ESFLU WG2 Training School – 2nd Grant Period


Swine influenza is a highly contagious respiratory disease in pigs caused by influenza A viruses (swIAV), leading to significant production losses. The intensification of pork production systems and the free movement of livestock across borders facilitate the spread of the virus in Europe. New variants, some with zoonotic potential, constantly emerge. Recent human pandemics have highlighted the zoonotic and reverse zoonotic potential of swine influenza and its risks to both animal and public health. Despite the burdens caused by swine influenza, surveillance across Europe is scant and fragmented. Available and upcoming swIAV genome sequence data are thus invaluable for understanding their spread in Europe. Understanding the dynamics of swIAV spread between European countries will enable the design of appropriate biosecurity measures to limit the spread of swIAV in Europe. Building capacity in swIAV-related laboratories across Europe is therefore crucial, enabling each research group to properly analyze the swIAV sequence data they generate in a standardized manner, fostering collaboration and phylogenetic comparisons between countries.

Training School Details

ESFLU WG2 is organizing a training school focused on building the capacity of swine influenza research teams in swIAV sequencing data analysis. This includes swIAV sequence alignment and cleaning, phylogenetic analyses using maximum-likelihood trees, as well as phylodynamic and phylogeographic analyses using Bayesian approaches. The goal is to train participants to better analyze and visualize the swIAV sequences they generate or will generate through their surveillance programs or research projects, without requiring prior knowledge of command-line or coding.

This training school is essential to enhance the skills of swIAV research teams in sequencing data analysis, as the number of swIAV sequences produced each year is increasing. Moreover, new surveillance programs are likely to be developed in certain countries, including Eastern European countries, which will require proper phylogenetic skills.

Table 1 – ESFLU WG2 training school main information

Training Scope Swine Influenza A viruses phylogenetics and phylodynamics
Dates 16th to 18th  October 2024
Duration 3 days
Location IZLER Headquarters, Via Antonio Bianchi, 7/9, 2 5124 Brescia BS, Italie
Number of trainees 15
Scientific coordination Dr Gautier Richard (ANSES, France)Dr Alex Byrne (Francis Crick Institute, UK)Dr Chiara Chiaponni (IZLER, Italy)Dr Alice Fusaro (IZSVe, Italy)
Application coordination Dr Dimitrios Papadopoulos (Aristotle University of Thessaloniki)

Profile of the candidates

Anyone can apply to this training school, as there are no requirements for command-line usage or coding skills. However, applicants should already be involved, or plan to be involved in the near future, in the phylogenetic analysis of swIAV sequencing data in their lab. They should dedicate a significant portion of their time to these phylogenetic-related tasks. Individuals who provide support for these activities in their lab, even if only a few times a year for publications or reports, are also eligible. Typically, only one person per lab will be selected to ensure capacity building across a wide array of swIAV-related laboratories, given the limited number of trainees. However, if you believe multiple people from your team should attend, please submit their profiles and explain why it is important for several members of your lab to participate in the training.


Due to the high expected number of applicants, candidates should submit a 400-word document explaining why they should attend this training, considering the aforementioned information.

Candidates must also provide a complete curriculum vitae, including a list of publications. All applications must be submitted via email to the Training Grants Coordinator of the Action, Dr. Papadopoulos Dimitrios (, with the subject line “ESFLU WG2 Training School 16th-18th Oct.”

All applications will be evaluated equally. Factors such as gender, geography, career stage, qualifications, and alignment with WG2 objectives will be considered. The deadline for application submissions is August 14, 2024 (17:00 CET).

Expenses Reimbursement

Trainers and trainees will receive a Daily allowance for each day and will be reimbursed for the travel expenses according to the COST travel reimbursement rules:

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