Postdoctoral research opportunity: Genetic and non-genetic determinants of cross-species transmission of highly pathogenic avian influenza viruses using phylodynamics

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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

Research context

Highly pathogenic avian influenza (HPAI) viruses have emerged as a serious global threat to animal and public health. Since 2020, these viruses have exhibited unprecedented spread, crossing geographical boundaries and affecting a wide range of species, including poultry, wildlife and humans¹. These viruses evolve rapidly, accumulating mutations that may facilitate adaptation to new species or increase the likelihood of transmissibility between species. Understanding how viral evolution shapes cross-species transmission is critical for predicting and preventing zoonotic emergence. Most knowledge about genetic mutations that could enable host shifts comes from laboratory experiments, where replication, virulence or shedding are measured under controlled conditions. While these studies are relevant in pinpointing candidate mutations, they do not necessarily capture the evolutionary dynamics that determine transmission success between hosts in field conditions. The capacity of a pathogen to expand is also scale-dependent: in lab conditions, it often relates to replication rates or competitive advantage (and commonly refered to as viral fitness), whereas at the population level, it is best defined by the virus’s ability to transmit between hosts^2,3. Increased replication in cell culture, for example, does not always translate into higher transmission between hosts in real-world settings. Recently, phylodynamic tools have been developed to quantify the transmission potential of viral lineages directly from surveillance data^4,5. By analyzing the branching patterns of time-scaled phylogenies, these methods estimate transmission potential, with more fit lineages producing more frequent branching and more sampled descendants. When combined with metadata, they can also disentangle the contributions of genetic and environmental factors to transmission potential, while accounting for confounders such as lineage structure and spatial heterogeneity.

Research objectives

This project aims to study the genetic and non-genetic determinants of cross-species transmission of HPAI viruses using large-scale genomic and epidemiological datasets. The key questions are: Which viral mutations are associated with higher transmission between host species? How much of the observed variations in transmission can be explained by viral mutations compared with host, environmental or management factors (host species, production type, putative implementation of vaccination, or geographic context)? The postdoctoral researcher will first compile a set of candidate mutations identified in experimental studies^6,7. Using phylodynamic methods^4,5, the postdoctoral researcher will infer lineage-specific fitness from dated phylogenies and examine whether lineages carrying particular mutations show consistently higher transmission potential within and between host species. The postdoctoral researcher will work on several case studies in which HPAI H5 clade 2.3.4.4b has circulated across different host species, while keeping the approach flexible to explore additional global datasets if sufficient quality data exist. This project will identify mutations that may facilitate cross-species transmission, and quantify the relative contribution of genetic mutations versus host and environmental factors. Results will help inform surveillance strategies and risk assessments for HPAI outbreaks.

Supervisors

The postdoc will be supervised by Claire Guinat (INRAE) and Mariette Ducatez (INRAE) who have a strong background on avian influenza viruses evolution and transmission. The position includes close collaboration with ETH Zurich (Computational Evolution group, Tanja Stadler) and North Carolina State University (Phylodynamics group, David Rasmussen), with potential short visits planned.

Environment and research group

The postdoctoral researcher will be affiliated to the mixed research unit Host-Pathogens Interactions (IHAP unit, epidesa group) at INRAE-ENVT located in Toulouse, France. The unit combines expertise in virology, epidemiology, phylodynamics and modelling for decision-making in animal health. The research project is part of the ZOOFLU project (ANR-23-PEPZ-0005 ZOOFLU, consortium INRAE, ANSES, CNRS-INSERM) funded by PEPR PREZODE and MIE, and focuses on the emergence mechanisms of zoonotic avian influenza viruses at the wildlife-domestic-human interface. It will offer excellent opportunities to advance career through participation at international conferences, collaboration with leading research groups in avian influenza surveillance, transmission and evolution, opportunities to co-supervise students and access to high-performance computing cluster.

Research location

The postdoctoral researcher will located on the National Veterinary School of Toulouse, in Toulouse, France. 

Key references

1.         Bellido-Martín, B. et al. Evolution, spread and impact of highly pathogenic H5 avian influenza A viruses. Nat. Rev. Microbiol. 1–16 (2025).

2.         Handel, A. & Rohani, P. Crossing the scale from within-host infection dynamics to between-host transmission fitness: a discussion of current assumptions and knowledge. Philos. Trans. R. Soc. B Biol. Sci. 370, 20140302 (2015).

3.         Xue, K. S. & Bloom, J. D. Linking influenza virus evolution within and between human hosts. Virus Evol. 6, veaa010 (2020).

4.         Rasmussen, D. A. & Stadler, T. Coupling adaptive molecular evolution to phylodynamics using fitness-dependent birth-death models. Elife 8, e45562 (2019).

5.         Kepler, L., Hamins-Puertolas, M. & Rasmussen, D. A. Decomposing the sources of SARS-CoV-2 fitness variation in the United States. Virus Evol. 7, veab073 (2021).

6.         European Food Safety Authority (EFSA) et al. Drivers for a pandemic due to avian influenza and options for One Health mitigation measures. EFSA J. 22, e8735 (2024).

7.         Suttie, A. et al. Inventory of molecular markers affecting biological characteristics of avian influenza A viruses. Virus Genes 55, 739–768 (2019).

Training and skills

Academic qualifications and experience

Applicants should hold a PhD in molecular epidemiology, evolutionary biology, or a related field, with strong skills in bioinformatics. Prior experience with phylodynamic analyses and proficiency in programming are required (R, BEAST2, bash). The ability to work independently and to contribute analytical approaches is expected throughout the project. An interest in infectious diseases and animal health is desirable. Proficiency in written and spoken English is essential, including the ability to present research at international conferences. Proficiency in French is not necessarily required. 

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

Please submit your CV, two reference letters and 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 to Claire Guinat (claire.guinat@envt.fr) by Feb 28^th 2026. 

Online interviews of shortlisted candidates will be held in March 2026.