PhD project title: Tracking minor variants in avian influenza genome RNA populations to investi[...]

French National Research Institute for Agriculture, Food and Environment (INRAE); France; Sur place; EUR 22 000 - 26 000; Plein temps

Résumé du poste

A leading research institute in agriculture is seeking a PhD student to study the evolution of avian influenza virus in vaccinated poultry populations. The position requires a Master Degree in virology or molecular biology, along with relevant skills in PCR, cloning, and computational biology. This role offers a unique opportunity to integrate interdisciplinary approaches in a project funded by Horizon Europe.

Qualifications

• Must not have a doctoral degree at the time of recruitment.
• Must comply with the mobility rule regarding previous residence in France.

Responsabilités

• Contribute to understanding evolution of avian influenza virus.
• Develop new sequencing methods for vaccine research.
• Investigate viral genomic RNA populations under vaccination.

Connaissances

Virology

Molecular biology

Computational biology

Good English writing skills

PCR and cloning techniques

Formation

Master Degree in virology or molecular biology

Description du poste

French National Research Institute for Agriculture, Food and Environment (INRAE)

Organisation/Company French National Research Institute for Agriculture, Food and Environment (INRAE) Department IHAP 1225 INRAE ENVT Research Field Biological sciences Medical sciences Researcher Profile First Stage Researcher (R1) Positions PhD Positions Country France Application Deadline 15 Dec 2025 - 20:00 (Europe/Paris) Type of Contract Temporary Job Status Full-time Offer Starting Date 1 Jan 2026 Is the job funded through the EU Research Framework Programme? Horizon Europe (other) Is the Job related to staff position within a Research Infrastructure? No

Offer Description

The present PhD student position and associated research project is part of the 13 PhD projects of the VIVACE Doctoral Network, funded by the Marie Sklodowska‑Curie action of the Horizon Europe programme.

Context on the VIVACE doctoral network

While outbreaks of highly pathogenic avian influenza viruses (HPAIV) in Europe used to be rare and geographically contained, the situation has dramatically changed in the last few years with thousands of outbreaks reported in domestic poultry and wild birds. Vaccination of poultry against avian influenza, which used to be prohibited in the European Union (EU) due to trade restrictions, is now being given full consideration, as it is becoming clear that traditional prevention and control approaches alone will not curb the accelerating pace of occurrence of devastating HPAIV epidemics. However, vaccinating poultry does not come without important challenges. The project VIVACE, gathering 15 leading universities or research institutes and 5 private companies, puts together an ambitious doctoral network to integrate poultry vaccination approaches into efficient management strategies for HPAIV. This interdisciplinary project offers funding for 13 PhD scholarships along the continuum from virology and immunology to spatial and molecular epidemiology, computer sciences, as well as social and behavioural sciences. Irrespective of their background, all doctoral candidates from VIVACE will benefit from a unique international training in these fields, as well as state‑of‑the‑art soft skill development. In doing so, the VIVACE consortium ambitions to train the next generation of scientists with integrated understanding and expertise in avian influenza management. More information about the project: https://vivace.hub.inrae.fr/avian-influenza-vaccination-context

Description and objectives of the PhD project

The overall objective of this project is to contribute to the understanding of evolution of avian influenza virus in poultry populations where vaccination is applied. Immune escape variants are more likely to arise when vaccination is suboptimal and DC5 will use models of suboptimal vaccination to develop and standardize robust methods to quickly identify minor variants before they become predominant immune escape variants. Specific objectives are (i) to overcome methodological challenges by developing new sequencing methods (ii) to develop standards to facilitate sensitive and reproducible variants quantification, (iii) to investigate the evolution of viral genomic RNA populations under suboptimal vaccination (modelled by imperfect vaccine/challenge homology and imperfect vaccine administration in animal or in vitro experiments), (iv) to investigate the evolution of viral genomic RNA populations in vaccinated vs. unvaccinated poultry in the field.

Supervision

This PhD project will be co‑supervised by Pr Romain Volmer (INRAE‑ENVT, Toulouse, France), Dr Steven van Borm (Sciensano, Brussels, Belgium), and Dr Isabella Monne (IZSVe, Padova, Italy). Romain Volmer is veterinary virologist working in the “Host pathogen interaction” research unit at INRAE‑ENVT in Toulouse, France. His research aims at better understanding the mechanisms regulating avian influenza virus evolution. Steven Van Borm is a veterinary virologist working in the “Avian Virology and Immunology” unit at Sciensano, Brussels, Belgium. His research focuses on the use of sequencing and other molecular biological methods to improve the diagnosis and characterization of priority animal viral diseases including avian influenza. Isabella Monne is a veterinary virologist at IZSVe, Padova, Italy. Her research focuses on the use of sequencing technologies and bioinformatics tools to study the evolution of RNA viruses, including influenza A viruses.

Hosting arrangements (including the secondment plans)

The PhD project will be primarily based at the INRAE‑ENVT, Toulouse. The PhD student will also perform research stays in the research team of Dr Steven van Borm (Sciensano, Brussels, Belgium), and Dr Isabella Monne (IZSVe, Padova, Italy).

Where to apply

E‑mail [e-mail]

Requirements

Research Field Agricultural sciences Education Level Master Degree or equivalent

Research Field Biological sciences Education Level Master Degree or equivalent

Skills/Qualifications

Academic qualifications and skills required

At the start sate, the candidate should hold a master degree in virology, molecular biology, ideally with skills in computational biology or at least a keen interest to develop skills in computational biology through dedicated training. The candidate should have a strong interest in veterinary/medical infectious diseases. Additionally, good English writing skills and proficiency in classical molecular biology laboratory techniques such as PCR and cloning.

To be eligible, the candidate:

• Must not have a doctoral degree at the time of recruitment
• Should comply with the mobility rule: must not have resided or carried out their main activity in France for more than 12 months in the 36 months immediately before their recruitment date. Short stays such as holidays and/or compulsory national service are not taken into account.

Languages ENGLISH Level Excellent

Additional Information

Selection process

Please send your applications as early as possible and no later than 15 December 2025 to [e-mail]

Shortlisted candidates will be contacted for online or onsite interviews.

Offer starting date: ideally 1 January 2026

Your application should include:

• your CV, including the contact details of two references
• 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