PhD position OT-21922

PhD project: Integrated surveillance strategies of highly pathogenic avian influenza viruses in complex ecosystems


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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

Highly pathogenic avian influenza (HPAI) viruses are rapidly crossing geographical boundaries, threatening poultry, wildlife and potentially evolving into global pandemics1,2. In South-East Asia, particularly in Cambodia, the ecosystem of live bird markets (LBMs) plays a crucial role in the emergence and spread of novel avian influenza viruses (AIV), increasing the risk of cross-species transmission and amplification within both domestic poultry and wild bird populations. Surveillance studies in Cambodian LBMs have revealed alarming high AIV detection rates in poultry3, often coupled with co-infections with different strains4 and sporadic human cases5. Effective surveillance strategies are imperative to promptly detect and mitigate the spread of these viruses in poultry and prevent human infections. This PhD project aims to generate crucial knowledge to design novel and powerful surveillance strategies to complement existing surveillance systems in the country, contributing to protecting animal and human health. Employing a multidisciplinary approach encompassing field work (interviews of traders about trading and biosecurity practices, bird and environment sampling), lab work (samples testing) and epidemiological analyses (spatial risk modelling, risk factor analysis, latent class modelling), this project aims to address the following specific objectives:

- Investigate anthropogenic, ecological and environmental factors contributing to HPAI infection and delineate high-risk areas for targeted surveillance and control
- Assess biosecurity and trading factors contributing to HPAI infection of poultry within LBMs and identify high-risk LBMs for focused surveillance and control
- Evaluate the effectiveness of sampling strategies in LBMs and determine the most optimized to enhance detection of HPAI viruses

This PhD project is part of the ERC Starting Grant project (No. 101116387) TrackFLU and will be pivotal for further studies in phylodynamics, aiming to understand the emergence, maintenance and transmission factors of HPAI viruses in LBM networks. Joining the ERC team offers a unique opportunity for the PhD student to be part of an innovative and dynamic research environment, collaborating closely with two postdoctoral researchers. The student will receive comprehensive training combining field and lab work, data analysis, setting them up for a successful career in infectious disease research. The project will involve interdisciplinary collaboration with INRAE and Institut Pasteur du Cambodge (IPC), as well as key local stakeholders, including National Animal Health and Production Research Institute (NAPHRI), Wildlife Conservation Society (WCS).


Dr Claire Guinat (INRAE, Toulouse, France) primary research focuses on the drivers shaping the transmission dynamics of animal infectious diseases, including avian influenza. She has a strong background in quantitative and phylodynamic approaches.

Dr Mathilde Paul (ENVT, Toulouse, France) focuses on understanding farmers’ behavior and anthropogenic factors influencing the spread of animal infectious diseases, particularly avian influenza. She has extensive experience in epidemiological tools and spatial statistics.

Dr Erik Karlsson (IPC, Phnom Penh, Cambodia) specializes in virology, surveillance, and diagnostics, with a particular emphasis on respiratory viruses, especially avian influenza viruses. His expertise lies in the detection and surveillance of endemic and emerging virusesat high-risk interfaces, especially in LMICs .

Key references
1. Wille, M. & Barr, I. G. Resurgence of avian influenza virus. Science 376, 459–460 (2022).
2. Cohen, J. Worries about bird flu in US cattle intensify. Sci. N. Y. NY 384, 12–13 (2024).
3. Horm, S. V. et al. Intense circulation of A/H5N1 and other avian influenza viruses in Cambodian live-bird markets with serological evidence of sub-clinical human infections. Emerg. Microbes Infect. 5, 1–9 (2016).
4. Horwood, P. F. et al. Co-circulation of influenza A H5, H7, and H9 viruses and co-infected poultry in live bird markets, Cambodia. Emerg. Infect. Dis. 24, 352 (2018).
5. World Health Organization. Avian Influenza A (H5N1)–Cambodia. Dis. Outbreak News Httpswww Who Intemergenciesdisease-Outbreak-Newsitem2023-DON445 Internet 26 Febr. 2023 (2023).

Research location
The PhD candidate will be affiliated with the epidesa group, a dynamic international team of
researchers involved in epidemiology and decision-making in animal health, with the Host-
Pathogens Interactions (IHAP) mixed research unit INRAE-ENVT. In the first year of the PhD,
the student will spend 12 months at the Institut Pasteur du Cambodge (IPC) in Cambodia,
engaging in extensive fieldwork. For the remainder of the PhD, the candidate will be mainly
based at the INRAE-ENVT campus (Toulouse, France) to focus on data analysis, with
occasional short missions to Cambodia for research dissemination purposes.

Training and skills

Master's degree/Engineering degree

Academic qualifications and experience
Candidates should hold a postgraduate Master’s degree in epidemiology, ecology, or a related
field. Prior experience with epidemiological data and/or statistical modelling would be
advantageous. An enthusiasm for field and lab work related to infectious diseases is desirable.
Mobility is required, as the project involves spending time in France and Cambodia. Proficiency
in English writing and willingness to present research work at international conferences are
essential. Proficiency in French is not necessarily required.

Gained skills
The candidate will have a unique opportunity to acquire practical experience in field and lab
work, develop analytical skills, and gain proficiency in epidemiology, particularly in the context
of animal infectious diseases. Through interdisciplinary collaboration with IPC and INRAE and
participation in the ERC Starting Grant project, the student will benefit from a dynamic scientific
environment for their career growth.
For further information, please contact Dr Claire Guinat (

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: trainingcareer 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

I send my CV and my motivation letter

Offer reference

  • Contract: PhD position
  • Duration: 36 months
  • Beginning: 02/09/2024
  • Remuneration: 2,100€ gross monthly
  • Reference: OT-21922
  • Deadline: 20/05/2024
Centre Occitanie-Toulouse

L'UMR INRAE-ENVT 1225 Interactions Hôtes-Agents Pathogènes (IHAP) 31076 TOULOUSE


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