PhD project: Susceptibility of ruminants to avian influenza viruses

Back to jobs listing

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

Objectives of the PhD project

Highly pathogenic avian influenza (HPAI) is a transboundary disease with zoonotic potential that poses significant threats to animal health, human health, and the global economy. Since 2020, the world has experienced unprecedented HPAI H5N1 epidemics of a particular lineage belonging to clade 2.3.4.4b. This epidemic has been associated with a wide geographical spread (5 continents), an increase in number of mammal infections and early 2024 cases in dairy cows in the US, with already 70 associated human infections in the USA as of April 2025. This highlights the concerning possibility that the virus has successfully crossed the species barrier and transmits efficiently. While HPAIV H5N1 has not caused cattle infections outside the USA so far, a recent study has shown that the American genotype (B3.13) infecting American cattle is not the only clade 2.3.4.4b strain able to efficiently infect dairy cow utter. In parallel, a recent infection of sheep in the UK was reported with a European genotype (DI) of HPAIV H5N1, and a serology study highlighted that cattle is exposed to swine and Human influenza A viruses.

In the present PhD project, we will thus tackle the question of ruminants susceptibility to avian and seasonal influenza viruses infection using in vitro and ex vivo approaches and looking in respiratory and mammary gland cells and tissues. Both HPAIV H5N1 (European and American lineage viruses) and low pathogenic avian influenza viruses will be tested. Molecular determinants of viral tropism will also be studied and a relevant strain will be selected for full phenotypic characterization in vivo.

Supervisor

Dr. Mariette Ducatez (INRAE, Toulouse, France) is lead scientist at INRAE. Her research activities are conducted in the VIRéMIE group of INRAE/ENVT IHAP unit that she co-leads. She has a strong interest in influenza viruses (genera A and D) circulating in animal species and at the animal-human interface. She co-authored more than 130 peer-reviewed research articles and supervised multiple graduate students.

 

Key references

1. European Food Safety Authority, European Centre for Disease Prevention and Control, European Union Reference Laboratory for Avian Influenza, Alexakis L., Buczkowski H., Ducatez M., Fusaro A., Gonzales J.L., Kuiken T., Ståhl K., Staubach C., Svartström O., Terregino C., Willgert K., Melo M., Kohnle L., Avian influenza overview December 2024-March 2025. EFSA Journal. 2025, doi: 10.2903/j.efsa.2025.9352.
2. Sanogo I.N., Guinat C., Dellicour S., Diakité M.A., Niang M., Koita O.A., Camus C., Ducatez M., Genetic insights of H9N2 avian influenza viruses circulating in Mali and phylogeographic patterns in Northern and Western Africa. Virus Evolution. 2024, 10(1):veae011. doi: 10.1093/ve/veae011.
3. Gaudino M., Lion A., Sagné E., Nagamine B., Oliva J., Terrier O., Errazuriz-Cerda E., Scribe A., Sikht F.Z., Simon E., Foret-Lucas C., Gausserès B., Lion J., Moreno A., Dordet-Frisoni E., Baranowski E., Volmer R., Ducatez M.F.*, Meyer G.*, The activation of the RIG-I/MDA5 signalling pathway upon Influenza D virus infection impairs the pulmonary pro-inflammatory response triggered by Mycoplasma bovis superinfection. Journal of Virology. 2023; e0142322. doi: 10.1128/jvi.01423-22.
4. Xie R., Edwards K.M., Wille M., Wei X., Wong S.S., Zanin M., El-Shesheny R., Ducatez M., Poon L.L.M., Kayali G., Webby R.J., Dhanasekaran V., The episodic resurgence of highly pathogenic avian influenza H5 virus. Nature. 2023, 622(7984): 810-817. doi: 10.1038/s41586-023-06631-2.
5. Gaudino M., Chiapponi C., Moreno A., Zohari S., O'Donovan T., Ryan E., Quineless E., Sausy A., Oliva J., Salem E., Fusade-Boyer M., Meyer G., Hübschen J., Saegerman C., Ducatez M.F.*, Snoeck C.J.*, Evolutionary and temporal dynamics of emerging Influenza D virus in Europe (2009-2022). Virus Evolution. 2022; 8(2):veac081. doi: 10.1093/ve/veac081.
6. Sanogo I.N., Djegui F., Akpo Y., Gnanvi C., Dupré G., Rubrum A., Jeevan T., McKenzie P., Webby R.J., Ducatez M.F., Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Virus in Poultry, Benin, 2021. Emerging Infectious Diseases. 2022; 8(12):2534-2537. doi: 10.3201/eid2812.221020.
7. Fusade-Boyer M., Djegui F., Batawui K., Byuragaba D.K., Jones J.C., Wabwire-Mangeni F., Erima B., Atim G., Ukuli Q.A., Tugume T., Dogno K., Adjabli K., Nzuzi M., Adjin R., Jeevan T., Rubrum A., Go-Maro W., Kayali G., McKenzie P., Webby R.J., Ducatez M.F., Antigenic and molecular characterization of low pathogenic avian influenza A(H9N2) viruses in sub-Saharan Africa from 2017 through 2019. Emerging Microbes and Infections. 10(1):753-761. 2021. doi: 10.1080/22221751.2021.1908097.
8. Lion A., Secula A., Rançon C., Boulesteix O., Pinard A., Deslis A., Hägglund S., Salem E., Cassard H., Näslund K., Gaudino M., Moreno A., Brocchi E., Delverdier M., Zohari S., Baranowski E., Valarcher J.F., Ducatez M.F., Meyer G., Enhanced Pathogenesis Caused by Influenza D Virus and Mycoplasma bovis Coinfection in Calves: a Disease Severity Linked with Overexpression of IFN-γ as a Key Player of the Enhanced Innate Immune Response in Lungs, Microbiology Spectrum. 2021; 9(3):e0169021. doi: 10.1128/spectrum.01690-21.

Research location

The PhD candidate will conduct his/her research at the French National Research Institute for Agriculture, Food, and Environment (INRAE), within the Host-Pathogen Interaction Unit (IHAP) on the campus of the National Veterinary School of Toulouse (ENVT), France. 

Training and skills

Training and skills

The ideal PhD candidate should possess a Master’s degree or equivalent in Virology, Infectiology, Microbiology, Veterinary Medicine, Biology, or a related field, with a solid academic foundation in infectious diseases, molecular and cellular biology. Candidates should have prior research experience in laboratory or field studies, particularly in virology, microbiology, or animal health, and demonstrate proficiency in molecular diagnostic techniques such as RT-qPCR and pathogen detection. Familiarity with cellular biology techniques is essential, skills in bioinformatics would be advantageous. The candidate should exhibit strong scientific writing and communication skills, with fluency in English; knowledge of French would be a bonus but not mandatory at all. Strong organizational and time-management skills, the ability to work independently and collaboratively within multidisciplinary teams, and a willingness to work in biocontainment facilities are crucial. 

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

How to apply

Please send your application before 31 May 2025 to Dr. Mariette Ducatez (mariette.ducatez@envt.fr).

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 contact Dr. Mariette Ducatez (mariette.ducatez@envt.fr).