Avian influenza: Diagnosis and molecular biological characterization
Grant: Veterinary contingency program. 2019-21. 2.5 million DKK.
In recent years, Denmark has experienced outbreaks of highly pathogenic avian influenza virus (HPAI) in wild birds, which has also led to a sharp increase in suspicion of outbreaks in commercial herds and hobby poultry. The project will increase our basic knowledge of the epidemiology of AIV in Danish conditions and will lead to the development of more refined diagnostic tests. Overall, the effort will significantly strengthen and upgrade veterinary preparedness in the field and improve response times on suspicion cases - of great importance to the authorities and the profession.
The overall aim of the project is to gain a better insight into the epidemiology of avian influenza in Denmark and in Europe, to develop molecular rapid methods for future outbreaks of highly pathogenic avian influenza and to investigate the pathogenesis of selected isolates in different bird species.
The project is carried out as a PhD project focusing on improving the diagnostic methods for detection of H5 / H7 virus in poultry to optimize the response time. In addition, detailed molecular biological characterization of isolates from the past three years will be carried out to investigate the epidemiology - how viruses spread in Denmark and which species of birds are susceptible. This will form the basis for improved surveillance in the future.
The project is divided into three work packages, but the following overall content:
WP-1. Detailed molecular biological characterization of Danish AI isolates.
Virus isolates collected from active and passive surveillance of domestic and wild birds over the past 3-5 years will be full genome NGS-sequencing. The results will be compared to available data from other countries In the same project, new, fast sequencing platforms will be tested (including "Minion" full-genic sequencing) to reduce the time needed to determine whether a virus is low or highly pathogenic.
WP -2. Development of high-through-put system for subtyping (HA and NA genes) of avian influenza isolates. We have developed a high- through -put PCR system (Fludigm) that cheaply and quickly tests e.g. 48 samples in 48 different assays for approx. the same price as an ordinary PCR study. The system is established and used for subtyping of swine flu. A chip with assays for all known HA and NA variants will be established. Using this chip will mean faster response time to the influenza virus subtype.
WP -3. Biological characterization of H5N8 and H5N6 HPAI virus from Denmark. The pathogenesis of various isolates of H5N8 and H5N6 isolated from swimming birds and birds of prey will be investigated by experimental infection of chickens and other bird species, including pheasants. The activity will be carried out by the PhD student as part of a stay abroad with partners in the UK, the USA and / or Poland.
Participants: Yung Liang, IVH; Charlotte K. Hjulsager, SSI; Anders Gorm Rasmussen, DTU