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Epidemiology of Fish and Wildlife Diseases
Birds

Samples of genetics and genomics research from the USGS Ecosystems Mission Area about the epidemiology of avian diseases.

A female Northern Pintail marked with a solar-powered satellite transmitter. Photo credit: Dr. Tetsuo Shimada, Izunuma-Uchinuma Environmental Foundation Common shellduck. Photo credit: Eric C. Palm, USGS

Avian influenza. Photo Credit: Cynthia Goldsmith, Centers for Disease Control and Prevention

Bird in flight. Photo credit: Don Becker, courtesy the USGS National Wildlife Health Center Avian Influenza Photo Gallery Bronzed cowbird. Photo credit: Wes Bailey, Fort Hood Natural Resources Management Branch
Avian Influenza: Genetic Assessment
(Pearce)
Avian Influenza: Rapid Detection
(Takekawa, Hill)
Avian Influenza: Spread from Eurasia into North America (Hall) Avian Influenza: Understanding Transmission, Spread, and Potential Risk (Hall) Genetics of Avian Immunity: Climate Change (Hahn, Fleischer)
Using mist nets to catch passerine birds for avian influenza virus testing. Photo credit: Hon Ip, USGS

Using mist nets to catch passerine birds for avian influenza virus testing. Photo credit: Hon Ip, USGS

Birds affected by avian cholera. Photo credit: USGS A male northern pintail duck. Photo credit: John Pearce, USGS  
Molecular Techniques in Pathogen Detection and Quantification (Ip) Viral Genetics--Nucleotide Sequences and Viruses that Effect Wildlife (Ip) Wild Bird Avian Cholera (Blehert) Avian Influenza Virus Genes in Alaska (Pearce)  

Genetic Assessment of Avian Influenza
Capture of Northern Pintails at Lake Izunuma-Uchinuma, Japan
Capture of Northern Pintails at Lake Izunuma-Uchinuma, Japan
A female Northern Pintail marked with a solar-powered satellite transmitter. Photo credit: Dr. Tetsuo Shimada, Izunuma-Uchinuma Environmental Foundation
A female Northern Pintail marked with a solar-powered satellite transmitter. Photo credit: Dr. Tetsuo Shimada, Izunuma-Uchinuma Environmental Foundation
Locations in Japan where Northern Pintail Ducks where captured and radiomarked.
Locations in Japan where Northern Pintail Ducks where captured and radiomarked.

Evaluating exchange of avian-borne pathogens between Asia and North America by migratory birds requires an understanding of patterns of contact among birds from each continent. Biologists at the Alaska Science Center (USGS) are comparing neutral nuclear and mitochondrial genetic similarities between Asian and North American pintails to evaluate the degree of reproductive isolation between these populations, and are assessing transcontinental transmission of avian influenza by comparing genetic similarities of low pathogenic (non-H5N1) virus strains in pintails wintering in California to those from Japan. Collaborators include the Laboratory of Biodiversity Science (University of Tokyo), USGS National Wildlife Health Center, Western Ecological Research Center, and the U.S. Fish and Wildlife Service.

Read about genetic analyses of avian influenza in Northern Pintails at following Progress Report:

Movements of Northern Pintail Ducks and Whooper Swans Marked with Satellite Transmitters in Japan

For more information contact John M. Pearce, Alaska Science Center.

 

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Rapid Molecular Techniques for Avian Influenza Detection in Wild Birds
Common shellduck (Tadorna tadorna) carrying a satellite transmitter as part of avian influenza surveillance efforts in Egypt. Photo credit: Eric C. Palm, USGS
Common shellduck (Tadorna tadorna) carrying a satellite transmitter as part of avian influenza surveillance efforts in Egypt. Photo credit: Eric C. Palm, USGS

