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Avian influenza is a viral disease caused by various strains of avian influenza viruses that can be classified as low pathogenic avian influenza (LPAI) or highly pathogenic avian influenza (HPAI).  It remains a global disease with potential high consequence with the potential to threaten wildlife, agriculture, and human health. 

The USGS National Wildlife Health Center (NWHC) in collaboration with multiple partners conducts research into the ecology of avian influenza virus and surveillance for highly pathogenic avian influenza (HPAI) viruses leading to several significant findings towards early detection and response to HPAI.

Avian Influenza (AI) is a global disease with potential high consequence. Wild birds, in particular certain species of waterfowl and shorebirds, are considered to be the natural reservoirs for avian influenza viruses. These subtypes that naturally occur in wild species usually cause little or no disease. In domestic birds, however, some AI viruses can be more pathogenic and mutation or recombination of a virus acquired from wild birds can increase disease potential. In recent years, spill-back has occurred negatively affecting wild birds. 

Avian influenza viruses (AIV) are classified by a combination of two groups of proteins found on the surface of the virus: hemagglutinin proteins (H), of which there are 16 (H1-H16), and neuraminidase proteins (N), of which there are 9 (N1-N9). There are 144 possible combinations or subtypes based upon this classification scheme. Additional information on avian influenza viruses are available in the Field Manual of Wildlife Diseases

AI strains are divided into two groups based on the pathogenicity of the virus, or the ability of the virus to produce disease. Most AI strains are classified as low pathogenic avian influenza (LPAI) and cause few clinical signs in infected birds. LPAI generally does not pose a significant health threat to humans. However, LPAI is monitored because two strains of LPAI— the H5 and H7 strains–can mutate into highly pathogenic forms. On the other hand, highly pathogenic avian influenza (HPAI) strains frequently fatal to birds and easily transmissible between susceptible species.  


Avian Influenza Movement in the Atlantic

Image: Brown Pelican and Gulls Along Coast 2

Brown pelicans and gulls float and fly along a coastline. (Credit: Elizabeth A. Sellers, USGS. Public domain.)

Highly pathogenic avian influenza outbreaks in domestic poultry cause large economic losses to the U.S. economy. It has been thought that Eurasian strains of avian influenza viruses enter the United States through the Pacific Flyway (Alaska to Baja California) and that this route is the most likely avenue for emerging Eurasian AIV strains to enter North America. However, AIV also frequently infects domestic poultry and wild ducks in Europe and Africa and migrating wild birds that use the east Atlantic flyway may also risk introducing Eurasian strain viruses to North America via this route. With the on-going European outbreaks of HPAI there is a risk of moving these viruses to North America as well.

The USGS National Wildlife Health Center, in collaboration with the National Institutes of Health Centers of Excellence for Influenza Research and Surveillance (CEIRS), the University of Iceland, and other partners, has explored the ecology and movement of AI viruses in the North Atlantic region since 2010. This research has demonstrated the importance of the migratory bird flyways in this region to the intercontinental movement of viruses between Europe and North America. AI viruses from both continents, as well as recombinations of both strains, were isolated in Iceland, sometimes from within a single flock of birds, showing that this region is a hotspot of virus movement and genetic reassortment. These studies also demonstrated the longer-term persistence of portions of these viruses within the North Atlantic avian community. 

Highly pathogenic AI viruses have been frequently found in wild and domestic European birds, significantly in 2006, and annually since then. This continued European epizootic increases the risk of HPAIV being transported from Europe to North America as bird populations migrate through the North Atlantic to breeding sites in Greenland and Canada, and highlights the importance of these studies.  Stakeholders include federal and state agencies, North Atlantic and European countries, and commercial poultry businesses who have an interest in protecting wildlife and/or domestic animals by identifying the risks of HPAIV entering the United States through North Atlantic wild bird flyways.  Significant findings from this research in the North Atlantic include:

  • Gulls and marine birds are an integral component of AIV ecology in this region;
  • Genetic sequence data revealed frequent mixing of North American and Eurasian AIV lineages in the North Atlantic;
  • Icelandic viruses were discovered to have genetic relationships with viruses causing seal mortalities in Europe; and
  • No HPAIV has been identified, however, viruses with genetic relationships to HPAIV H5N1 viruses have been detected in Iceland. 

HPAI and other influenzas circulate in freshwater waterfowl. It is also possible that sea ducks, which regularly move between continents, could play a role in how HPAI moves and evolves around the world. In collaboration with CEIRS, State Wildlife Agencies, Ducks Unlimited, and hunting guides, the NWHC has conducted surveillance in wild sea ducks in the Northeastern United States, Alaska, Canada, and Iceland over the past 6 years. This research has shown that sea duck avian influenzas often differ from those carried by freshwater ducks. This research is currently defining environmental factors that affect AI transmission in marine environments.

Alaska is an international crossroads for millions of migratory birds that winter in Asia, Oceania, South America and the lower

Migration flyways (Public domain)


Quantitative Applications in Disease Ecology

Human, agricultural, and wildlife health depend on each other. Therefore, risk assessment, prediction, and management of wildlife diseases are important for our nation’s health and economy. However, monitoring and evaluating wildlife health is difficult and expensive. This leads to incomplete and biased datasets that are difficult to analyze with traditional methods. A project is underway to develop new statistical and mathematical techniques and package them into user-friendly tools. Some examples of new tools in development are the ability to analyze and interpret complex data, assess risk of future or ongoing disease outbreaks, estimate the effects of disease on individuals, populations, and ecosystems, and evaluate potential management solutions. This project, performed in partnership with the Department of Statistics at the University of Wisconsin-Madison, is broadly applicable to a variety of wildlife diseases, but is currently working on new statistical methods for predicting virus isolation of avian influenzas.


Minor Spillover of Avian Influenza Between Wild and Domestic Birds

Commercial Poultry farm

Commercial poultry farm (Public domain)

In another study, NWHC reserachers also analyzed the genomes of HPAIV that spread in the United States during 2014-2015 and resulted in over $3 billion in losses to the U.S. poultry industry. As infection and transmission of pathogens in wild birds are difficult to measure during a fast-moving outbreak, the NWHC used cutting-edge modeling techniques to analyze genetic similarity between HPAIVs infecting wild birds and poultry. Analyses indicated that even though the viruses likely evolved in Asia, they easily infected and spread among North American wild birds. The viruses were also able to spread between domestic and wild birds (i.e., spillover). However, the rate of spillover was minor, and the poultry outbreak persisted without need for ongoing transmission from wild birds. Techniques used in this study can also be used to examine transmission and adaptation of avian influenza within waterfowl populations and between waterfowl and poultry.


Avian Influenza Surveillance

The USGS National Wildlife Health Center is a member of the U.S. Interagency Steering Committee for Surveillance for Highly Pathogenic Avian Influenza in Wild Birds. The NWHC performs both passive and active surveillance for the detection and monitoring of avian influenza. Check out the Avian Influenza Surveillance page to learn more.