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Postdoctoral research opportunity: Genetic and non-genetic determinants of cross-species transmission of

Référence : 2025-2136187

  • Fonction publique : Fonction publique de l'État
  • Employeur : Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE)
    Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE)
  • Localisation : 23 chemin des capelle 31076 toulouse
Domaine : Recherche
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Date limite de candidature : 31/03/2026

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  • Nature de l’emploi Emploi ouvert uniquement aux contractuels
  • Nature du contrat Non renseigné
  • Expérience souhaitée Non renseigné
  • Rémunération Fourchette indicative pour les contractuels Between 3,000 and 3,500€ gross € brut/an Fourchette indicative pour les fonctionnaires Non renseignée
  • Catégorie Catégorie A (cadre)
  • Management Non renseigné
  • Télétravail possible Non renseigné

Vos missions en quelques mots

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. 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. 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.

Profil recherché

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.

Niveau d'études minimum requis

  • Niveau Niveau 8 Doctorat/diplômes équivalents

Éléments de candidature

Documents à transmettre

Pour postuler à cette offre, l'envoi du CV et d'une lettre de motivation est obligatoire

Personnes à contacter

claire.guinat@envt.fr

Qui sommes-nous ?

NOTRE AMBITION : AGIR POUR LA VIE, L’HUMAIN, LA TERRE

Premier organisme de recherche spécialisé au monde en agriculture, alimentation et environnement, INRAE est né le 1er janvier 2020 de de la fusion entre l’INRA et IRSTEA. Nous sommes une communauté de travail de 12 000 personnes, avec plus de 200 unités de recherche et une quarantaine d’unités expérimentales implantées dans 18 centres sur toute la France.

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À propos de l'offre

  • 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).

  • Vacant à partir du 01/04/2026

  • Chercheuse / Chercheur

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