Efficient methods for the detection of avian influenza (AI), particularly those subtypes that are lethal to humans, poultry and wild birds, are necessary for the prevention of outbreaks. Rapid detection methods also represent a breakthrough for research that seeks to unravel the role of wild birds in the spread of the virus. The ability to determine the host status of wild birds at the time of field sampling, makes it possible to deploy satellite transmitters to track the movement of the host. This information would enhance understanding of whether wild birds can act as vectors for highly pathogenic subtypes such as the lethal subtype, H5N1. Recently developed molecular methods, such as real-time reverse transcriptase polymerase chain reaction (rRT-PCR) offers one of the most accurate and sensitive techniques for diagnosis of AI in the laboratory. Most rRT-PCR assays are capable of characterizing the AI subtype, even at the low titer levels shed by wild birds. However, maintenance of wet PCR reagents at a constant cold temperature has prohibited the use of rRT-PCR in field settings. Our current work aims to validate the use of various portable rRT-PCR units that use freeze-dried reagents, eliminating the need for refrigeration in the field. Such technologies would lend themselves to use in remote locations throughout Eurasia where avian influenza H5N1 has become entrenched.

For more information view Satellite Tracking Migratory Birds: Determining Migratory Connectivity and Routes for Distinct Populations and contact John Y. Takekawa and Nichola J. Hill, Western Ecological Research Center.

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Examining Virus Isolates from Birds in the North Atlantic for Eurasian Strains of Avian Influenza
Avian influenza. Photo Credit: Cynthia Goldsmith, Centers for Disease Control and Prevention
Avian influenza. Photo Credit: Cynthia Goldsmith, Centers for Disease Control and Prevention

Avian influenza is thought to be spread in part, by migrating wild birds. The risks of introduction of HPAI H5N1 into North America are generally believed to be greatest in Alaska. However, many birds migrate from Eurasia into the North Atlantic where they mingle with migrants from North America and could transmit the virus to birds that would be able to carry the virus to the U.S. We will examine virus isolates from birds in the North Atlantic for genetic evidence of Eurasian strains of AI being introduced into these populations. These data will provide information on the risks of HPAI being introduced into N. America by this route.

For more information contact Jeffrey S. Hall, National Wildlife Health Center.

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Understanding the Dynamics of Avian Influenza: Transmission, Spread, and Potential Risk
Bird in flight. Photo credit: Don Becker, courtesy the USGS National Wildlife Health Center Avian Influenza Photo Gallery
Bird in flight. Photo credit: Don Becker, courtesy the USGS National Wildlife Health Center Avian Influenza Photo Gallery

A highly pathogenic strain of avian influenza (HPAI) virus subtype H5N1 emerged in Asia and is circulating in Asia, Europe, and Africa causing mortality in domestic birds, wild waterfowl, and causing human deaths. Numerous avian and mammalian species have been shown to be susceptible to infection and mortality in the field and laboratory, but little is known about the full spectrum of species susceptible to the virus, transmission among wildlife species, or factors that determine immunity or resistance, and whether long-term carriers may exist for some species. This task will examine these dynamics in a selected variety of wildlife species, using both low and high pathogenicity AI viruses, to better understand the potential effect H5N1 HPAI may have on North American wildlife, and the dynamics of infection that will enable us to better understand its transmission, spread, and potential risk to domestic fowl and humans should it be introduced to the U.S. We also study the within-host population genetics of influenza viruses to shed light on recombination, reassortment, virus variation and mutation of these viruses.

For more information contact Jeffrey S. Hall, National Wildlife Health Center.

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Genetics of Avian Immunity: Resilience in the Face of Emerging Zoonoses and Climate Change
Bronzed cowbird. Photo credit: Wes Bailey, Fort Hood Natural Resources Management Branch
Bronzed cowbird. Photo credit: Wes Bailey, Fort Hood Natural Resources Management Branch

To improve ecologists’ ability to predict disease epidemics in wildlife and human populations, it is fundamental to understand the ecological conditions that have favored the evolution of strong immune systems. Avian species are effective model species for studying the evolution of immunity in a variety of habitats and ecosystem. One important region of the genome responsible for immune system responses is the major histocompatibility complex (Mhc), a focal area for much biomedical research. Wildlife research offers promising insights into design, structure and function of Mhc proteins, and we are examining the role of increased Mhc gene sequence diversity of in a group of parasitic birds that have had unusual exposure to diverse parasites, in comparison to related, 'control' non-parasitic species. We hypothesize that these parasitic birds, the New World cowbirds, and related icterid blackbirds, are a good model group for documenting the evolution of increased diversity of the MHC as a result of exposure to increasing diversity of environmental parasites. We are applying classical PCR and next generation sequencing methods to obtain multilocus genotypes for individuals of two or more cowbird species and two or more related non-parasitic icterid species.

