Doctorat Project

Offer Reference

•  Contract: PhD position
•  Duration: 36 mounth
•  Beginning: 01/10/2025
•  Remuneration: 2 200€ per month (gross salary)
•  Reference: OT-25716
•  Deadline: 14/05/2025

Work environment, missions and activities

The intensification of livestock production is a major factor influencing the emergence of zoonotic pathogens. In many settings, this process creates a complex mosaic of animal production and distribution modes. Yet, the ways in which the resulting networks – through which animals are raised, traded and consumed – shape pathogen transmission and persistence remain poorly understood. This is particularly true in regions at high risk of disease emergence, such as Bangladesh, where poultry production is rapidly intensifying and multiple avian influenza virus (AIV) lineages, including highly pathogenic H5N1, circulate endemically.

This PhD project aims to explore how the structure of poultry production and distribution networks influence AIV transmission dynamics, and to assess the effectiveness of structural interventions to mitigate disease risk. The successful candidate will develop mechanistic models and apply a novel modelling framework, EPINEST, to simulate the spread of AIVs in Bangladesh. The project will leverage extensive datasets on network structure, viral prevalence and genetic sequences. A key focus will be the integration of phylodynamic analysis to inform the mechanistic models, linking viral genomic data to transmission patterns. Control strategies altering the network structure will be simulated and their impact of AIV transmission risk will be explored.

The PhD student will be primarily based in the EPIA unit (EPIdémiologie des maladies Animales et zoonotiques), on the VetAgroSup campus near Lyon, France, and collaborate closely with the Royal Veterinary College (United Kingdom), Chattogram Veterinary and Animal Science University and the Bangladesh Livestock Research Institute (Bangladesh). The position will involve on-site visits at the Royal Veterinary College.

Through this PhD programme, the student will develop robust skills in mechanistic modelling and phylodynamic analyses. Furthermore, as part of an international collaboration, the candidate will thrive in a stimulating interdisciplinary environment. This setting will not only enhance their research skills but also broaden their professional network and expose them to diverse scientific perspectives and methodologies.

References :

•  Pinotti et al, 2024, EPINEST, an agent-based model to simulate epidemic dynamics in large-scale poultry production and distribution networks. PLOS Computational Biology, 20(2):e1011375
• Pinotti F et al, 2024, Modelling the transmission dynamics of H9N2 avian influenza viruses in a live bird market. Nature Communications, 15(1):3494.
•  Carnegie et al (2023) H9N2 avian influenza virus dispersal along Bangladeshi poultry trading networks. Virus Evolution, 9(1):vead014.

Training and skills

Master's degree/Engineering degree

• Completion of a postgraduate degree, or at least an undergraduate degree, in epidemiology, network science, biostatistics, computational biology, mathematics, physics, or another relevant quantitative discipline.
• Proficiency in both written and spoken English.
• Willingness to supervise research degree students, and to be able to work as part of a multidisciplinary team.
• Knowledge in mathematical modelling, a prior experience in quantitative analyses and in modelling the spread of infectious diseases would be an asset, as well as proficiency in R and/or a computer programming language such as C/C++ or Python.

Personne à contacter

•   FOURNIE Guillaume - Cf. personal page - guillaume.fournie@inrae.fr