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

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.

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. Using phylodynamic methods, 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.

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.

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 ) by Feb 28th 2026. Online interviews of shortlisted candidates will be held in March 2026.

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

---