GenEpi-BioTrain - Virtual training 25 - Mobile labs and field sequencing during outbreaks

Topic outline

• Welcome to the virtual training on Mobile labs and field sequencing during outbreaks

  Welcome to the virtual training on Mobile labs and field sequencing during outbreaks

  Course description

  This virtual training provides an overview of how mobile laboratories and field-deployable sequencing technologies support rapid response during infectious disease outbreaks. Through insights from experts in emergency biological intervention, field epidemiology, and outbreak surveillance coordination, participants will examine the operational, logistical, and analytical components required to deploy mobile diagnostics in crisis settings.

  Target audience

  Public health microbiologists, epidemiologists, or bioinformaticians interested in learning about the deployment strategies of mobile labs to the field during outbreaks and the role of genomic surveillance during an outbreak investigation. 

  Format

  This virtual training consists of two half-day sessions held in the mornings of Monday 13 April and Wednesday 15 April, from 09:00 to 12:30 (CEST).

  Outline (see detailed agenda below)

  Session 1: 

  Part 1: The Role of Rapid Response Mobile Laboratories (RRMLs) in the European and Global Health Security Architecture

  Part 2: Laboratory for Urgent Response to Biological Threats (CIBU) - presentation of the mobile laboratory

  Part 3: Deployment of the Mobile Lab - Mayotte

  Part 4: Practical exercise: Virtual deployment for unknown disease outbreak

  
  

  Session 2: 

  Part 1: Virtual deployment discussion (practical)

  Part 2: The European Mobile Laboratory: field experience in emerging infection surveillance and response

  Part 3: History and development of sequencing on the field

  • ForumAnnouncements
  • PagePresenters' biography
  • PageVirtual training organisation credits
  • PageLegal terms and conditions
• Collapse allExpand all
  Aim and objectives

  Aim and objectives

  The course will highlight how rapid pathogen detection, genomic data generation, and on-site analytics contribute to timely public health decision-making, including case management, transmission tracking, and implementation of countermeasures. Across two interactive sessions, participants will gain a practical understanding of field workflows, real-world constraints, and best practices for integrating mobile sequencing into outbreak investigation and control.

  Upon completing this workshop, participants will be able to:

  • Describe the operational role of mobile laboratories in outbreak response, including their deployment, logistical requirements, and integration into emergency public health interventions.
  • Explain the principles and workflows of field-deployable sequencing technologies, including sample processing, rapid diagnostics, and portable genomic sequencing approaches.
  • Interpret how genomic data generated in field settings can support outbreak investigation, including pathogen detection, strain characterization, and situational awareness for response teams.
  • Apply basic concepts of mobile laboratory deployment through a simulated outbreak scenario, including interpretation of initial diagnostic results and consideration of operational decision-making.
  • Recognise the evolution and future directions of field sequencing initiatives, including global and European efforts to strengthen genomic surveillance capacity during epidemics.
• Pre-requisites

  Pre-requisites

  This training, specifically the practical exercise, has some Prerequisites. In anticipation of the second session on 15 April 2026, we invite you to:

  1. Read carefully the 'Software requirements' and prepare your tools.

  
  

  • FolderSoftware Requirements
• Summary of tools and software employed during the training

  Summary of tools and software employed during the training

  RAMPART https://github.com/artic-network/rampart

  Amplicon-nf 

  https://github.com/artic-network/amplicon-nf (command line only)

  https://artic.network/amplicon-nf/amplicon-nf-epi2me-simple-sop.html

   with EPI2ME Desktop application (https://epi2me.nanoporetech.com/downloads) 

  MAFFT https://mafft.cbrc.jp/alignment/software/

  MEGA https://www.megasoftware.net/

  IQ-TREE https://github.com/iqtree/iqtree2

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

  
  

  • FolderPractical exercise material
• Session 1

  Session 1
  • FileAGENDA

    
    

  • Opening of session 1
  • Part 1: The Role of Rapid Response Mobile Laboratories (RRMLs) in the European and Global Health Security Architecture 

     
    
