Optimizing poultry vaccination strategies against highly pathogenic avian influenza to support policy

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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

Background 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. Despite being an intensive field of research, many unknowns remain as we are still struggling to predict HPAIV incursion in poultry, avoid viral spread and limit the socio-economic impact entailed predominantly by control measures. 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 aims at putting together an ambitious doctoral network, composed of 13 PhD scholarships, to contribute to fully integrate poultry vaccination approaches into efficient management strategies for HPAIV. This will be done by unravelling the impact current and upcoming EU vaccination policies will have on avian influenza virus evolution, surveillance and control strategies and societal burden of HPAI. For this, VIVACE will use a combination of disciplines from life sciences, epidemiology, computer sciences and social and behavioural sciences. The consortium gathers 15 leading universities or research institutes and 5 private companies, securing both inter-sectoriality and wide geographic distribution with tailored epidemiological and vaccination contexts.

More info on the VIVACE doctoral network can be found here https://www.inrae.fr/en/news/management-avian-influenza-vaccination-context

Objectives of the PhD project

In this PhD project, we aim at developing data-driven model-based decision-support tools to identify efficient poultry vaccination strategies. Specific objectives are 1) to further develop existing between-farm transmission models of HPAI conceived at the host institutions by incorporating vaccination strategies taking into account (i) its impact on virus transmissibility and HPAI clinical manifestation (ii) its impact on surveillance effectiveness and (iii) its impact on biosecurity compliance, 2) to calibrate the transmission model using recent HPAI epidemics and preliminary results from vaccination challenges and (pre) clinical trials and 3) to identify optimised vaccination strategies that allow to minimise HPAI epidemiological impact while minimizing the number of vaccine doses. This project is expected to generate new knowledge on the impact poultry vaccination has on HPAI epidemic dynamics and evidence-based recommendations on HPAI prevention and management, including vaccination.

Supervisors

Dr Timothée Vergne (INRAE, Toulouse, France) is an Associate Professor of Veterinary Public Health at the National Veterinary School of Toulouse (ENVT). He leads the Epidesa group, a dynamic international team of researchers dedicated to the improvement of livestock and farmers well-being through the use of modern epidemiological techniques. His primary research interests include the understanding of detection and transmission processes of infectious diseases using statistical and mathematical modelling tools, in order to optimize the way infectious diseases are managed. He is one of the three co-coordinators of the VIVACE project.

Dr Jose Gonzales Rojas (Wageningen Research, Lelystad, The Netherlands) is a senior scientist at Wageningen Bioveterinary Research (WBVR). He leads the Epidemiology and Risk Assessment expertise group, an international team of researchers dedicated to improve animal and public health through high-level scientific research. WBVR is a FAO reference centre for veterinary epidemiology. Jose’s primary research focus lies in the prevention and control of infectious diseases through the understanding of the mechanism leading to onset of infection and transmission.

 

Host institutions

The PhD candidate will be hosted by the Epidesa group, within the mixed research unit Host-Pathogens Interactions (IHAP), located on the campus of the National Veterinary School of Toulouse, France. Over the course of the project, the doctoral candidate is expected to visit the co-host institution (WBVR, Lelystat, The Netherlands) to complete his/her training on infectious disease modelling, to calibrate the models and to develop simulation protocols for the vaccination strategy optimization. 

If you want to know more about what it means to study epidemiology in Epidesa, have a look at this short video.

Training and skills

The suitable candidate would ideally be a biologist (e.g. ecologist, veterinarian, animal scientist or agronomist) with a master of science in bio-statistics, applied mathematics or epidemiology with proven quantitative analytical skills. Candidates with a background in applied mathematics and an interest for biology are also warmly encouraged to apply. A strong interest in programming (preferably in R) would be highly advantageous. An enthusiasm for infectious diseases, animal health and interdisciplinary work is desirable. Mobility is required, as the project involves spending time in France and The Netherlands. Proficiency in English writing and willingness to present research work at international conferences are essential. Proficiency in French is not necessarily required. As VIVACE is a doctoral network (Marie Sklodowska-Curie Action), eligible candidates must not have resided or carried out their main activity (work, studies, etc.) in France for more than twelve months in the three years immediately before the beginning of the PhD project.

