GenEpi-BioTrain - Virtual Training 28 - Genomics and epidemiology of polioviruses: How a virus resists eradication

Topic outline

• Welcome to the virtual training on genomics and epidemiology of polioviruses

  Welcome to the virtual training on genomics and epidemiology of polioviruses

  Course description

  The aim of this virtual training is to provide participants with a comprehensive understanding of poliovirus biology, genomics, epidemiology, and public health strategies. It will focus on poliovirus surveillance, the evolution of vaccine-derived strains and eradication efforts. Participants will have the opportunity to analyse poliovirus genomic data and to learn how these data can be integrated into the epidemiological surveillance of poliovirus.

  Target audience

  Public health microbiologists and virologists, epidemiologists, or bioinformaticians interested in learning about the biology and epidemiology of polioviruses and the role of genomic surveillance in global eradication efforts.

  Format

  This virtual training consists of two half-day sessions held in the afternoons of Friday 17 July from 13:00 to 16:30 and Monday 20 July from 14:30 to 18:00 (CEST).

  Outline (see detailed agenda below)

  Session 1: 

  • Introduction to poliovirus evolution 
  • Poliovirus surveillance in the EU/EEA
  • Epidemiology and genomic surveillance 
  • Practical exercise: Genomic analysis of human poliovirus

  
  Session 2: 

  • Guided correction of practical exercises and discussion 
  • Wastewater monitoring of polioviruses
  • Vaccination and Evolution of vaccine-derived strains
  • Future directions in polio research and eradication efforts 

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  Aim / Objectives

  Aim / Objectives

  This virtual training will focus on poliovirus surveillance, the evolution of vaccine-derived strains and eradication efforts. Participants will have the opportunity to analyse poliovirus genomic data and to learn how these data can be integrated into the epidemiological surveillance of poliovirus. Participants will also learn about surveillance efforts across the EU/EEA and discover the role that environmental surveillance played in understanding recent outbreaks.

  Upon completing this training, participants will be able to:

  • Describe the biology, genomic organisation, and epidemiology of polioviruses, including the characteristics of different serotypes and their role in disease transmission.
  • Explain how genomic and environmental surveillance contribute to poliovirus detection, outbreak investigation, and monitoring of transmission dynamics.
  • Apply basic genomic epidemiology approaches to classify polioviruses, identify serotypes, and reconstruct outbreaks using sequence data.
  • Interpret phylogenetic and genomic analyses to investigate the emergence and spread of vaccine-derived polioviruses (VDPVs).
  • Assess the impact of vaccination strategies on poliovirus evolution, including the transition from OPV to IPV and the factors associated with VDPV emergence.
    
  • Discuss current challenges and future directions in global polio eradication efforts, including the integration of genomic data into public health decision-making and outbreak response.
• Pre-requisites and required software

  Pre-requisites and required software

  This training, especially the practical session, has some prerequisites.

  1. Minimal computer requirements

  Before attending the workshop, please ensure your computer meets the following minimum specifications:

  CPU: At least 6 processor cores

  Memory (RAM): At least 16 GB

  Operating System: Windows 10/11, macOS, or Linux

  Windows users (required before installing command-line software)

  Participants using Windows should first install Windows Subsystem for Linux (WSL2) with the Ubuntu distribution. This provides a Linux environment that will be used throughout the workshop for running command-line tools.

  Follow Microsoft's installation guide:

  Install WSL | Microsoft Learn

  https://learn.microsoft.com/windows/wsl/install

  Software	Purpose	Installation method
  AliView	View and edit sequence alignments	GUI installer or Conda
  FigTree	Visualize phylogenetic trees	GUI installer or Conda
  TempEst	Assess temporal signal (root-to-tip regression)	GUI installer
  BEAST	Bayesian phylogenetic analysis	GUI installer or Conda
  BEAGLE	Accelerates BEAST analyses	Conda
  MAFFT	Multiple sequence alignment	Conda
  IQ-TREE	Maximum likelihood phylogenetic inference	Conda

  2. Software requiring Conda
  

  Before installing MAFFT and IQ-TREE, install Miniforge (recommended) or Miniconda.

  2.1 Install Miniforge

  Download the installer for your operating system:

  https://conda-forge.org/download/

  Windows users: Install Miniforge inside your Ubuntu (WSL2) environment, not in Windows itself.

  2.2 Install MAFFT and IQ-TREE

  Open a terminal (Linux/macOS or Ubuntu in WSL) and run:

  conda --version

  Install MAFFT

  conda install -c bioconda mafft

  Verify:

  mafft --version

  Install IQ-TREE

  conda install -c bioconda iqtree

  Verify:

  iqtree --version

  If that command is not found:

  iqtree2 --version

  
  

  3. AliView

  Visit:

  https://ormbunkar.se/aliview/

  Download the version for your operating system.

  Install using the default settings.

  Launch AliView to verify that it opens successfully.

  4. FigTree

  Visit: https://tree.bio.ed.ac.uk/software/figtree/
  

  
  

  5. TempEst

  Visit: https://tree.bio.ed.ac.uk/software/tempest/

  6. BEAST

  Visit: https://beast.community/

  Download the latest release. Install using the default settings.

  Launch BEAUti to verify that the installation was successful.

  7. Install BEAGLE (Linux/WSL)

  Windows and macOS versions of BEAST generally include BEAGLE automatically.
  