Collaboration of Caldwell Hahn, Patuxent Wildlife Research Center, and Robert C. Fleischer, Smithsonian Institution.

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Molecular Techniques in the Detection and Quantification of Pathogens
Swabbing sea gulls for H5N1 virus detection. Photo credit: Hon Ip, USGS
Swabbing sea gulls for H5N1 virus detection. Photo credit: Hon Ip, USGS

Rapid advances in the detection of genetic material (both DNA and RNA) from viral pathogens have greatly aided in the identification and the study of viruses in wild animals.  The Diagnostic Virology Laboratory in the National Wildlife Health Center has worked, in collaboration with the USDA National Veterinary Services Laboratory and the USDA Southeast Poultry Research Laboratory, to improve the real time RT-PCR test for the detection of the H7 subtype avian influenza viruses in North American wild birds.  The previous test was developed to detect H7 viruses from domestic sources and failed to detect H7 viruses from wild birds. The new test can detect viruses from both groups with equal efficacy and has since been deployed to network laboratories.  Molecular methods are also amenable to high throughput strategies.  As part of the national surveillance program, a sustained capacity of over 1,000 samples can be tested for avian influenza per day has been established.  Molecular testing can also help in situations when viable samples are difficult or impossible to obtain.  In a study performed by collaborators at the University of Kansas and the USDA, it was not possible to send samples from Chinese tree birds containing viable viruses to the US. Instead samples were preserved in alcohol, which preserved the genetic material and had the added advantage of allowing for room temperature storage and shipping.  Using molecular techniques, we were able to determine that tree birds in China may be significant reservoirs of avian influenza viruses.  This is contrary to the current paradigm of passerine birds having few viruses.  Moreover, the study found that the majority of the tree birds that were positive were migratory species, raising the possibility of these birds being able to transmit the highly pathogenic H5N1 virus during migration.

For more information, please contact Hon S. Ip at the National Wildlife Health Center in Madison, Wisconsin.

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Viral Genetics--What Can Nucleotide Sequences Tell Us about Viruses that Infect Wildlife?
Using mist nets to catch passerine birds for avian influenza virust testing. Photo credit: Hon Ip, USGS
Using mist nets to catch passerine birds for avian influenza virus testing. Photo credit: Hon Ip, USGS

The Diagnostic Virology Laboratory at the National Wildlife Health Center works on the identification and characterization of emerging and established viruses that affect wildlife from around the world.  Besides the use of viral phylogenetic analysis to validate the basis of the nation avian influenza surveillance program (see USGS National Wildlife Health Center Avian Influenza), we use the genetics of viruses to understand their relationship to those from historic outbreaks.  For example, large-scale sequencing and phylogenetic studies have been conducted in the evolution of Newcastle Disease Virus (NDV) in collaboration with the US Department of Agriculture (USDA), and on the worldwide distribution of avian poxviruses with the Szent István University in Hungary.  Such studies allow us to put into perspective the viruses isolated from new mortality events to inform resource managers whether they are dealing with resurgence of an existing disease or confronting the introduction of a novel virus.  Moreover, detailed sequence analysis coupled with experimental studies can identify mutations that are associated with virulence or host-range expansion.

For more information, please contact Hon S. Ip at the National Wildlife Health Center in Madison, Wisconsin.

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Interspecific Exchange Of Avian Influenza Virus Genes In Alaska: The Influence Of Trans-Hemispheric Migratory Tendency And Breeding Ground Sympatry
A male northern pintail duck. Photo credit: John Pearce, USGS
Photo: A male northern pintail duck.
Photo credit: John Pearce, USGS

Avian cholera, an infectious disease caused by the bacterium Pasteurella multocida, kills thousands of North American wild waterfowl annually.  Pasteurella multocida serotype 1 isolates cultured during a laboratory challenge study of mallard ducks (Anas platyrhynchos) and collected from wild birds and environmental samples during avian cholera outbreaks were characterized using amplified fragment length polymorphism (AFLP) analysis, a whole-genome DNA fingerprinting technique.  Comparison of the AFLP profiles of 53 isolates from the laboratory challenge demonstrated that P. multocida underwent genetic changes during a three month period. 

