PhD position OT-25769
PhD project title: Tracking minor variants in avian influenza genome RNA populations to investigate virus evolution under suboptimal vaccination
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
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, (ii) 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), (iii) 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).
Training and skills
At the start sate of the PhD, which is negotiable, 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.
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
The application deadline is 6 June 2025.
Selected candidates will be interviewed either on site in Toulouse, France or online in June 2025
Please send your application before 6 June 2025 to viroihap@gmail.com
Your application should include:
- your CV
- two reference letters
- 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
Online interviews of shortlisted candidates will be held in June 2025.
For further information, please send questions to viroihap@gmail.com
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)