Dynamics of avian influenza
in a changing world

The Friedrich-Loeffler-Institut (FLI) is a federal research institute and independent higher federal authority under the Federal Ministry for Food, Agriculture and Consumer Protection. At present, the Friedrich-Loeffler-Institut has approximately 900 employees in eleven specialist institutes at five locations. The work of the FLI focuses on farm animal health and welfare and on the protection of humans from zoonoses. The FLI is one of the leading research institutes for animal health in Europe. The project-related major tasks are the prevention of diseases by developing and improving new diagnostic technologies including rapid diagnostics, and providing the background for modern surveillance and control strategies for animal diseases and zoonoses. The FLI performs basic and applied research in different scientific areas, including epidemiology, immunology, virology, bacteriology, and parasitology. The FLI operates state-of-the-art experimental virology labs and experimental animal facilities up to BSL-4, also for experiments with both domestic and wild birds, in which all the virology, molecular biology, pathology and immunology techniques necessary for this project are fully operational.

The Institute of Diagnostic Virology (IVD) studies important virus diseases of animals, mainly in terms of diagnosis, differential diagnosis, molecular epidemiology and pathogenesis. Special attention is given to notifiable diseases and zoonoses. Nineteen different reference laboratories, e.g. for Avian Influenza (also OIE and FAO reference laboratory), Foot-and-Mouth-Disease or African Swine Fever are part of the Institute of Diagnostic Virology. In addition, new molecular diagnostics, including next-generation sequencing techniques (Ion Torrent, Illumina and MinIon platforms), automated nucleic acid extraction, DNA chip technology and real-time (multiplex) PCR are major tasks. Influenza A viruses are a major focus of the institute including molecular diagnostics, virus isolation, sequencing, phylogeny, molecular epidemiology, and pathogenesis. Infection studies with all types of birds, pigs, mice and ferrets are a special expertise of the institute under both BSL2 and BSL3 conditions. 

The Institute of Molecular Virology and Cell Biology (IMVZ) investigates pathogen-host cell interactions on the molecular level using selected viruses, which are of importance in veterinary medicine. Research at the institute focuses on herpesviruses, rhabdoviruses, orthomyxoviruses, paramyxoviruses, and asfarviruses. Using the most recent molecular virological, biochemical and cell biological techniques, their genome organization and regulation of gene expression are investigated and viral gene products are identified and characterized with regard to their function and interaction with host cell components. In addition to genetic engineering methods for targeted modification of viral genomes, the platforms for proteome analysis and for “Live-Cell Imaging” which are part of the institute play a central role. In addition, the Institute of Molecular Virology and Cell Biology houses the National Reference Laboratories for Aujeszky's Disease, Rabies, and Infectious Laryngotracheitis. Molecular biology including reverse genetics of influenza A viruses is a major expertise and recombinant viruses and reassortants are generated and characterized routinely. 

Erasmus MC is the largest university medical centre in the Netherlands. The Department of Viroscience at Erasmus MC (see www.virosciencelab.com) employs more than 110 persons of different disciplines and runs an extensive research program on viral infections of humans and animals, with specific interests in viral zoonoses, pathogenesis and transmission and natural and vaccine-induced immunity. There are 6 principal investigators at the professor level, each representing an essential skill in infectious diseases, including professors in 1) General Virology; 2) Molecular Virology; 3) Immunology; 4) Pathology; 5) Epidemiology; 6) Clinical Virology, as well as assistant/associate professors specialized in specific virus fields. Viruses under research include influenza A and B virus, RSV, hMPV, measles virus, coronaviruses, HIV-1, HIV-2, hepatitis A, B and C viruses, West Nile virus, dengue viruses, monkey pox virus, and herpes viruses. The department houses the National Influenza Centre, the national reference centre for emerging viral diseases, and the international reference centres for viral haemorrhagic fevers and measles for WHO. The department has built up an extensive track record in the identification of several novel human viruses, including Middle Eastern Respiratory Syndrome (MERS) coronavirus, human metapneumovirus (HMPV), human H5N1 infection in Hong Kong, SARS-CoV, and hCoVNL63. In collaboration with the department of Zoology at Cambridge University, UK, the department has developed methods for improving human influenza virus surveillance and vaccine strain selection (2004), which have been adopted by the WHO as an integral part of the annual vaccine strain selection process. The department of Viroscience is Co-Coordinator of the H2020 COMPARE project, and participates in numerous other H2020 projects. It is or has been the Coordinator of several FP7 large scale integrating projects (ANTIGONE, EMPERIE, FLUNIVAC, ASKLEPIOS, VECTORIE) and participates in numerous other FP7 projects of relevance to emerging disease preparedness, including disease in animals. Its research includes the characterization of viral variants and the pathological and serological response generated in the susceptible host species of many viral infections of humans and animals.

