Environmental detection of avian influenza virus
A collaborative project 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.
Highly pathogenic avian influenza (HPAI) continues to circulate internationally, causing record numbers of deaths in both wild birds and domestic poultry. In 2022, HPAI was recognized as the cause of death for both terrestrial and aquatic mammals. Initially the fatal infections in aquatic mammals were believed to be from the consumption of infected birds. Recent findings, however, have suggested that the aquatic mammals may become infected from contact with their contaminated water habitat.
The research group is working to answer research questions such as what is the environment's role in presence, transmission, and persistence of AIVs? What does the detection of infectious low pathogenicity AIV in water mean for HPAI risk?
Method development to recover infectious avian influenza virus from the aquatic environment
Since 2018, the USGS has been working to optimize a method to recover infectious AIV from the aquatic environment. Improvements to methods included avoiding AIV inactivation during collection and processing of water samples and inhibitor removal for molecular detection of viral RNA. A series of spiked laboratory experiments were conducted to optimize recovery of infectious AIV. Several water matrices, filtering techniques, pump speeds, elution solutions, and concentration methods were tested.
Infectious virus is potentially transmitted between birds, poultry, mammals, and even humans. Past research indicates avian influenza virus can persist for extended periods of time in the environment. However, detection of virus in the environment has mostly focused on molecular detection of AIV, which does not indicate transmission potential of the virus.
Infectious highly pathogenic avian influenza virus recovered from Iowa wetlands
In response to the 2021-2023 HPAI H5 outbreak, an AIV environmental outbreak
response study was conducted using a One Health approach. An optimized method was used to temporally sample (April and May 2022) and analyze (culture and molecular methods) surface water from five water bodies (four wetlands and one lake used as a comparison location) in areas near confirmed HPAI detections in wild bird or poultry operations.
Examining avian influenza virus isolate subtypes isolated from both waterbodies and wild birds
During the fall 2022 migration of wild birds, recovery and persistence of infectious HPAI and LPAI and viral RNA were examined in wetlands in Alaska, Minnesota, and Iowa. During the spring 2023 migration, four wetlands in Louisiana were sampled to continue research on recovery and persistence of AIV from the environment. Several wetlands were sampled after wild birds departed to assess persistence of AIV in the environment. The study includes comparison of the genetic sequences of viruses isolated from wetland water to genetic sequences for wild bird origin viruses, where they are available.
Research Questions:
- Is 2.3.4.4b HPAI A(H5N1) virus or other AIV isolated from wetlands in different latitudes?
- If virus (LPAI or HPAI) is isolated from a wetland during time periods when migratory waterfowl are present, is there evidence that the virus persist in the environment after migratory waterfowl depart? Are there environmental factors that contribute to persistence (e.g., water temperature)?
- Do the genome constellations of viruses isolated from wetlands match those isolated from wild birds congregating in the wetland?
Can water level manipulation on refuges inactivate avian influenza virus?
Recent HPAI outbreaks have highlighted the difficulty in controlling the spread of AIV transmission among wild birds. The environment, specifically water, is a probable reservoir of infectious avian influenza virus with potential for transmission. Several chemical agents are used to disinfect/inactivate AIV, however, implementation in the field is limited to poultry production facilities and equipment. Less is known how to safely and effectively inactivate AIV in the environment, for instance, in National Wildlife Refuge System wetlands and pools. Recently, strategies have been suggested to limit spread and exposure to AIV on affected wetlands. One management action suggested is the manipulation of water levels to facilitate inactivation of the virus, as lowering water levels generally enables increased water temperature and ultraviolet light penetration.
Surveillance of avian influenza virus in National Park Waterbodies
Many park units have experienced avian mortalities due to HPAI including endangered California condors. One possible source of transmission is HPAI virus contaminated water by fecal material of infected birds. This study will assess the importance of waterbodies in maintaining avian influenza virus within natural and constructed ecosystems. Selected park units include waterbodies which are important migratory and breeding habitat for birds and are also frequently used for human drinking water sources and recreation. This project will assist park units in preserving wildlife and natural resources while managing safety of visitors, recreators, and surrounding tribal communities.
