowledge and preferably are familiar with the software R. 

    IMPORTANT: All participants are expected to bring a laptop with R installed on it.

    Additional prerequisites for this course

    Basic educational experience in genetics and evolutionary biology is helpful but not required.  

    Relevant literature


    Back to main page of ESPIDAM


  • Sources for R

    Instructions for installing R, introduction to R?

  • Wednesday, June 26

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  • Thursday, June 27

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  • Friday, June 28

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