Key references

1. Andronico, A., Courcoul, A., Bronner, A., Scoizec, A., Lebouquin-Leneveu, S., Guinat, C., Paul, M.C., Durand, B., Cauchemez, S., 2019. Highly pathogenic avian influenza H5N8 in south-west France 2016-2017: A modeling study of control strategies. Epidemics 28, 100340. https://doi.org/10.1016/j.epidem.2019.03.006
2. Bauzile, B., Durand, B., Lambert, S., Rautureau, S., Fourtune, L., Guinat, C., Andronico, A., Cauchemez, S., Paul, M.C., Vergne, T., 2023. Impact of palmiped farm density on the resilience of the poultry sector to highly pathogenic avian influenza H5N8 in France. Vet. Res. 54, 56. https://doi.org/10.1186/s13567-023-01183-9
3. EFSA Panel on Animal Health and Animal Welfare (AHAW), European Union Reference Laboratory for Avian Influenza, Nielsen, S.S., Alvarez, J., Bicout, D.J., Calistri, P., Canali, E., Drewe, J.A., Garin-Bastuji, B., Gonzales Rojas, J.L., Gortázar, C., Herskin, M., Michel, V., Miranda Chueca, M.Á., Padalino, B., Roberts, H.C., Spoolder, H., Stahl, K., Velarde, A., Winckler, C., Bastino, E., Bortolami, A., Guinat, C., Harder, T., Stegeman, A., Terregino, C., Aznar Asensio, I., Mur, L., Broglia, A., Baldinelli, F., Viltrop, A., 2023. Vaccination of poultry against highly pathogenic avian influenza – part 1. Available vaccines and vaccination strategies. EFSA J. 21, e08271. https://doi.org/10.2903/j.efsa.2023.8271
4. EFSA Panel on Animal Health and Animal Welfare (AHAW), Influenza, E.U.R.L. for A., Nielsen, S.S., Alvarez, J., Bicout, D.J., Calistri, P., Canali, E., Drewe, J.A., Garin-Bastuji, B., Gortázar, C., Herskin, M.S., Michel, V., Miranda Chueca, M.Á., Padalino, B., Roberts, H.C., Spoolder, H., Stahl, K., Velarde, A., Viltrop, A., Winckler, C., Bortolami, A., Guinat, C., Harder, T., Stegeman, A., Terregino, C., Lanfranchi, B., Preite, L., Aznar, I., Broglia, A., Baldinelli, F., Gonzales Rojas, J.L., 2024. Vaccination of poultry against highly pathogenic avian influenza – Part 2. Surveillance and mitigation measures. EFSA J. 22, e8755. https://doi.org/10.2903/j.efsa.2024.8755
5. Gonzales, J.L., Elbers, A.R.W., van der Goot, J.A., Bontje, D., Koch, G., de Wit, J.J., Stegeman, J.A., 2012. Using egg production data to quantify within-flock transmission of low pathogenic avian influenza virus in commercial layer chickens. Prev. Vet. Med. 107, 253–259. https://doi.org/10.1016/j.prevetmed.2012.06.010
6. Vergne, T., Gubbins, S., Guinat, C., Bauzile, B., Delpont, M., Chakraborty, D., Gruson, H., Roche, B., Andraud, M., Paul, M., Guérin, J.-L., 2021. Inferring within-flock transmission dynamics of highly pathogenic avian influenza H5N8 virus in France, 2020. Transbound. Emerg. Dis. 68, 3151–3155. https://doi.org/10.1111/tbed.14202

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 December 2024 to Dr Timothée Vergne (timothee.vergne@envt.fr). Your application should include:

• your CV in two pages
• 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 January 2024.

For further information, please contact Dr Timothée Vergne (timothee.vergne@envt.fr).