The Animal and Plant Health Agency (APHA) was launched on the 1 October 2014. It merged the former Animal Health and Veterinary Laboratories Agency with the Plant and Bee Health and GM Inspectorates and the Plant Varieties and Seeds Office, creating a single agency responsible for animal, plant and bee health. It is an executive agency working on behalf of Defra, Scottish Government and Welsh Government.

The APHA currently employs around 2,300 members of staff including scientists, administrators, inspectors laboratory attendants, animal technicians and veterinarians and brings together this considerable experience in dealing with pest and disease outbreaks and other animal and plant health threats. 

The APHA is the national and international reference laboratory for a wide range of animal diseases. It comprises 16 laboratories including a 368-acre site at Weybridge in Surrey, 15 regional laboratories across the UK and five farms on the Weybridge site. The majority of the veterinary resource within APHA is based at the regional laboratories, engaged in surveillance within the UK. There are also two Surveillance Centres provided under contract by the Liverpool and London Veterinary Schools. Research activities underpin the surveillance work and provide robust scientific evidence required by the UK Department for Environment, Food and Rural Affairs (Defra) and international organizations (EU, OIE, WHO, FAO) to inform policy and control strategies. Surveillance involves consultancy, maintenance of expertise, fieldwork, laboratory testing and test development. The APHA is the Community Reference Laboratory (EU reference laboratory) for Newcastle Disease (ND), Avian Influenza (AI) and Transmissible Spongiform Encephalopathy’s (TSE’s). The current laboratory facilities at the APHA allow for research to be undertaken in BSL 3 containment laboratories on SAPO-listed group 4 / ACDP group 3 pathogens.

The majority of the human resources for this project lie within the Virology Department, specifically the Avian Virology and Mammalian Influenza Group. Other groups, including Pathology, Epidemiology and Biomathematics and Risk Research also provide additional resources to specific projects.

IZSVe is a governmental organization and part of the network of the Istituti Zooprofilattici Sperimentali in Italy. It provides scientific and technical support to the Central and Regional governments regarding animal health and welfare, veterinary public health, environmental protection and food safety. Within the framework of its national and international engagements, IZSVe is involved at the frontline in the surveillance and characterization of viral agents with animal and public health impacts, such as influenza viruses. The IZSVe conducts extensive research and surveillance activities on AIVs, particularly in North-East Italy, which is one of the most AI-prone areas in Europe. Because of its unique environmental setting (i.e. high poultry density, large wetlands harboring many resident wild birds and being the crossroad for many migratory birds), this area has faced some of the most devastating AI epidemics in poultry in Europe, with recurrent AIV incursions from wild birds. This led to a strengthening of eco-epidemiological research intelligence and AI outbreak preparedness and response capacity, as well as to the establishment of a high standard surveillance infrastructure through which detailed data on poultry and wild bird populations and on the local environment are collected and analyzed on a routine basis. The Department of Comparative Biomedical Sciences of IZSVe hosts national and international (FAO/OIE) reference laboratories for AIV and the OIE Collaborating centre for diseases at the Human-Animal Interface. The team counts on a staff of 53 persons including veterinarians, biotechnologists and technicians (13M/40F, average age 38). Over the years, the group has stood out as an international reference centre for research on avian influenza by studying the evolutionary dynamics, the pathogenesis, the transmission patterns and the virological factors driving the host-species jump of influenza A viruses. Within this framework, several poultry models poultry (chickens, turkeys, Pekin ducks, quails and pigeons) have been validated and are available at the IZSVe. The Institute is also equipped with BSL3 facilities for conventional and experimental diagnosis of viral diseases of animals, zoonotic viral agents (isolation in tissue culture, embryonated eggs, electron microscopy, histopathology, etc.) and molecular diagnosis (RT-PCR; Real Time PCR; sequencing, Pyrosequencing, NGS, etc.). A BSL3 animal facility for birds, small mammals and pigs is also on the premises. IZSVe has direct access to next generation sequencing (NGS) platforms and has a well-established experience in the application of NGS technologies to study the evolution and molecular epidemiology of viruses.

