Avian Influenza

Research by the U.S. Geological Survey and Partners

What is Avian Influenza?

Avian influenza (AI) is a viral infection of wild birds that cannot been seen with the naked eye. It is caused by a group of viruses known as type A influenzas. During the current outbreak, we have also seen AI infect wild mammals (terrestrial, freshwater, and marine).

Avian influenza viruses occur naturally in wild birds such as ducks, geese, swans, and gulls. These low pathogenic viruses do not generally cause illness; however, highly pathogenic viruses cause illness and death in backyard birds and commercial poultry. During this outbreak, we have also seen other  food animals  infected, such as dairy cows, goats, and alpacas.

 Recent evidence  has shown that highly pathogenic avian influenza is an emerging threat to wild birds and other wildlife. 

Outbreaks may cause devastating agricultural economic losses and some viral strains have the potential to infect people directly. Furthermore, the combination of avian influenza viruses with mammalian viruses can result in strains that can transmit from person to person, possibly leading to viruses with pandemic potential.

"Conceptual diagram depicting the generalized ecology of avian-origin influenza A (AI) viruses. Arrows depict common directionality of cross-species transmission events for AI viruses, including those with a highly pathogenic (HP) phenotype among wildlife, agricultural, and human sectors." From  Ramey et al 2022 

Federal Response to Avian Influenza 

The Interagency Steering Committee for Surveillance for Highly Pathogenic Avian Influenza (HPAI) in wild birds facilitates a coordinated and cooperative approach among many federal and state agencies for the surveillance of wild birds to detect avian influenza viruses in the U.S. The Steering Committee currently includes representatives from the U.S. Department of Agriculture (USDA), U.S. Fish and Wildlife Service (USFWS), U.S. Geological Survey (USGS), the National Flyway Council (NFC), and the Association of Fish and Wildlife Agencies (AFWA).

USGS Role in Federal Response

The USGS is the science bureau of the U.S. Department of the Interior (DOI) and has been conducting research on avian influenza since 2006.

The DOI works with the USDA to actively coordinate with State and Federal wildlife, agricultural, and human health agencies to understand avian influenza distribution and dynamics to aid natural resource managers, agricultural officials, and the food animal industry. 

In collaboration with these partners, the USGS developed a national science strategy for Highly Pathogenic Avian Influenza (HPAI) for 2016-2020. This science plan augments on-going research to forecast disease spread by wild birds, detect novel strains, characterize factors that control persistence of HPAI in the environment, and develop risk assessments for livestock, natural resources, and human health. 

USGS AI Science Strategy

Implementation of novel objectives and proposed research actions with international, Federal, State, Tribal, and academic partnerships served as the basis for developing robust decision-making frameworks to aid resource managers and policymakers faced with the biological threat of HPAI. The strategy encompasses five long-term research science goals.

The USGS AI science team is currently working on a new science plan based on emergent needs.

Science Goal 1

Augment National HPAI Surveillance Plan

  • An interagency effort to revise a national surveillance plan for HPAI in wild migratory birds in the United States, fill data gaps and avoid data redundancy 

Objective 1: Develop tools and strategies for early HPAI detection in wildlife and the environment

Proposed Action 1: Develop new detection strategies for HPAI in environmental samples

Proposed Action 2: Detect potential HPAI introductions into the United States


Objective 2: Conduct HPAI surveillance in wild birds and peridomestic wildlife (wildlife living in and around human occupied areas)

Proposed Action 1: Implement the National Interagency Surveillance Plan for HPAI in waterfowl

Proposed Action 2: Collaborate with USDA to conduct HPAI surveillance of potential hosts near poultry facilities

Proposed Action 3: Conduct meta-analysis of HPAI surveillance strategies

Science Goal 2

Determine mechanisms of HPAI disease spread in wildlife and the environment

  • Understand the spread and persistence of HPAI in wildlife, water, and sediments; work with resource managers to assess prevalence of AI viruses and population outcomes for wildlife, poultry, and public health

Objective 1: Determine mechanisms of HPAI spread and persistence in wildlife.

Proposed Action 1: Conduct experimental HPAI studies to understand the role of sea ducks in the movement, transmission, and evolution of these viruses.

Proposed Action 2: Examine the role of filter-feeding organisms in HPAI persistence, transmission, or inactivation.


