GenEpi-BioTrain - Virtual training 24 - Antigen surveillance: from evolution to immune escape

Topic outline

• Welcome to the virtual training on antigen surveillance: from evolution to immune escape

  Welcome to the virtual training on antigen surveillance: from evolution to immune escape

  Course description

  This virtual training provides an overview of how viral and bacterial pathogens undergo antigenic evolution, potentially leading to immune escape and reduced effectiveness of prophylaxis and treatment. With case studies and real-world examples, it highlights the critical role of continuous genomic surveillance, alongside the need to research and develop novel immunisation and neutralisation strategies to sustain effective pathogen control.

  Target audience

  Public health microbiologists, epidemiologists, or bioinformaticians interested in learning about antigen evolution and novel immunisation strategies. 

  Format

  This virtual training consists of two half-day sessions held in the mornings of Monday 23 March and Wednesday 25 March, from 09:00 AM to 12:30 PM (CET).

  Outline

  Session 1: Antigen evolution, from viruses to bacteria

  Part 1: SARS-CoV-2 variants: increased fitness and immune evasion

  Part 2: Respiratory Syncytial Virus (RSV)

  Part 3: Genomic epidemiology applied to pertussis cases

  Part 4: Pertussis antigen detection (practical)

  
  

  Session 2: Bacterial antigen evolution and pandemic preparedness

  Part 1: Case study discussion (practical)

  Part 2: Streptococcus pneumoniae: vaccine strategies and antigenic variation

  Part 3: Neisseria meningiditis: virulence, immune evasion and cross-reactivity

  Part 4: Future directions: AI in pandemic preparedness and vaccines development

  
  

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  Aim and objectives

  Aim and objectives

  Across two sessions, participants will gain insights from research and public health experts involved in the surveillance of diverse viral and bacterial pathogens that are known to mutate and escape established immunisation methods over time. The training also includes a practical hands-on experience of bioinformatic tools used for the detection of the whooping-cough agent’s antigens and tracking of strain evolution. Finally, the course offers a forward-looking perspective on pandemic preparedness, exploring how emerging approaches—including AI-driven antigen prediction—could enable faster and more adaptive responses, particularly in vaccine development.

  Upon completing this workshop, participants will be able to:

  • Explain the genetic and evolutionary mechanisms underlying antigenic variation and immune escape in bacterial and viral pathogens.
  • Describe how genomic surveillance supports the detection and monitoring of antigenic evolution, vaccine escape, and reduced vaccine effectiveness.
  • Interpret examples of antigen-driven pathogen evolution using case studies from SARS-CoV-2, Respiratory Syncytial Virus, Streptococcus pneumoniae, Neisseria meningitidis and Bordetella pertussis.
  • Apply bioinformatic tools to detect antigen variants and track strain evolution, using pertussis as a practical use case.
  • Recognise emerging approaches in pandemic preparedness, including the role of AI-driven antigen prediction and accelerated vaccine development pipelines.
• Summary of tools and software employed during the training

  Summary of tools and software employed during the training

  No specific software installations are required. The webinar will use online platforms, including BIGSdb-Pasteur, blastN, GrapeTree. 

  
  
• Session 1: Antigen evolution, from viruses to bacteria

  Session 1: Antigen evolution, from viruses to bacteria
  • FileAGENDA

    
    

  • Opening of session 1

  • Part 1: SARS-CoV-2 variants: increased fitness and immune evasion 

    
    

  • File1. SARS-CoV-2 variants: increased fitness and immune evasion
  • Part 2: Respiratory Syncytial Virus (RSV) 

    
    
  • File2. Respiratory Syncytial Virus (RSV)
  • Part 3: Genomic epidemiology applied to pertussis cases 

     
    
  • File3. Genomic epidemiology applied to pertussis cases
  • Part 4: Pertussis antigen detection (practical) 

    
    

  • File4. Practical exercise: Pertussis antigen detection
• Session 2: Bacterial antigen evolution and pandemic preparedness

  Session 2: Bacterial antigen evolution and pandemic preparedness
  • Opening of session 2  

     
    

  • Part 1: Case study discussion (practical)  

    
    

  • File1. Practical exercise: correction
  • Part 2: Streptococcus pneumoniae: vaccine strategies and antigenic variation 

    
    

  • File2. Streptococcus pneumoniae: vaccine strategies and antigenic variation
  • Part 3: Neisseria meningiditis: virulence, immune evasion and cross-reactivity 

    
    

  • File3. Neisseria meningiditis: virulence, immune evasion and cross-reactivity
  • Part 4: Future directions: AI in pandemic preparedness and vaccines development 

    
    

  • File4. Future directions: AI in pandemic preparedness and vaccines development
• 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 ECDC Helpdesk at front.office@ecdc.europa.eu.