Postdoctoral position OT-30570
Postdoctoral research project: Drivers of avian influenza viruses evolution and transmission in live bird market networks
31076 TOULOUSE
INRAE presentation
The French National Research Institute for Agriculture, Food, and Environment (INRAE) is a major player in research and innovation. It is a community of 12,000 people with 272 research, experimental research, and support units located in 18 regional centres throughout France. Internationally, INRAE is among the top research organisations in the agricultural and food sciences, plant and animal sciences, as well as in ecology and environmental science. It is the world’s leading research organisation specialising in agriculture, food and the environment. INRAE’s goal is to be a key player in the transitions necessary to address major global challenges. Faced with a growing world population, climate change, resource scarcity, and declining biodiversity, the Institute has a major role to play in building solutions and supporting the necessary acceleration of agricultural, food and environmental transitions.
Work environment, missions and activities
Context
Highly pathogenic avian influenza (HPAI) viruses are rapidly crossing geographical boundaries, threatening poultry, wildlife and potentially evolving into global pandemics1,2. In South-East Asia, particularly in Cambodia, the ecosystem of poultry production and trade plays a crucial role in the emergence and spread of novel avian influenza viruses, increasing the risk of cross-species transmission and amplification within both domestic poultry and wild bird populations. Surveillance studies in Cambodian live bird markets have revealed alarming high avian influenza virus detection rates in poultry3, often coupled with co-infections with different strains4 and sporadic human cases5. Effective surveillance strategies are imperative to promptly detect and mitigate the emergence and spread of viruses in poultry and prevent human infections.
Position summary
We are seeking a highly motivated postdoctoral researcher to join our group (epidesa, epidemiology and decision-making in animal health, https://epidesa.inrae.envt.fr) at the Host-Pathogens Interactions (IHAP) research unit at INRAE. The postdoctoral researcher will investigate the drivers of avian influenza virus evolution in live bird market networks in Cambodia, using an original longitudinal dataset generated by the TrackFLU project (https://trackflu.inrae-envt.com). Over one year, TrackFLU has followed 20 poultry sites in Cambodia, including live bird markets, farms and slaughterhouses, with information on poultry production, trading and biosecurity practices, alongside sampling of poultry for avian influenza viruses. The resulting viral genomic data will provide an unprecedented opportunity to link virus evolution and transmission with the epidemiological and ecological context in which viruses circulate. The postdoctoral researcher will analyse the whole-genome sequences generated through the project using phylodynamic and computational analyses, together with the longitudinal practices data to identify factors that are associated with viral co-circulation and reassortments. This position offers an exciting opportunity to work at the intersection of pathogen genomics and infectious disease epidemiology, leading efforts to understand the emergence and spread of avian influenza viruses in live bird market networks in Cambodia.
Environment and research group
This postdoctoral position is part of the TrackFLU project (No. 101116387) funded by the ERC Starting Grant. Joining the TrackFLU project offers excellent opportunities to advance your career through participation at (inter)national conferences, collaboration with Institut Pasteur du Cambodge, local stakeholders, including Animal Health and Production Research Institute (NAPHRI), and leading research group in phylodynamics (ETH Zürich, Institut Pasteur Paris), opportunities to co-supervise master and PhD students, access to sequencing laboratories at IPC and high-performance computing cluster at INRAE.
Supervisors
Dr Claire Guinat (INRAE, Toulouse, France) primary research focuses on the drivers shaping the transmission dynamics of animal infectious diseases, including avian influenza. She has a strong background in quantitative and phylodynamic approaches.
Dr Arthur Kocher (INRAE, Toulouse, France) studies human and animal disease ecology and evolution using molecular approaches combined with Bayesian statistics and phylogenomics.
Key references
1. Wille, M. & Barr, I. G. Resurgence of avian influenza virus. Science 376, 459–460 (2022).
2. Cohen, J. Worries about bird flu in US cattle intensify. Sci. N. Y. NY 384, 12–13 (2024).
3. Horm, S. V. et al. Intense circulation of A/H5N1 and other avian influenza viruses in Cambodian live-bird markets with serological evidence of sub-clinical human infections. Emerg. Microbes Infect. 5, 1–9 (2016).
4. Horwood, P. F. et al. Co-circulation of influenza A H5, H7, and H9 viruses and co-infected poultry in live bird markets, Cambodia. Emerg. Infect. Dis. 24, 352 (2018).
5. World Health Organization. Avian Influenza A (H5N1)–Cambodia. Dis. Outbreak News Httpswww Who Intemergenciesdisease-Outbreak-Newsitem2023-DON445 Internet 26 Febr. 2023 (2023).
Research location The postdoctoral researcher will be affiliated to INRAE (epidesa group, IHAP unit) located on the National Veterinary School of Toulouse campus, Toulouse, France, with potential short missions to Cambodia for research activities and dissemination purposes.
Training and skills
Academic qualifications and experience
Candidates should hold a PhD degree in disease evolution, epidemiology or related disciplines. Prior experience with phylodynamic analyses is required. A strong interest in biological and epidemiological questions related to pathogen evolution and transmission is required. Ability to work with different types of data, including genomic and epidemiological data is required, as well as strong analytical and scientific writing skills. Strong organizational skills and the ability to work independently is desirable. Proficiency in English writing and willingness to present research work at international conferences are essential. Proficiency in French is not necessarily required.
For further information, please contact Claire Guinat (claire.guinat@envt.fr).
INRAE's life quality
By joining our teams, you benefit from (depending on the type of contract and its duration):
- up to 30 days of annual leave + 15 days "Reduction of Working Time" (for a full time);
- parenting support: CESU childcare, leisure services;
- skills development systems: training, career advise;
- social support: advice and listening, social assistance and loans;
- holiday and leisure services: holiday vouchers, accommodation at preferential rates;
- sports and cultural activities;
- collective catering.
How to apply
How to apply
Please submit your CV, a short motivation letter (max 1 page) where you state why you are interested and what experience you have to address the aspects of the project, and two reference letters to Claire Guinat (claire.guinat@envt.fr) by October 25th 2026. Online interviews of shortlisted candidates will be held early November 2026.
All persons employed by or hosted at INRAE, a public research establishment, are subject to the Civil Service Code, particularly with regard to the obligation of neutrality and respect for the principle of secularism. In carrying out their functions, whether or not they are in contact with the public, they must not express their religious, philosophical or political convictions through their behaviour or by what they wear. > Find out more: fonction publique.gouv.fr website (in French)