The Laboratory of Virology, Faculty of Veterinary Medicine, Ghent University includes 30 persons: 2 professors, 2 post-docs, 19 PhD students and 7 technicians. Three PhD students are working on influenza in swine under the guidance of Prof. Van Reeth.

The laboratory has a long track record in swine influenza virus (SIV) research. In 1979, the group was the first to isolate the European avian-like H1N1 SIV, which continues to be the predominant virus lineage in European swine populations. A swine influenza vaccination-challenge model was already established in the 1980s and the group contributed significantly to the understanding of the organ and cellular pathogenesis of swine influenza. The classical virological and serological techniques for influenza have been in use since then. Kristien Van Reeth was the first to study the role of cytokines in the pathogenesis of SIV in pigs in 1998.

The group has a strong interest in both the veterinary and public health aspects of swine influenza. One of the current and very timely research themes is the role of pigs in the influenza virus ecology and emergence of novel pandemic influenza viruses for humans. The second major research theme is cross-protection between antigenically distinct influenza viruses from swine and between viruses from swine and other species (humans and birds).

The proposed research fits entirely within the first theme. It aims to obtain a better understanding of the role of pigs in influenza pandemics by studying avian influenza virus adaptation to pigs. Combined with detailed surveillance for influenza in pigs and critical analysis of potential risk factors, this knowledge will be indispensable for the control of future influenza pandemics. The proposed research is a continuation of the FP7 European research project “FLUPIG” (2010-14) for which Kristien Van Reeth was coordinator. During the FLUPIG project, the group has invested heavily in the development of a pig transmission model for avian influenza viruses and in the infrastructure to perform serial pig passages and transmission studies in pigs.

The Roslin Institute (RI) at the University of Edinburgh (UEDIN) is one of eight National Institutes of Bioscience in the UK that receive core-strategic funding from the Biotechnology & Biological Sciences Research Council. It is the research arm of the Royal (Dick) School of Veterinary Studies (the top-rated UK veterinary school) within the University of Edinburgh (a world top 20 university) and has over 500 staff and students. The RI undertakes research within the framework of BBSRC Institute Strategic Programs focused on the health and welfare of animals, and applications of basic animal sciences in human and veterinary medicine, the livestock industry and food security. Immunology, virology, vaccinology, and genomics are all major strengths of the Institute and therefore we are well-fitted to the tasks in which we are involved in this proposal. The Division of Infection and Immunology has built up an extensive track record in livestock infectious disease research with over two dozen members of staff heading groups that focus on a variety of immunological, viral, bacterial and parasite-oriented projects. It has particular strengths in avian immunology and influenza A virus research.

Although Sweden’s youngest university, Linnaeus University (LNU) is founded upon a long tradition of high-quality teaching and advanced scientific accomplishment. As a merger of Växjö University and the University College of Kalmar, LNU opened its doors on 1 January 2010. With 35,000 students and 2,000 employees, LNU is one of the larger universities in Sweden. The University’s five faculties offer about 150 courses of study and more than 2,500 individual courses in roughly 100 subjects. Research at LNU is multifaceted, and has both depth and breadth, with well-developed collaboration between disciplines as well as surrounding industries, region and society as a whole. The areas of inquiry span over the humanities, social sciences, natural sciences and engineering, with a number of well-established research specialties. All of the University’s faculties offer postgraduate programs, and more than 400 postgraduate students are currently at work in more than fifty different disciplines. For this call, the Linnaeus Centre for Ecology and Evolution in Microbial Model Systems (EEMiS: lnu.se/en/eemis/) will be involved. EEMiS is a center of excellence within the university, comprised of six full professors and their research groups that collaborate on science at the intersection of their disciplines (zoonotic ecology, microbiology, aquatic ecology and evolutionary ecology). Within EEMiS, substantial experience exists in conducting research on avian pathogens in free-living wild birds. This includes the long-term disease surveillance of Influenza A virus (IAV) in migratory mallards, carried out at Ottenby Bird Observatory on the island of Öland. This program started in 2002 and it is now on its 15th year and has provided key insights in IAV disease dynamics, including temporal variation of IAV occurrence, subtypic and genotypic variation at population and individual levels at both temporal and spatial scales, as well as targeted studies to investigate the effect of IAV infection on bird movements, behaviors and condition. EEMiS houses a fully equipped virology laboratory for detection, isolation and characterization of IAV from bird samples that has already investigated more than 60,000 samples in the last ten years. Importantly, in the laboratory of the main PI, Professor Waldenström, there is longstanding experience in conducting eco-immunological research on avian pathogens, particularly to combine methods used in ornithology (such as capturing birds for ringing purposes, collecting data on birds’ condition and health status, and applying methods for remote sensing of bird movements) with virology methods. At our disposal is the Ottenby Bird Observatory – one of the oldest and largest bird observatories in Europe – with its field personnel trained in capturing waterfowl using both fixed duck decoy traps and mobile field methods.