Objective 2: Determine mechanisms of HPAI spread and persistence in the environment

Proposed Action 1: Determine hydrologic characteristics that facilitate persistence of HPAI in fresh and brackish waters

Proposed Action 2: Examine persistence of AI viruses in sediment

Proposed Action 3: Characterize AI transport in groundwater

Proposed Action 4: Investigate climate variability and change as a driver of AI persistence and spread


Objective 3: Determine mechanisms of HPAI spread and persistence in peridomestic wildlife found near poultry operations

Proposed Action 1: Interagency workshop on the wildlifedomestic animal HPAI interface

Proposed Action 2: Field research to examine the role of wild birds in HPAI movement

Proposed Action 3: Experimental studies to understand the role of wild birds in HPAI movement, transmission, and evolution

Proposed Action 4: Conduct research to examine the role of non-avian species in HPAI movement and transmission


Objective 4: Determine implications of High and Low Pathogenic Avian Influenza (HPAI and LPAI) exposure for wildlife

Proposed Action 1: Investigate population level impacts of HPAI exposure on DOI trust species

Proposed Action 2: Determine the genetic factors associated with HPAI resistance and susceptibility

Proposed Action 3: Compare wildlife HPAI immune responses for targeted HPAI surveillance and management

Science Goal 3

Characterize HPAI viruses circulating in wildlife

  • Genomic and bioinformatics characterization of AI viruses circulating in wildlife and the environment and a spatiotemporal assessment of risk to poultry production, wildlife, and public health

Objective 1: Characterize AI viruses circulating in wild birds

Proposed Action 1: Characterize HPAI viruses in wild birds across North America

Proposed Action 2: Characterize LPAI viruses in wild birds across North America

Proposed Action 3: Characterize LPAI and HPAI strains in peridomestic wild birds near poultry operations


Objective 2: Characterize AI viruses circulating in wild mammals

Proposed Action 1: Characterize AI viruses circulating in peridomestic mammals near poultry operations

Proposed Action 2: Characterize AI viruses circulating in feral swine


Objective 3: Characterize HPAI viruses circulating outside North America and on the continental fringes with potential of introduction

Proposed Action 1: Characterize AI viruses circulating in wildlife outside of North America

Proposed Action 2: Characterize AI viruses on continental fringes of North America

Science Goal 4

Understand implications of avian ecology on HPAI spread

  • Clarify how intercontinental migration and avian community interaction influence HPAI spread

Objective 1: Map spatial and temporal distributions of wild and domestic avian populations for risk model development

Proposed Action 1: Develop wild and peridomestic bird distribution models as inputs for disease risk assessments

Proposed Action 2: Develop high resolution models of poultry densities as inputs for disease risk assessments

Proposed Action 3: Examine the influence of climate change on bird migration and its implications on AI dynamics


Objective 2: Address AI-relevant information gaps in avian migratory connectivity data

Proposed Action 1: Develop quantitative flyway maps of AI reservoir species

Proposed Action 2: Determine population connectivity of avian AI reservoir species through genetic analyses

Proposed Action 3: Characterize landscape connectivity between avian AI reservoirs and wild birds susceptible to HPAI disease


Objective 3: Investigate HPAI transmission in avian communities and the impact of HPAI on avian populations

Proposed Action 1: Determine HPAI transmission pathways within ecological communities

Proposed Action 2: Assess impact of HPAI on North American avian populations

Science Goal 5

Develop HPAI forecasting and decision-making tools

  • Conduct decision analyses and develop risk and decision models from the first four goals (and prior USGS research) to integrate into risk assessment and decision models to improve AI detection and improve outbreak prevention strategies in poultry and wildlife management outcomes

Objective 1: Provide decision support to management agencies

Proposed Action 1: Work with management agencies to develop a quality HPAI decision making framework

Proposed Action 2: Synthesize HPAI decision analyses from different management agencies to identify common information gaps and critical uncertainties

Proposed Action 3: Refine HPAI research priorities based on management partner needs


Objective 2: Develop HPAI risk assessment and predictive models

Proposed Action 1: Develop dynamic occupancy models to estimate probabilities of AI occurrence

Proposed Action 2: Conduct a meta-analysis of existing AI mechanistic models

Proposed Action 3: Develop geospatial models of HPAI transmission risk at the wild-to domestic bird interface

Proposed Action 4: Develop Landsat-based HPAI risk maps

Proposed Action 5: Develop hydrologic HPAI risk maps

Proposed Action 6: Develop models of HPAI transmission risk for avian communities


Objective 3: Develop online HPAI data visualization tools

Proposed Action 1: Improve existing collaborative databases to store historical and future HPAI data

Proposed Action 2: Develop an HPAI data visualization tool

USGS AI Research Centers

The USGS conducts research on AI at multiple science centers and Cooperative Research Units (CRUs) across the nation and has amassed substantial internationally recognized expertise investigating this disease.

