PhD position OT-23142
PhD project title: Ecological niche modelling and phylodynamic assessments of avian influenza risk and dispersal in the context of vaccination implementations
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://www.inrae.fr/en/news/management-avian-influenzavaccination-context
Description and objectives of the PhD project
The overall objective of the PhD project will be to inform vaccination strategies by analysing the epidemiological and dispersal dynamics of circulating AIV lineages in countries associated with different vaccination settings and unravelling the environmental factors impacting their dispersal. We will focus on three distinct study areas: Morocco, Egypt where poultry vaccination against H5N8, H5N1 and H9N2 has been ongoing since 2006, and France which only recently initiated H5N8 vaccination in ducks in October 2023. These diverse settings provide a unique opportunity to assess how vaccination strategies might influence AIV evolution and spread. The specific aims of the PhD project will consist in (i) training ecological niche models predicting the risk of local circulation given local environmental conditions, (ii) estimating key epidemiological parameters using multi-type birth-death phylodynamic models, (iii) performing spatially explicit phylogeographic reconstructions of the dispersal history of AIV lineages using a relaxed random walk diffusion model, and (iv) investigating the impact of environmental and anthropogenic factors on the dispersal of AIV lineages using landscape phylogeographic methods.
Supervision
This PhD project will be co-supervised by Dr Simon Dellicour (University of Brussels, ULB, Belgium) and Dr Claire Guinat (INRAE, Toulouse, France). Dr Simon Dellicour is a molecular epidemiologist with a recognised expertise in viral and landscape phylogeography, a field where he and his team have performed and applied several methodological developments over the last eight years (https://spell.ulb.be/subject/landscape-phylogeography/). Simon Dellicour is currently heading the Spatial Epidemiology Lab (SpELL) of the University of Brussels (ULB). The research activities of the SpELL (https://spell.ulb.be/) resolve around the broad field of spatial epidemiology and aim to study the effect of spatial factors on the emergence, spread, persistence and evolution of diseases and invasive species. In particular, the SpELL has a recognised expertise in risk mapping through ecological niche modelling. Dr Claire Guinat primary research focuses on the drivers shaping the transmission dynamics of animal infectious diseases, with a particular focus on avian influenza. She has a strong experience in using quantitative and phylodynamic approaches to analyse epidemiological and pathogen genetic data to provide insights that can guide disease control efforts.
Five key publications on the topic
- Guinat C, Valenzuela Agüí C, Vaughan TG, Scire J, Pohlmann A, Staubach C, King J, Świętoń E, Dán Á, Černíková L, Ducatez MF, Stadler T (2022). Disentangling the role of poultry farms and wild birds in the spread of highly pathogenic avian influenza virus in Europe. Virus Evolution 8: veac073
- Klitting R, Kafetzopoulou LE, Thiery W, Dudas G, Gryseels S, Kotamarthi A, Vrancken B, Gangavarapu K, Momoh M, Demby Sandi J, Goba A, Alhasan F, Grant DS, Garry RF, Smither AR, Zeller M, Pauthner MG, McGraw M, Hughes LD, Duraffour S, Günther S, Suchard MA, Lemey P, Andersen KG, Dellicour S (2022). Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades. Nature Communications 13: 5596
- Dellicour S, Lequime S, Vrancken B, Gill MS, Bastide P, Gangavarapu K, Matteson N, Tan Y, du Plessis L, Fisher AA, Nelson MI, Gilbert M, Suchard MS, Andersen KG, Grubaugh ND, Pybus OG, Lemey P (2020). Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework. Nature Communications 11: 5620
- Dellicour S, Lemey P, Artois J, Lam TT, Fusaro A, Monne I, Cattoli G, Kuznetsov D,Xenarios I, Dauphin G, Kalpravidh W, Von Dobschuetz D, Claes F, Newman SH, Suchard MA, Baele G, Gilbert M (2020). Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference – application to H5N1 spread in the Mekong region. Bioinformatics 36: 2098-2104
- Dellicour S, Baele G, Dudas G, Faria NR, Pybus OG, Suchard M, Rambaut A, Lemey P (2018). Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak. Nature Communications 9: 2222
The PhD project will be based at the University of Brussels (ULB, Belgium, “La Plaine” campus: https://spell.ulb.be/page/access/), in the research team of Dr Simon Dellicour at the Spatial Epidemiology Lab (SpELL, https://spell.ulb.be/). The PhD student will also perform several long research stays in the research team of Dr Claire Guinat at the Epidemiology lab (Epidesa, https://epidesa.weebly.com) located on the INRAE-ENVT campus, Toulouse, France.
Training and skills
The candidate should hold a master degree in (bio)engineering, computational biology, epidemiology, or a scientific field such as biology/veterinary/medical sciences, ideally with analytical skills in modelling and spatial analyses, should have a strong interest in epidemiology. Additionally, good English writing skills and proficiency in computer-based work are required, as well as the willingness to present research work at international conferences. Knowledge and use of the programming language R is required. 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 send your application before January 15 (2025) to Simon Dellicour (simon.dellicour@ulb.be) and Claire Guinat (claire.guinat@envt.fr). Your application should include: a twopage CV demonstrating your relevant experience, a maximum of two reference letters, as well as a 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 or onsite interviews of shortlisted candidates will be held between 20 and 24/01/2025.
For further information, please contact Simon Dellicour (simon.dellicour@ulb.be) and Claire Guinat (claire.guinat@envt.fr).
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)