Flavivirus infections in poultry : from transmission and host adaption to vaccination strategies

Mosquito-borne flaviviruses (MBFVs) include several important pathogens such as Yellow fever virus, Dengue virus, West Nile virus, Japanese encephalitis virus, and Zika virus. Many of these viruses use birds as natural reservoirs. Poultry, characterized by large population sizes, high-density farming, and close contact with humans, may therefore play an important role in the ecology and emergence of flaviviruses. In 2010, an outbreak of Tembusu virus (TMUV) occurred in duck farms in China, causing severe economic losses and highlighting the importance of monitoring flavivirus infections in poultry. However, the mechanisms underlying host range, transmission, and adaptation of flaviviruses in poultry remain poorly understood. In this thesis, we first investigated the pathogenicity and transmission routes of a cluster 3 TMUV strain (SD) in ducks and chickens. TMUV SD infected both species, but virus shedding from the oropharyngeal and cloacal routes and direct contact transmission were observed only in ducks. In contrast, no virus shedding or direct transmission occurred in chickens. However, Culex pipiens mosquitoes were able to acquire the virus from infected chickens and subsequently transmit it to naïve chickens, indicating that mosquito vectors remain essential for TMUV transmission in chickens. To explore the molecular basis of host expansion, we compared an early cluster 2 TMUV strain (FX2010) with the recent cluster 3 strain (SD). While SD replicated systemically in chickens, FX2010 couldn’t infect chicken. Using chimeric virus approaches, we identified the viral envelope (E) protein as a key determinant of host range. In particular, a serine residue at position 69 was required for efficient infection, pathogenicity, and tissue tropism in chickens, and this residue has become predominant in recent cluster 3 strains. We further examined the role of the prM and E proteins from different flaviviruses by introducing their prME regions into a common TMUV-FX2010 backbone. Comparative analyses in duck and mouse models demonstrated that the prME region is a major determinant of viral infectivity in ducks and of the ability to initiate infection via the intranasal route in mice. Finally, using the TMUV vaccine strain FX2010-180P as a backbone, we developed chimeric live-attenuated vaccine candidates expressing the prM-E proteins of West Nile virus. These candidates induced strong neutralizing antibody responses in ducks, demonstrating that the TMUV vaccine platform can be used for the development of flavivirus vaccines for poultry. Overall, this work improves our understanding of flavivirus host adaptation and transmission in poultry and provides insights for surveillance, prevention, and vaccine development against emerging flaviviruses in poultry.