  • File1. The Role of Rapid Response Mobile Laboratories (RRMLs) in the European and Global Health Security Architecture
  • FileWHO RRML Teaser video
  • Part 2: Laboratory for Urgent Response to Biological Threats (CIBU) - presentation of the mobile laboratory 

     
    
  • File2. CIBU – Presentation of the Mobile Laboratory
  • Part 3: Deployment of the Mobile Lab - Mayotte 

     
    
  • File3. Deployment of the Mobile Laboratory – Mayotte
  • Part 4: Practical exercise: Virtual deployment for unknown disease outbreak 

     

  • File4. Practical exercise: Virtual deployment for unknown disease outbreak
  • You completed session 1

    If you see this message, it means that you have either attended session 1 live or watched the recording of session 1. This is pre-requisite to access the certificate

    
    

    Not available unless any of:

    • The activity Online session 1 — Virtual training 25 is marked complete
    • All of:
      • The activity OPENING OF SESSION 1 Webinar Room VT25 ... is marked complete
      • The activity PART 1:THE ROLE OF RAPID RESPONSE MOBILE ... is marked complete
      • The activity PART 2:LABORATORY FOR URGENT RESPONSE TO ... is marked complete
      • The activity PART 3:DEPLOYMENT OF THE MOBILE LAB - ... is marked complete
      • The activity PART 4:PRACTICAL EXERCISE: VIRTUAL DEPLOYMENT ... is marked complete
• Session 2

  Session 2
  • Opening of session 2

    
    

  • Part 1: Virtual deployment discussion (practical) 

     
    

  • File1. Virtual deployment discussion (practical)
  • FileRAMPART exercise video
  • FileAmplicon-nf video part 1
  • FileAmplicon-nf video part 2
  • FilePhylogenetic analyses video
  • Part 2: The European Mobile Laboratory: field experience in emerging infection surveillance and response 

      
    

  • File2. The European Mobile Laboratory: field experience in emerging infection surveillance and response
  • Part 3: History and development of sequencing on the field 

     
    

  • File3. History and development of sequencing on the field
  • You completed session 2

    If you see this message, it means that you have either attended session 2 live or watched the recording of session 2. This is pre-requisite to access the certificate.

    Not available unless any of:

    • The activity Online session 2 — Virtual training 25 is marked complete
    • All of:
      • The activity OPENING OF SESSION 2 Webinar Room VT25 ... is marked complete
      • The activity PART 1:VIRTUAL DEPLOYMENT ... is marked complete
      • The activity PART 2: THE EUROPEAN MOBILE LABORATORY: FIELD ... is marked complete
      • The activity PART 3:HISTORY AND DEVELOPMENT OF SEQUENCING ON... is marked complete
• Activities visible only to the participants of the live sessions

  Activities visible only to the participants of the live sessions
  • SeminarOnline session 2 — Virtual training 25

    View all events
  • SeminarOnline session 1 — Virtual training 25

    View all events
  • FeedbackSuggest a topic for a future virtual training
  • ForumQuestions and Answers (Q&A) Forum
• Further learning

  Further learning
  • Here is a selection of training materials that might interest you:

    The expanding role of mobile laboratories in global health crises

    Recording of ESCAIDE side session (2024)

    Guidance for rapid response mobile laboratory (‎RRML)‎ classification

    WHO guidance (2021)

    Open guidance

    Rapid Response Mobile Laboratories (‎RRML)‎ Network: at a glance

    WHO technical document (2023)

    Open article

    Rapid Response Mobile Laboratories (‎RRMLs)‎: what’s in a mobile laboratory?

    WHO technical document (2023)

    Open article

    Strategic Group for Diagnostic Surge Capacities of the Global Outbreak Alert and Response Network (GOARN)

    WHO publication (2025)

    Open publication

    Integrating mobile laboratories into global health security: advancing collaboration through GOARN-DiSC

    Open access article in BMJ (2025)

    Open article

    Minimum operational standards and typology for rapid response mobile laboratories

    WHO standard (2025)

    Consult standard
• 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.