Analysis of 120 P. multocida serotype 1 isolates collected from wild birds and environmental samples revealed that isolates were distinguishable from one another based upon regional and temporal genetic characteristics.  Thus, AFLP analysis had the ability to distinguish P. multocida isolates of the same serotype by detecting spatiotemporal genetic changes and provides a tool to advance the study of avian cholera epidemiology.  Further application of AFLP technology to the examination of wild bird avian cholera outbreaks may facilitate more effective management of this disease by providing the potential to investigate correlations between virulence and P. multocida genotypes, to identify affiliations between bird species and bacterial genotypes, and to elucidate the role of specific bird species in disease transmission. Abstract: http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2010.04908.x/abstract

For more information contact John Pearce, Alaska Science Center.

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Wild Bird Avian Cholera
Distribution of P. multocida serotype 1 isolates cultured from wild birds and environmental samples collected in Central California. Isolates are represented on the map according to their collection location using dendrogram branch designations from figure 3a. Collection sites are indicated with triangles
Distribution of P. multocida serotype 1 isolates cultured from wild birds and environmental samples collected in Central California.  Isolates are represented on the map according to their collection location using dendrogram branch designations from figure 3a.  Collection sites are indicated with triangles. Larger view
Principal components analysis of P. multocida serotype 1 isolates cultured from wild birds and environmental samples. Each isolate is designated according to its collection location and the cluster encompassing 49 of the 61 Central California P. multocida isolates is circled
Principal components analysis of P. multocida serotype 1 isolates cultured from wild birds and environmental samples.  Each isolate is designated according to its collection location and the cluster encompassing 49 of the 61 Central California P. multocida isolates is circled. Larger view
Birds affected by avian cholera. Photo credit: USGS
Birds affected by avian cholera. Photo credit: USGS

Avian cholera, an infectious disease caused by the bacterium Pasteurella multocida, kills thousands of North American wild waterfowl annually.  Pasteurella multocida serotype 1 isolates cultured during a laboratory challenge study of mallard ducks (Anas platyrhynchos) and collected from wild birds and environmental samples during avian cholera outbreaks were characterized using amplified fragment length polymorphism (AFLP) analysis, a whole-genome DNA fingerprinting technique.  Comparison of the AFLP profiles of 53 isolates from the laboratory challenge demonstrated that P. multocida underwent genetic changes during a three month period. 

Analysis of 120 P. multocida serotype 1 isolates collected from wild birds and environmental samples revealed that isolates were distinguishable from one another based upon regional and temporal genetic characteristics.  Thus, AFLP analysis had the ability to distinguish P. multocida isolates of the same serotype by detecting spatiotemporal genetic changes and provides a tool to advance the study of avian cholera epidemiology.  Further application of AFLP technology to the examination of wild bird avian cholera outbreaks may facilitate more effective management of this disease by providing the potential to investigate correlations between virulence and P. multocida genotypes, to identify affiliations between bird species and bacterial genotypes, and to elucidate the role of specific bird species in disease transmission.

For more information contact David S. Blehert, National Wildlife Health Center.

 

 

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Featured Publications

Northern pintail. Photo credit: USFWSRamey, A. M., C. R. Ely, J. A. Schmutz, J. M. Pearce, and D. J. Heard. 2012. Molecular detection of hematozoa infections in Tundra Swans relative to migration patterns and ecological conditions at breeding grounds. PLoS One, 7(9): e45789.

Pearce, J. M., A. B. Reeves, A. M. Ramey, J. W. Hupp, H. S. Ip, M. Bertram, M. J. Petrula, B. D. Scotton, K. A. Trust, B. Meixell, and J. A. Runstadler. 2011. Interspecific exchange of avian influenza virus genes in Alaska: The influence of trans-hemispheric migratory tendency and breeding ground sympatry. Molecular Ecology 20:1015 - 1025.

Reeves, A. B, J. M. Pearce, A. M. Ramey, B. W. Meixell, and J. A. Runstadler. 2011. Interspecies transmission and limited persistence of low pathogenic avian influenza genomes among Alaska dabbling ducks. Infection, Genetics, and Evolution 11:2004-2010.

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