GenEpi-BioTrain - Virtual training 13 - RSV Insights: Genomic Evolution, Treatments, and Public Health Strategies

Topic outline

• RSV Insights: Genomic Evolution, Treatments, and Public Health Strategies (GenEpi-BioTrain — Virtual Training 13)

  RSV Insights: Genomic Evolution, Treatments, and Public Health Strategies (GenEpi-BioTrain — Virtual Training 13)

  ℹ️ Please Note

  You are welcome to explore the available resources and video recordings. Please note that the resources in this course come from the Virtual Training 13 held in December 2024, and certificates are only issued to participants who attended the live webinar sessions.

  
  Introduction
  

  Welcome to the virtual training on "Introduction to building basic bioinformatics workflows"!

  This course aims at providing you with skills to create and maintain workflows for automating routine bioinformatics tasks.

  Description

  An important skill in bioinformatics is the ability to install and use command line tools to perform analysis of whole genome sequence data. For the purpose of performing routine bioinformatics tasks associated with WGS-based public health surveillance, automation plays a vital role. The first step towards automation is to set up a basic workflow for small-scale use. Small-scale workflows are easy to maintain and can be developed by a small number of people. However, the use of such workflows depends on the involvement of developers. A sustainable solution is to convert a workflow into a pipeline. Creating and configuring bioinformatic pipelines is somewhat complex and requires expertise in workflow management systems such as Snakemake and Nextflow. Learning how to set up basic workflows is a precursor to learning how to build pipelines.

  In this course, participants will learn about basic workflows and how to set them up. Participants will set up their own simple workflow to produce raw read QC reports, whole genome assemblies and basic antimicrobial resistance genotyping. Participants will be given a brief introduction on how to extend their workflow with additional bioinformatics tools, and will be given inspiration on how to advance their workflows into pipelines.

  Intended audience

  The target audience for this training is mainly beginners in bioinformatics, who have some familiarity with navigating and interacting with Unix terminals, creating and running simple bash scripts, and creating and working with virtual environments through the Conda ecosystem (see Prerequisites). 

  What you will not learn

  In this virtual training, participants will not learn how to use the Unix terminal, how to code, and what bioinformatics tools or commands do. To these purposes, please explore the already available GenEpi-BioTrain virtual trainings freely available on the ECDC Learning Portal. Additionally, participants will not learn how to use workflow management systems like Nextflow and/or Snakemake.

  Outline of sessions

  The two sessions take place on 19 and 21 March 2025 at 09:00-12:30 (CET) on each day.
  

  As with all GenEpi-BioTrain Virtual Trainings, the webinars will be recorded and you will be able to access the recordings at any time, provided you are enrolled in the course.

  Welcome to this virtual training space on EVA.

  Below you will see the two online sessions and their support materials.

  In anticipation for the live sessions, we encourage participants to:

  1. Explore the materials available; 

  2. Install the software indicated below;

  3. Suggest topics of interest for future virtual trainings.

  • ForumAnnouncements
  • PagePresenters' biography
  • PageVirtual training organisation credits
  • PageLegal terms and conditions
  • International RSV Symposium

    The 13th International RSV Symposium will take place in Brazil from 12 to 15 March 2025. For more details, visit this link: https://www.rsv2025.org/

    Early bird registration closes on 18 December!

• Aim and Objectives

  Aim and Objectives

  The aim of this virtual training is to provide participants with in-depth knowledge of RSV (Respiratory Syncytial Virus), including its genomic diversity, evolution, available treatments, and emerging vaccine strategies. The focus will be on how genomic data informs public health responses, the impact of RSV on vulnerable populations, and ongoing advancements in treatment and prevention. The training will also explore regulatory frameworks and public health strategies for managing RSV outbreaks.
  

  
  

  Upon completing this workshop, participants will be able to:

  • Understand the virology, epidemiology, and clinical impact of RSV on global health.

  • Explain RSV genomic diversity, evolutionary trends, and their implications for public health.

  • Use bioinformatics tools to analyze RSV genomic sequences, variants, and interpret phylogenetic data.

  • Analyze genomic data to better understand RSV transmission patterns and outbreaks.

  • Describe current RSV treatment options and advancements in monoclonal antibodies.

  • Understand the status and challenges in developing RSV vaccines, particularly for vulnerable groups like pregnant women.

