Increase sharing and analyses of surveillance and virology data
Aim
- To facilitate data sharing and analysis (surveillance, virulence, antigenicity, other viral characteristics) on swine Influenza viruses (swIAVs) within the network and with national and international organizations like OFFLU.
- To build and disseminate expertise for the detection and characterization of swIAVs that are undergoing constant diversification in pig populations
- To provide data that will fill knowledge gaps on incidence and variability of swIAV and improve national and international surveillance systems
- To provide development opportunities and training for early career scientists and increase expertise regarding swIAV, particularly with respect to technical innovation and bioinformatic data analysis
Main Deliverables
European Swine Influenza Network Report on Swine Influenza A Viruses Evolution and Diversity in Europe from October 2022 to September 2023: https://zenodo.org/records/10598312
Expected Deliverables
- A bi-annual report of pan-European swIAV diversity through the analysis of surveillance data shared by the working group members using a common template.
- Complete pan-European antigenic maps of swine influenza viruses and reference sera established and regularly updated
- Workshops on the necessary bioinformatics / phylogenetics / antigenic maps analyses aspects
- Paper analysing the swIAV spread dynamics between European countries through phylodynamic and phylogeographic analyses of the sequences collected during the action.
Past and future activities
- March 2023: WG2 online kick-off meeting to present the main goals and future action of the working group.
- April 2023: WG2 in-person meeting in Barcelona, Spain, to discuss the upcoming activities and priorities for the working group for the next years.
- September 2023: organisation of a NGS Consensus Sequences Ring Trial to compre bioinformatics pipelines of the teams generating swIAV sequences in Europe. The sequences have been collected from all partners and data analyses are on going to compare the reproducibility of the generated sequences, based on a set of common FASTQ files of different quality.
- October 2023: Short Term Scientific Mission concerning phylodynamic and phylogeographic data analyses on swine influenza A viruses sequences. Hosted by Alice Fusaro and Bianca Zecchin at the Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Viral Genomics and Transcriptomics, Padova, Italy.
- December 2023 (upcoming): publication of the first ESFLU swIAV evolution and diversity in Europe report #1 covering the October 2022 to September 2023 with about 250 analysed strains covering 16 countries, thanks to the joint effort of the working group members.
- 2024 (upcoming): ESFLU Phylogenetics and Phylodynamics Training School (dates and location to be determined).
- 2024 (upcoming): ESFLU swIAV evolution and diversity in Europe report #2 & #3.
Members and Sub-groups Organisation
The ESFLU Working Group 2 encompasses 74 members with 24 countries represented and is gender balanced. 35% of the members are young researchers. The members are divided in 4 subgroups:
- Sequencing and bioinformatics: from sequencing data to consensus sequences.
- Phylogenetics and Phylodynamics: from consensus sequences to phylogenetic trees and phylodynamic analyses
- Antigenic tests and data analysis: from strains antigenic data to antigenic maps.
- Epidemiology data analysis: to determine the most useful metadata to collect alongside sequences to combine phylogenetic and epidemiology data.
Main Experts Profiles and Scientific Expertise
The working group 2 scientific expertise is wide, as shown by the word cloud below. The main experts driving the working group display skills related to phylogenetics, sequencing and bioinformatics.