A collaborative project 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.
Highly pathogenic avian influenza (HPAI) continues to circulate internationally, causing record numbers of deaths in both wild birds and domestic poultry. In 2022, HPAI was recognized as the cause of death for both terrestrial and aquatic mammals. Initially the fatal infections in aquatic mammals were believed to be from the consumption of infected birds. Recent findings, however, have suggested that the aquatic mammals may become infected from contact with their contaminated water habitat.
The research group is working to answer research questions such as what is the environment's role in presence, transmission, and persistence of AIVs? What does the detection of infectious low pathogenicity AIV in water mean for HPAI risk?
Method development to recover infectious avian influenza virus from the aquatic environment
Since 2018, the USGS has been working to optimize a method to recover infectious AIV from the aquatic environment. Improvements to methods included avoiding AIV inactivation during collection and processing of water samples and inhibitor removal for molecular detection of viral RNA. A series of spiked laboratory experiments were conducted to optimize recovery of infectious AIV. Several water matrices, filtering techniques, pump speeds, elution solutions, and concentration methods were tested.
Infectious virus is potentially transmitted between birds, poultry, mammals, and even humans. Past research indicates avian influenza virus can persist for extended periods of time in the environment. However, detection of virus in the environment has mostly focused on molecular detection of AIV, which does not indicate transmission potential of the virus.
Infectious highly pathogenic avian influenza virus recovered from Iowa wetlands
In response to the 2021-2023 HPAI H5 outbreak, an AIV environmental outbreak
response study was conducted using a One Health approach. An optimized method was used to temporally sample (April and May 2022) and analyze (culture and molecular methods) surface water from five water bodies (four wetlands and one lake used as a comparison location) in areas near confirmed HPAI detections in wild bird or poultry operations.
Examining avian influenza virus isolate subtypes isolated from both waterbodies and wild birds
During the fall 2022 migration of wild birds, recovery and persistence of infectious HPAI and LPAI and viral RNA were examined in wetlands in Alaska, Minnesota, and Iowa. During the spring 2023 migration, four wetlands in Louisiana were sampled to continue research on recovery and persistence of AIV from the environment. Several wetlands were sampled after wild birds departed to assess persistence of AIV in the environment. The study includes comparison of the genetic sequences of viruses isolated from wetland water to genetic sequences for wild bird origin viruses, where they are available.
Research Questions:
- Is 2.3.4.4b HPAI A(H5N1) virus or other AIV isolated from wetlands in different latitudes?
- If virus (LPAI or HPAI) is isolated from a wetland during time periods when migratory waterfowl are present, is there evidence that the virus persist in the environment after migratory waterfowl depart? Are there environmental factors that contribute to persistence (e.g., water temperature)?
- Do the genome constellations of viruses isolated from wetlands match those isolated from wild birds congregating in the wetland?
Can water level manipulation on refuges inactivate avian influenza virus?
Recent HPAI outbreaks have highlighted the difficulty in controlling the spread of AIV transmission among wild birds. The environment, specifically water, is a probable reservoir of infectious avian influenza virus with potential for transmission. Several chemical agents are used to disinfect/inactivate AIV, however, implementation in the field is limited to poultry production facilities and equipment. Less is known how to safely and effectively inactivate AIV in the environment, for instance, in National Wildlife Refuge System wetlands and pools. Recently, strategies have been suggested to limit spread and exposure to AIV on affected wetlands. One management action suggested is the manipulation of water levels to facilitate inactivation of the virus, as lowering water levels generally enables increased water temperature and ultraviolet light penetration.
Surveillance of avian influenza virus in National Park Waterbodies
Many park units have experienced avian mortalities due to HPAI including endangered California condors. One possible source of transmission is HPAI virus contaminated water by fecal material of infected birds. This study will assess the importance of waterbodies in maintaining avian influenza virus within natural and constructed ecosystems. Selected park units include waterbodies which are important migratory and breeding habitat for birds and are also frequently used for human drinking water sources and recreation. This project will assist park units in preserving wildlife and natural resources while managing safety of visitors, recreators, and surrounding tribal communities.