PhD project: Leveraging pathogen genomics and phylodynamics to track highly pathogenic avian influenza viruses in wild birds

Highly pathogenic avian influenza (HPAI) is a transboundary disease with zoonotic potential that poses significant threats to animal health, human health, and global economy. The HPAI clade 2.3.4.4b H5N1 has affected more than 70 countries across Africa, the Americas, and Eurasia, resulting in the death of over half a billion poultry and potentially millions of wild birds across a diverse range of species. These outbreaks are of substantial conservation concern for wild birds, with some facing dramatic population declines. France has been one of the most affected European countries, with devastating outbreaks in poultry farms and wild bird populations. It is not clear what role wild bird’s species play in the maintenance and transmission of HPAI viruses. It is also unclear whether certain wild bird species transmit the virus more than others or if certain mutations are more specific to certain hosts. Additionally, the environmental and landscape factors that may influence the spread of the virus in wild birds are not fully understood. By obtaining genome data from detected wild bird cases, and incorporating genomic and epidemiological data into phylodynamic models, this project will provide novel and powerful means to decipher the transmission dynamics of HPAI viruses in wild birds, and at the domestic-wild bird interface. The findings from this research will inform surveillance strategies in wild bird populations, as well as the prevention and control of HPAI at the domestic-wild bird interface. Findings will ultimately contribute to protecting animal and human health.

This project aims to use pathogen genomics and phylodynamics to investigate transmission and evolution patterns of HPAI viruses in wild birds, with the following specific objectives:

• Quantify the transmission dynamics of the virus among different species of infected wild birds and at the domestic-wild bird interface
• Assess differences in evolution patterns among different species of infected wild birds
• Evaluate the impact of environmental and landscape factors on the spatial spread of virus in infected wild birds at the domestic-wild bird interface

Supervisors
Dr Guillaume Le Loc’h (ENVT, Toulouse, France)’s primary research interest is wildlife eco-pathology, with a particular focus on avian influenza. He has extensive experience in studying the interactions between wild birds and domestic poultry and how these interactions can facilitate the spread of avian influenza.
Dr Claire Guinat (INRAE, Toulouse, France) is a spatial and molecular epidemiologist with a particular interest in the transmission dynamics of animal infectious diseases. She has a strong experience in using quantitative and phylodynamic approaches to analyze pathogen genome data and to provide insights that can guide disease control efforts.

The PhD candidate will have the opportunity to work in a multidisciplinary supervisory team and will be based at the National Veterinary School of Toulouse (ENVT, Toulouse, France), providing access to a collaborative research environment. The student will greatly benefit from expertise, networks and opportunities available through the epidesa group, an international team of researchers involved in epidemiology and decision-making in animal health. Throughout the project, the student will develop core skills in epidemiology, ecology, phylodynamics and gain familiarity with virus genomics and animal infectious diseases.

The PhD candidate will work in close partnership with the national reference laboratory for avian influenza virus (ANSES PPN, France) and the French Biodiversity Agency (OFB, France) what will allow the candidate to access samples and associated surveillance data from infected poultry and wild birds in France. In addition, the PhD candidate will have the opportunity to interact with researchers at ETH Zurich (Computational Evolution group, cEvo, Switzerland) and Université Libre de Bruxelles (Spatial Epidemiology Lab, SpELL, ULB, Belgium) who are core groups in the development of phylodynamic and phylogeography approaches, allowing the candidate to benefit from the expertise of these established research groups.

Eligibility
Open to international applicants.

Academic qualifications and experience
Candidates should hold a postgraduate Master’s degree in computational biology, ecology, epidemiology, or a related field. Experience working with sequence data and/or mathematical modelling would be an asset. An enthusiasm for infectious diseases, animal health and interdisciplinary work is desirable.

Skills/Attributes
The successful candidate should demonstrate a willingness and ability to learn new computational skills, and should have an interest in wildlife ecology and epidemiological mechanisms of disease transmission. Additionally, good English writing skills and proficiency in computer-based work are required, as well as the willingness to present research work at international conferences. Proficiency in French is not necessarily required.

For further information, please contact Dr Claire Guinat (claire.guinat@envt.fr).
Key references

1. Chakraborty D, Guinat C, Muller NF, Briand FX, Andraud M, Scoizec A, et al. Phylodynamic analysis of the highly pathogenic avian influenza H5N8 epidemic in France, 2016-2017. Transbound Emerg Dis. 2022 Sep;69(5):E1574–83.
2. Guinat C, Valenzuela Agüí C, Vaughan TG, Scire J, Pohlmann A, Staubach C, et al. Disentangling the role of poultry farms and wild birds in the spread of highly pathogenic avian influenza virus in Europe. Virus Evol. 2022;8(2):veac073.
3. Lambert S, Durand B, Andraud M, Delacourt R, Scoizec A, Le Bouquin S, et al. Two major epidemics of highly pathogenic avian influenza virus H5N8 and H5N1 in domestic poultry in France, 2020–2022. Transbound Emerg Dis. 2022;
4. Guinat C, Vergne T, Kocher A, Chakraborty D, Paul MC, Ducatez M, et al. What can phylodynamics bring to animal health research? Trends Ecol Evol. 2021;36(9):837–47.
5. Gall-Ladevèze L, Guinat C, Fievet P, Vollot B, Guérin JL, Cappelle J, et al. Quantification and characterisation of commensal wild birds and their interactions with domestic ducks on a free-range farm in southwest France. Sci Rep. 2022;12(1):1–13.
6. Hirschinger J, Vergne T, Corre T, Hingrat Y, Guerin JL, Le Loc’h G. Exposure assessment for avian influenza and Newcastle disease viruses from peridomestic wild birds in a conservation breeding site in the United Arab Emirates. Transbound Emerg Dis. 2022;69(4):2361–72.