USGS Scientists are

  1. Defining the role of migratory birds in viral spread
  2. Characterizing genetics of viruses in wild birds
  3. Determining environmental conditions affecting survival of the viruses in wetlands
  4. Examining the potential role of non-waterfowl hosts
  5. Investigating the potential ecological consequences of infection in migratory birds

Alaska Science Center (ASC)

Alaska Science Center (ASC). Click to expand.

Anchorage- Juneau- Fairbanks, AK

Western Ecological Research Center (WERC)

Western Ecological Research Center (WERC). Click to expand.

Sacramento, CA

Montana Cooperative Research Unit (MCRU)

Montana Cooperative Research Unit (MCRU). Click to expand.

Missoula, MT

Upper Midwest Environmental Sciences Center (UMESC)

Upper Midwest Environmental Sciences Center (UMESC). Click to expand.

La Crosse, WI

National Wildlife Health Center (NWHC)

National Wildlife Health Center (NWHC). Click to expand.

Madison, WI | Honolulu, HI

Upper Midwest Water Science Center (UMid WSC)

Upper Midwest Water Science Center (UMid WSC). Click to expand.

Several locations across WI, MI, MN

Eastern Ecological Science Center (EESC)

Eastern Ecological Science Center (EESC). Click to expand.

Kearneysville, WV | Beltsville, MD

Alaska Science Center (ASC)

Anchorage- Juneau- Fairbanks, AK

The mission of the Alaska Science Center is to provide objective and timely data, information, and research findings about the earth and its flora and fauna to Federal, State, and local resource managers and the public to support sound decisions regarding natural resources, natural hazards, and ecosystems in Alaska and circumpolar regions.

Western Ecological Research Center (WERC)

Sacramento, CA

WERC's research spans from the California coast and mountains to San Francisco Bay and the central Valley, from the Sierra Nevada Mountains to the plains and ranges of the Great Basin, and from urbanized southern California to the deserts of the southwest and Mexico.

Montana Cooperative Research Unit (MCRU)

Missoula, MT

The Montana Cooperative Wildlife Research Unit performs research designed to address the needs of cooperators, bridging the gap between applied and basic wildlife science. Our studies provide new insights useful to management and conservation, based on understanding the ecological mechanisms that underlie habitat requirements and demography of individual and coexisting wildlife species. 

Upper Midwest Environmental Sciences Center (UMESC)

La Crosse, WI

The majority of ecological research conducted at the Upper Midwest Environmental Sciences Center (UMESC) supports Department of the Interior (DOI) issues and lands in the Upper Midwest. UMESC also coordinates its research with other U.S. Geological Survey (USGS) Science Centers, to broadly address ecological and population concerns throughout the Nation's heartland.

National Wildlife Health Center (NWHC)

Madison, WI | Honolulu, HI

The USGS National Wildlife Health Center is the only national center dedicated to wildlife disease detection, control, and prevention in the United States. Our mission is to advance wildlife health science for the benefit of animals, humans, and the environment.

Upper Midwest Water Science Center (UMid WSC)

The Upper Midwest Water Science Center (UMid WSC) is working with Federal and university partners working toward the goal of understanding avian influenza viruses (AIVs) in the environment: early detection, enhancing biosurveillance, and mitigation to reduce spread into domestic poultry and potential occupational or recreational exposure to humans.

Eastern Ecological Science Center (EESC)

Kearneysville, WV | Beltsville, MD

The Eastern Ecological Research Center aligns scientific capabilities with the most pressing conservation and management challenges; establish an engaged workforce that fosters high relationship trust with employees, partners and the public.

Reporting Bird Mortalities: WHISPers

WHISPers stands for Wildlife Health Information Sharing Partnership - event reporting system. It is a partner-driven, web-based repository for sharing basic information about historic and ongoing wildlife mortality (death) and/or morbidity (illness) events. WHISPers provides a place and a reporting structure for natural resource managers to enter event information and for anyone, including the public, to learn about verified (laboratory diagnosed) wildlife disease events. 


AI Publications

Recent peer-reviewed articles by USGS and partners

All photographs by U.S. Geological Survey unless otherwise noted.

Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

"Conceptual diagram depicting the generalized ecology of avian-origin influenza A (AI) viruses. Arrows depict common directionality of cross-species transmission events for AI viruses, including those with a highly pathogenic (HP) phenotype among wildlife, agricultural, and human sectors." From  Ramey et al 2022