Avian Influenza Research

Science Center Objects

Since 2006, the USGS Alaska Science Center has been part of the State and Federal interagency team for the detection and response to highly pathogenic (HPAI) viruses in North America. Avian influenza or "bird flu" is a viral disease that primarily infects domestic poultry and wild birds. Avian influenza viruses are naturally occurring in wild birds such as ducks, geese, swans, and gulls. These viruses generally do not cause illness in wild birds, however, when spread to poultry they can be highly pathogenic and cause illness and death in backyard and commercial farms.

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Graphic depicting five bird migration flyways of the Pacific Ocean basin

Graphic depicting five bird migration flyways of the Pacific Ocean basin.
(Credit: Mary Whalen, USGS. Public domain.)

Through the Science Strategy for Highly Pathogenic Avian Influenza (HPAI) in Wildlife and the Environment, the USGS will assess avian influenza (AI) dynamics in an ecological context to inform decisions made by resource managers and policymakers from the local to national level. Research on avian influenza has revealed important patterns of virus movement and transmission in migratory birds. Ongoing work includes surveillance for foreign-origin pathogens and study of intercontinental links between Asia and North America.

Alaska is a geographically important focus of the surveillance program because it lies within the migratory routes of birds that move between North America and Asia. Research at the Alaska Science Center (ASC) strengthens the efficiency and effectiveness of HPAI surveillance across North America, while increasing our understanding of virus ecology in wild bird hosts. The ASC uses migratory, genetic and immunological data to: identify likely routes of virus introduction, determine priority species and regions to sample, and document changes to the genetic diversity of avian influenza that will strengthen future decision-making.




Examining the Role of Migratory Birds the Movement of Avian Pathogens between and within Continents 

Man releasing duck in Japan. He wears a face mask for protection from disease

USGS Scienctist Andrew Ramey releases a Northern Pintail Duck in Japan. 
(Credit: John Reed, USGS. Public domain.)

Past research on molecular characteristics of avian disease by the USGS and collaborators has documented host prevalence, transmission patterns, genetic origins, and inter-continental movement of disease agents between Alaska and East Asia. This project takes these findings further by examining new pathogens, demographic impacts, and new host populations.

Since 2011, USGS studies have examined emerging avian diseases, links between disease and climate change, environmental persistence of avian viruses, blood parasite prevalence and transmission, and fitness consequences of specific pathogens. Molecular detection and characterization of these pathogens is one of the primary objectives and novel methods being developed to take advantage of new techniques in the area of molecular genetics. Study locations include: Anchorage, Colville River Delta, Minto Flats State Game Refuge, Izembek National Wildlife Refuge, Yukon Delta National Wildlife Refuge, and Izunuma Lake, Northern Honshu, Japan.


Avian Influenza Genomics

Molecular ecology laboratory procedure

USGS Scienctist Rob Wilson adding prepared genetic material to a gel in the Alaska Science Center Molecular Ecology Laboratory.
(Credit: Yvette Gillies, USGS. Public domain.)

The USGS Alaska Science Center has conducted genome sequencing of avian influenza viruses since 2006 to gather information on how migratory birds are involved in the movement of influenza genes between Eastern and Western Hemispheres. More recently, the USGS has used next generation sequencing platforms to more rapidly and thoroughly obtain genetic information on avian influenza viruses.  USGS research has documented more inter-hemispheric viruses in Alaska than elsewhere in North America and evidence of a complete genome virus that was moved between Asia and Alaska via migratory birds.   Ongoing genomics research at the Alaska Science is directed towards improving our understanding of how viruses are transmitted between host species and transported among geographic locations. Such information can be used to improve future surveillance efforts for avian influenza viruses and other microbes that infect wild birds.


A flock of shorebirds flying near the upper Alaskan Peninsula, Alaska

Dunlin flock near Egegik, Alaska.
(Credit: Daniel Ruthrauff, USGS. Public domain.)

Bird Migration and Influenza

  • Mallard
  • Blue-winged Teal
  • Northern Pintail
  • Tundra Swan
  • Shorbirds
  • Gulls


Research and Surveillance

The USGS Alaska Science Center conducts research and surveillance activities to assess the role of wild birds in the introduction and spread of avian influenza viruses in North America via migratory flyways.

Ongoing Avian Influenza Virus Surveillance at Izembek National Wildlife Refuge

Since 2010, the USGS has conducted collaborative surveillance sampling for influenza A viruses in wild birds at Izembek National Wildlife Refuge. This project samples selected species at an intercontinental crossroads for migratory waterfowl. Genetic sequencing of the viruses obtained provides information on subtype diversity, patterns of interspecies transmission, and the evolution and persistence of Eurasian origin viral genes in western Alaska. Findings are informing future surveillance activities for foreign origin influenza viruses in Alaska and elsewhere in North America.

Priority Species for Sampling

In early 2006, an Alaska Interagency Avian Influenza Working Group was formed to develop a ranking matrix for selecting priority species to be sampled within Alaska. Most wild bird species with populations that utilize areas of both Alaska and Asia were identified and considered in the ranking exercise. Based on scoring criteria, 28 target species were chosen for sampling based on five factors: 1) proportion of the population occurring in Asia, 2) contact with a known ‘hot spot’ or source of highly pathogenic avian influenza, 3) habitats used in Asia in context with exposure potential, 4) population size in Alaska, and 5) ability to obtain a representative sample of sufficient size.  Information about these species can be found here.

However, as USGS and other agency partners began to look at the virus data from wild bird sampling, it became clear that some birds and regions were not useful for obtaining viral genetic information that informed future surveillance plans (see Ramey et al. 2010).  Thus, currently, the USGS now samples annually at Izembek National Wildlife Refuge in the fall and only samples a handful of species, such as northern pintail, emperor geese, and glaucous-winged gulls.  By reducing the scale of our sampling, we obtain valuable information on avian influenza for a much smaller cost.

Previous Research and Surveillance

Avian Influenza Virus Surveillance in Western Alaska

The Yukon-Kuskokwim Delta in western Alaska is an important breeding ground for thousands of birds and is located in an area where multiple migratory flyways converge, providing opportunities for infectious agents, like avian influenza virus, to spread. Earlier work by the USGS found a high frequency of Eurasian origin genes in western Alaska, indicating movement of viruses into North America. In addition, results suggest that species readily share introduced viruses in areas such as the the Yukon-Kuskokwim Delta where thousands of individuals from numerous species and multiple international migratory flyways co-occur. 

H5N1 Surveillance Activities

Following the outbreaks of Asian H5N1 highly pathogenic avian influenza (HPAI), it was determined that if H5N1 HPAI viruses were to spread to North America via migratory birds, the the most likely location for initial detection in North America would be in Alaska because of the overlap of major migratory bird flyways in this region. The USGS summarized available research on migration and distribution of birds in Alaska to determine a list of priority species for sampling that would maximize the probability of detection should Asian H5N1 HPAI be present in Alaska.  The criteria used to determine priority species by the USGS can be found in Attachment 4 of the 2006 document, "Interagency Strategic Plan for Avian Influenza Surveillance in Migratory Birds" [PDF 1.98 MB].