The Li Ka Shing (LKS) Faculty of Medicine at The University of Hong Kong is one of the world-leading teaching and research institutes for emerging infectious diseases including SARS, avian influenza viruses, and MERS. The Centre of Influenza Research at the School of Public Health adopts a multi-disciplinary research program that integrates virology, molecular biology, epidemiology, immunology, cell biology, aerobiology, and bioinformatics to study influenza and related respiratory pathogens. The Centre of Influenza Research is one of the WHO H5 reference laboratories since 2004 while the School of Public Health has been designated as a WHO Collaborating Centre for Infectious Disease Epidemiology and Control since 2014. The research interests of the principle investigators (seven professoriate staffs) at the Centre of Influenza Research are to elucidate the evolutionary path of emerging viral pathogens from animal reservoirs, to understand viral, host, and environment determinants facilitating transmission of influenza and other related respiratory pathogens, to assess the risk of animal influenza viruses for their pandemic potential in humans, to analyze the virus-host interactions on interspecies transmissions or immunopathogenesis, to develop evidence-based control measures for influenza and other related respiratory pathogens in humans and at the human-animal interface.

Southeast Poultry Research Laboratory (SEPRL) is the largest poultry health research laboratory in the USA, and is within the U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture. SEPRL is the in-house USDA high biocontainment laboratory for research on poultry viral diseases. SEPRL is a world leader in developing research solutions to the most deadly poultry diseases such as highly pathogenic avian influenza (HPAI) and Newcastle disease, which have devastated poultry and wild bird populations around the world. This includes playing a key role in developing rapid genetic diagnostic tests and vaccines used to control these diseases, not only in the United States but also globally. The experience of the laboratory nationally and internationally has translated into being designated a Collaborative Center on Research on Emerging Avian Diseases by the World Organization for Animal Health (OIE), a Reference Laboratory for Avian Influenza by the Food and Agriculture Organization (FAO) of the United Nations and an OIE/FAO Expert Animal Influenza Laboratory. The SEPRL scientific program will continue to play a key role in developing the next platform of vaccines against these diseases and new diagnostic tests that will keep these devastating diseases out of the United States. The existing scientific programs focuses on the needs of the poultry industries and, importantly, the needs of government action agencies responsible for controlling poultry diseases with epizootic and pandemic potential. To accomplish its mission, ARS has 11 scientists, and 44 FTE support staff. Both endemic and Select Agents are be safely studied.

The National Center for Foreign Animal Disease (NCFAD) is part of the Canadian Food Inspection Agency (CFIA)’s National Centers for Animal Disease. CFIA is responsible for enforcing food safety standards and sets standards and carries out enforcements and inspection for animal health and plant protection.

The National Centre for Foreign Animal Disease (NCFAD), located in the Canadian Science Centre for Human and Animal Health in Winnipeg, Manitoba, (Canada) is part of the Canadian Food Inspection Agency (CFIA)’s National Centres for Animal Disease. NCFAD is co-located with the Public Health Agency of Canada’s National Microbiology Laboratory. NCFAD provides state-of-the-art scientific expertise and technologies for the prevention, detection, control and reporting of foreign animal diseases (FAD) and emerging animal diseases. The laboratory has diagnostic capabilities for a large number of FADs including, but not limited to: avian influenza, foot-and-mouth disease, classical and African swine fevers, Rift Valley fever, Ebola and Nipah and Hendra virus infections.

The NCFAD has received designations by the World Organization for Animal Health (OIE) as a reference laboratory for both highly pathogenic avian influenza (HPAI) and for classical swine fever, in recognition of excellence in diagnostic competency, test method development, validation, research, collaboration and training. The NCFAD is also accredited to the international quality standard, ISO/IEC 17025 for both diagnostics and research. ISO accreditation means that an international level of standardization has been met; this ensures state-of-the-art technology, worldwide compatibility and competence in diagnostic and research activities.

The mandate of the NCFAD is to provide scientific and laboratory services for the rapid and accurate identification and reporting of foreign animal diseases. The lab has five main functions: Testing services; technology development and research; training; scientific advice; and international consultation.