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

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.

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 (

PhD position
Closing date
May 20th, 2024
Posted on
May 2nd, 2024 10:42
Last updated
May 2nd, 2024 10:42