  
  
• Agenda

  Agenda
  • 
    

  • PageClick here for a detailed agenda
• Software requirements

  Software requirements

  No specific software installations are required as only online tools will be used, such as:

  • Sequence annotation: https://clades.nextstrain.org
  • Phylogenetic tree inference: https://ngphylogeny.fr/
  • Phylogenetic tree visualization: https://itol.embl.de/
  • Follow-up of epidemics: https://nextstrain.org/
  • Databases (public ones): https://www.ncbi.nlm.nih.gov/ & https://www.bv-brc.org/
  • Databases (private ones // Account + activation of the EPIRSV tab needed): https://www.gisaid.org/ 
  • Mutation of interest detection: https://rsvsurver.bii.a-star.edu.sg/ 

  
  
• Session 1: Virology, Evolution, and Analysis of Genomic Data (10 December)

  Session 1: Virology, Evolution, and Analysis of Genomic Data (10 December)

  1. Introduction to RSV: Virology, Epidemiology, Global Impact and Pathogenesis (50 min) — Pr. Peter Openshaw (Imperial College, London)

  • RSV Biology and Transmission: Understanding virus structure and life cycle

  • Global Disease Burden: Impact on different populations and seasonal patterns.

  • Early attempts at vaccination, augmentation of disease and immunopathogenesis.
    

  • Q&A (5min)

  
  

  2. Genomic Diversity and Evolution of RSV (40 min) — Frédéric Lemoine and Jérome Bourret (Institut Pasteur, Paris)

  • Genomic Variability: RSV genetic diversity, subtypes, and mutations.

  • Evolutionary Trends: How RSV evolves and implications for public health.

  • Tracking Lineages: Phylogenetic analysis and understanding RSV spread.

  • Q&A (5/10min)

  
  

  3. Practical Exercise: Analyzing RSV Genomic Data (1hour) — Dr. Frédéric Lemoine and Dr. Jérome Bourret (Institut Pasteur, Paris)

  A. Bioinformatics Tools for RSV Analysis (20min) 

  • Overview of Tools: Introduction to bioinformatics platforms for RSV analysis (e.g., viral genome databases, sequence alignment tools, visualization tools).

  • Interactive Tool Demo: Live demonstration of a bioinformatics tool for RSV analysis.

  • Q&A

  B. Practical Exercise: Analyzing RSV Genomic Data (40min) 

  • Hands-On Exercise: Participants will use online tools to analyze RSV genomic sequences.

  • Task: Identify genetic variants, construct phylogenetic trees, and interpret results.

  • BREAK (30 min)

  • Correction

  • 1. Opening session

  • 2. Introduction of participants

  • 3. Introduction to RSV: Virology, Epidemiology, Global Impact and Pathogenesis 

  • 4. Q&A

  • 5. Genomic Diversity and Evolution of RSV

     

  • 6. Q&A

  • 7. Bioinformatics Tools for RSV Analysis

  • 8. Q&A

  • 9. Exercise

  • 10. Correction of the exercises

  • 11. Concluding Remarks

  • Lectures

  • FolderLectures
  • Practical

    Here, you will find the guidelines and datasets to be used in Session 1. Please download both in advance to have them ready for the exercises.
    A demonstration of the online tools and the corrections of the exercises will be provided during Session 1.

  • FileGuidelines
  • FolderDatasets
  • Additional resources

  • PageRSV Gene Duplications articles
  • PageIdentification of duplication events
• Session 2: Surveillance, Treatment, and Vaccine Strategies (13 december)

  Session 2: Surveillance, Treatment, and Vaccine Strategies (13 december)

  1. RSV Treatment and Vaccine Development (50 min) — Marie-Anne Rameix Welti (Institut Pasteur, Paris)

  • Vaccination (pregnant women and elderly) and monoclonal antibodies: status, challenges in development, and recent advancements.

  • Antiviral treatments: development and challenges

  • Case Study: “Genotypic and phenotypic characterisation of respiratory syncytial virus after nirsevimab breakthrough infections: a large, multicentre, observational, real-world study”.

  • Q&A (5min)

  
  

  2. RSV Surveillance (35 min) — Dr. Marie-Anne Rameix-Welti (Institut Pasteur, Paris) and Dr. Nick Bundle (ECDC, Sweden)

  • Overview of the National Reference Center for RSV in France — 15min (Dr. Marie-Anne Rameix-Welti)

  • Overview of RSV monitoring and data collection methods in EU — 15min (Dr. Nick Bundle)

  • Q&A (5min)

  
  

  3. RSV Surveillance, Immunisation and Public Health Policy (35min) — Dr. Lisa Domegan (HPSC Ireland)

  • Overview of RSV monitoring and data collection methods in Ireland

  • How genomic and epidemiological data are integrated for public health responses

  • Implementation of Public Health measures, (e.g. vaccination or mAb administration).

  • Q&A (5min)

  
  

  • 1. Opening

  • 2. RSV treatment and vaccine development

  • 3. RSV surveillance 

  • 4. RSV surveillance, immunisation and public health policy

  • Lectures

  • FolderLectures
• 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 - ICT Front Office ICT.FrontOffice@ecdc.europa.eu.