Postdoctoral research project: Drivers of avian influenza viruses evolution and transmission in live bird market networks

Context 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 poultry production and trade plays a crucial role in the emergence and spread of novel avian influenza viruses, increasing the risk of cross-species transmission and amplification within both domestic poultry and wild bird populations. Surveillance studies in Cambodian live bird markets have revealed alarming high avian influenza virus 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 emergence and spread of viruses in poultry and prevent human infections.  Position summary We are seeking a highly motivated postdoctoral researcher to join our group (epidesa, epidemiology and decision-making in animal health, https://epidesa.inrae.envt.fr) at the Host-Pathogens Interactions (IHAP) research unit at INRAE. The postdoctoral researcher will investigate the drivers of avian influenza virus evolution in live bird market networks in Cambodia, using an original longitudinal dataset generated by the TrackFLU project (https://trackflu.inrae-envt.com). Over one year, TrackFLU has followed 20 poultry sites in Cambodia, including live bird markets, farms and slaughterhouses, with information on poultry production, trading and biosecurity practices, alongside sampling of poultry for avian influenza viruses. The resulting viral genomic data will provide an unprecedented opportunity to link virus evolution and transmission with the epidemiological and ecological context in which viruses circulate. The postdoctoral researcher will analyse the whole-genome sequences generated through the project using phylodynamic and computational analyses, together with the longitudinal practices data to identify factors that are associated with viral co-circulation and reassortments. This position offers an exciting opportunity to work at the intersection of pathogen genomics and infectious disease epidemiology, leading efforts to understand the emergence and spread of avian influenza viruses in live bird market networks in Cambodia.  Environment and research group This postdoctoral position is part of the TrackFLU project (No. 101116387) funded by the ERC Starting Grant. Joining the TrackFLU project offers excellent opportunities to advance your career through participation at (inter)national conferences, collaboration with Institut Pasteur du Cambodge, local stakeholders, including Animal Health and Production Research Institute (NAPHRI), and leading research group in phylodynamics (ETH Zürich, Institut Pasteur Paris), opportunities to co-supervise master and PhD students, access to sequencing laboratories at IPC and high-performance computing cluster at INRAE.  Supervisors 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 Arthur Kocher (INRAE, Toulouse, France) studies human and animal disease ecology and evolution using molecular approaches combined with Bayesian statistics and phylogenomics. 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).