Genomic sequence data of viruses can greatly improve our understanding of viral spread within and between populations. These data provide insights into transmission links between humans or animals, which are undetectable by epidemiological data. By integrating genetic, epidemiological and immunological data, we can study the processes shaping phylogenetic trees (Grenfell et al. 2004). This upcoming field, called phylodynamics, has proven useful in understanding outbreaks of, for instance, Covid-19. In PROVED, these models will enhance our knowledge of two viruses in swine.

Your job
Phylodynamic studies can aid control of infectious diseases in animals, which is crucial to improve animal health and welfare and human health in case of zoonoses. However, phylodynamic models are not yet frequently applied to viruses in animal populations (Guinat et al. 2021), even though animal populations are interesting to study in light of contact structures that are incomparable to human populations.

We have a unique genomic dataset of two viruses in swine. Swine Influenza A virus (SIV) and Porcine Reproductive and Respiratory Syndrome virus (PRRSv) are significant causes of respiratory disease in swine and have been circulating in swine herds for decades, even though vaccines are available for both pathogens. Control of these viruses is hampered by extensive genetic diversity and continuous evolution by mutations, reassortment and recombination. By tracking the evolution of SIV and PRRSv within individual pigs, farms, and regions, and connecting this to vaccination status and epidemiological parameters, this project will provide novel means to decipher the transmission dynamics of the viruses in swine populations. The results of this research will contribute to the development and application of phylodynamic models in animal populations and to the control of respiratory viruses in swine herds. The findings will ultimately contribute to protecting animal and human health.

As PhD candidate in this project, you will use existing genomic data of SIV and PRRSv, movement data of pigs, and farm characteristics and locations, to model transmission of the viruses across countries, between farms, and within farms. Moreover, you will gather information about current vaccination practices applied by farmers, and evaluate the impact of vaccination protocols and other management factors on the evolution and dynamics of the viruses in farms. You will work in close partnership with Wageningen Bioveterinary Research for access to genomic data and expertise in virology, and with Royal GD for surveillance data from affected swine farms. Throughout the project, you will develop core skills in epidemiology and phylodynamics, and gain familiarity with virus genomics and animal infectious diseases.

This PhD project may be the right fit for you if:

• you hold an MSc degree from an internationally recognised institution in computational biology, bioinformatics, epidemiology, ecology or a related field;
• you are willing to learn new computational skills, and are interested in mechanisms of viral spread and evolution and animal infectious diseases;
• you have proficiency in English speaking and writing. Proficiency in Dutch is not necessarily required.

Proficiency in computer-based work is required, as well as the willingness to present research at international conferences. Experience working with sequence data and/or mathematical modeling would be an asset.

We offer:

• a position for one year, with an extension to a total of four years upon a successful assessment in the first year, and with the specific intent that it results in a doctorate within this period;
• a working week of 36 to 40 hours and a gross monthly salary between €2,770 and €3,539 in the case of full-time employment (salary scale P under the Collective Labour Agreement for Dutch Universities (CAO NU));
• 8% holiday pay and 8.3% year-end bonus;
• a pension scheme, partially paid parental leave and flexible terms of employment based on the CAO NU.

In addition to the terms of employment laid down in the CAO NU, Utrecht University has a number of schemes and facilities of its own for employees. This includes schemes facilitating professional development, leave schemes and schemes for sports and cultural activities, as well as discounts on software and other IT products. We also offer access to additional employee benefits through our Terms of Employment Options Model. In this way, we encourage our employees to continue to invest in their growth. For more information, please visit Working at Utrecht University.

Universiteit Utrecht

A better future for everyone. This ambition motivates our scientists in executing their leading research and inspiring teaching. At Utrecht University, the various disciplines collaborate intensively towards major strategic themes. Our focus is on Dynamics of Youth, Institutions for Open Societies, Life Sciences and Pathways to Sustainability. Sharing science, shaping tomorrow.

At the Faculty of Veterinary Medicine we train the veterinarians and researchers of the future, provide care for animals and conduct leading and societal relevant research. That is what we are good at. We see that the health and welfare of animals, humans and the environment are interconnected. By sharing our knowledge and working together, we make positive impact, both nationally and internationally. Our 1,500 students and 950 staff members inspire and strengthen each other. Our engagement connects us. The drive to, from an integral perspective, make the world a better place.

You will become part of the epidemiology group in the Department of Population Health Sciences, led by prof. Arjan Stegeman. The epidemiology group is an international group of more than 20 employees with expertise in modeling infectious diseases, evidence-based veterinary medicine, surveillance, economics of animal health and field and experimental epidemiology. As a team, we prioritise collaboration, ongoing feedback, and both professional and personal development.