  On Linux or WSL:

  conda install -c conda-forge -c bioconda beagle-lib

  Verify:

  beagle_info

  Software with graphical installers

  The installation should also provide:

  BEAUti

  BEAST

  TreeAnnotator

  LogCombiner

  Tracer (depending on the version, this may be installed separately)

  8. Tracer

  Visit the official Tracer website: https://beast.community/tracer

  
  
  

  • FileVT28 Prerequisites
• Materials for the training

  Materials for the training
  • FileVT28 - S1 - Exercise instructions
  • • Practical exercise materialPractical exercise material
      • Background_dataset.fastaBackground_dataset.fasta
      • ECDC_metadata_Figtree.txtECDC_metadata_Figtree.txt
      • ECDC_metadata_microreact.csvECDC_metadata_microreact.csv
      • Practical_Activity_Guideline.pdfPractical_Activity_Guideline.pdf
      • renamed_DRC_DDNS_ECDC.fastarenamed_DRC_DDNS_ECDC.fasta
• Session 1

  Session 1

  Hours	Session	Content
  13:00-13:10	ECDC introduction and rules of conduct Presenter: Dr Luca Freschi, ECDC, Sweden
  13:10-13:55	Introduction to poliovirus evolution (45 min) Presenter: Dr Maël Bessaud, Institut Pasteur, Paris, France	Poliovirus & other enteroviruses: genome organization & evolution Poliovirus vaccine strains: attenuation determinants & reversion Importance of poliovirus genetic characterization for eradication Q&A
  13:55-14:05	Break
  14:05-14:50	Poliovirus surveillance in the EU/EEA (45 min) Presenters: Dr Silvia Funke, Dr Luca Freschi, ECDC, Sweden	Surveillance objectives and ongoing efforts European genomic surveillance of Polio Q&A
  14:50-15:00	Break
  15:00-15:45	Epidemiology and genomic surveillance (45-60 min) Presenters: Dr Alexander Shaw, Dr Darlan De Silva Candido, Imperial College London, UK	Alexander: Nanopore sequencing and introduction to DDNS (method overview) Intro to Piranha and demo Darlan: Virus evolution Genomic epidemiology Applications and examples from other outbreaks Q&A
  15:45-16:15	Practical exercise: Genomic analysis of Human poliovirus (15-30 min) Presenter: Dr Darlan De Silva Candido, Imperial College London, UK	Introduction of the exercises: Virus and serotype identification using VP1 sequences (publicly available data) Outbreak analysis using sequences from DDNS from DRC (tbc)
  16:15-16:30	Conclusion and Q&A

  • FileAGENDA S1 pdf
  • Opening of session 1

  • Introduction to poliovirus evolution  

    
    

  • FileIntroduction to poliovirus evolution
  • Poliovirus surveillance in the EU/EEA 

    
    

  • FilePoliovirus surveillance in EU/EEA
  • Epidemiology and genomic surveillance (DDNS and Piranha) 

    
    
  • FileDDNS and Piranha
  • Epidemiology and genomic surveillance (Application examples)  

    
    

  • FileViral evolution and epidemiology: application examples
  • Instructions for the exercise 

     
    

  • FilePractical exercise
  • Questions & Answers and closing remarks
• Session 2

  Session 2

  Hours	Session	Content
  14:30-14:40	ECDC introduction and rules of conduct Presenter: Dr Luca Freschi, ECDC, Sweden
  14:40-15:25	Guided correction of practical exercises and discussion (30-45 min) Presenter: Dr Darlan De Silva Candido, Imperial College London, UK	Step-by-step correction of exercises Background on evolutionary models and basic phylogenetics Sequence alignment Maximum likelihood phylogenies Serotype and virus type identification Vaccine-derived outbreak reconstruction in the DRC: overlaying time and space Q&A
  15:25-16:10	Wastewater monitoring of polioviruses (45 min) Presenters: Dr Sindy Böttcher, Dr Cornelius Rau, Robert Koch Institute, Germany	Wastewater monitoring for poliovirus in Germany Detections of cVDPV2 and WPV1 in wastewater in Germany Public health response to poliovirus detections in wastewater in Germany Q&A
  16:10-16:20	Break
  16:20-16:50	Vaccination and Evolution of vaccine-derived strains (30 min) Presenter: Dr Corey Peak, Gates Foundation, USA	Transition from OPV (Oral Polio Vaccine) to IPV (Inactivated Polio Vaccine) Risk factors for VDPV (Vaccine-Derived Polio Virus) emergence and evolution of vaccine-derived strains Genomic differences between wild-type poliovirus, OPV strains, and circulating VDPVs Q&A
  16:50-17:00	Break
  17:00-18:00	Future Directions in Polio Research and Eradication Efforts (30 + 30 min) Presenters: Dr Kathleen Rankin, Ms Kaija Hawes, Gates Foundation, USA	Kathleen: Global Polio Eradication Initiative (GPEI) updates Strategies to improve immunization in low-coverage areas Use of genomic data in outbreak response Kaija: The role of bioinformatics in long-term monitoring Challenges in maintaining polio eradication Q&A
  18:00	Conclusion and Q&A

  • FileAGENDA S2 pdf
  • Opening of session 2

    
    

  • Guided correction of practical exercises and discussion  

    
    

  • FileCorrection of practical exercise
  • Wastewater monitoring of polioviruses 

    
    

  • FileWastewater monitoring of polioviruses
  • Vaccination and Evolution of vaccine-derived strains 

    
    

  • FileVaccination and Evolution of vaccine-derived strains
  • Future Directions in Polio Research 

    
    
  • FileFuture directions in polio research
  • Maintaining a Polio-Free World 

    
    

  • FileMaintaining a Polio-free world
  • Closing remarks

• Contacts

  Contacts

  For any questions regarding the this webinar series, please use the discussion forum.

  If you have questions regarding other training initiatives please contact: courses@ecdc.europa.eu.

  If you have technical issues please contact the ECDC Service Desk at servicedesk@ecdc.europa.eu.