45k birds checked for avian influenza in US

A massive surveillance program monitors virus spread in wild birds from coast to coast.

440 people died worldwide from avian influenza H5N1, bird flu, since 2003. Responding to this outbreak, the United States formed a committee that monitors avian influenza in wild birds. Tom Deliberto is a leader of this collaboration of federal and state agencies.

Check the project on ResearchGate for current numbers of tested and infected birds.

ResearchGate: Why is it necessary to monitor wild bird populations to track the spread of avian influenza?

Tom Deliberto: Wild birds are the natural reservoirs for all avian influenza viruses. Avian influenza viruses evolve in these natural hosts. These primarily consist of ducks, geese, swans, shorebirds, gulls, terns, and other birds generally associated with water and aquatic environments. For the most part the viruses are harmless and don’t infect poultry or people. But the thing about influenza viruses is that they have the ability to change and mix up genetic material among themselves and create a whole new virus. Sometimes, when that happens, it allows a virus to infect poultry. Once in poultry, these viruses can evolve to be what we call highly pathogenic and cause severe mortality. We conduct the surveillance to find out what’s going on with these native viruses. But once in a while, one of these highly pathogenic viruses evolves.

RG: This was the case in Asia several years ago and this is also what your current project is about. Can you tell us more?

Deliberto: A virus that evolved from the Asian H5N1 combined with another virus and created this whole new set of viruses we call – caution, very technical term – H5 Avian influenza clade This sort of nomenclature is a way for virologists to say how these viruses evolved. In 2014, this new virus, H5N8, really took foothold and started spreading in Asia. It probably emerged in the Korean peninsula, then it spread to Japan in the spring of 2014. In the summer we saw it in the breeding grounds in the Russian far East, up in Siberia. In the fall we saw it back down South in China. It then enters Europe and, finally, in later fall, we see it cross over the Pacific and into the North American continent.

Once this new virus got here it starts acting almost like an invasive species. It’s got this whole new environment. It’s got all of these wild ducks. It has all this poultry that’s unfamiliar with this virus. This causes the virus to spread and reproduce in the winter of 2014/5. Thanks to our surveillance program we were able to tell that it spread along the entire Pacific flyway, right down to California and Utah, including Idaho, Nevada, Oregon and Washington. We could track how the virus moved in wild birds. In spring 2015, we see it made a jump into the Central and Mississippi flyways of the North American continent.


RG: Why was this spread problematic?

Deliberto: This virus has never seen our North American bird species and it’s never interacted with the strains of influenza circulating in these species. Remember I said that these viruses can mix their genetic material up if they infect a common host? What we believe happened is that relatively quickly H5N8 mixed with a harmless North American N2 virus. This created a new virus called H5N2. This virus turns out to be highly pathogenic. The H5N2 virus moved out of the Pacific flyway in fall or winter 2015 and into the Central part of the US and started infecting poultry. That’s when we started having many poultry outbreaks in the US. That’s a little history of what’s happened in the last year.

RG: How many birds were affected?

Deliberto: In wild birds to date, as of end of May 2016, we had a total of 100 cases in wild birds from July 2014 to June 2016 and 65 of those have been confirmed positive through virus isolation and/or genetic sequencing.

RG: That doesn’t sound like much. What damage did this do?

Deliberto: The damage was done when the virus left the wild birds populations and went into poultry. H5N2 had a genetic sequence that indicated that it was a high-path virus, meaning it would infect poultry and likely spread easily. This virus in particular killed a lot of domestic chickens and turkeys.

The cost to control that whole outbreak was close to 1 billion USD. That included not only the loss of chickens and turkeys, but also the cost of responding to calls that poultry were either sick or exposed to the high path-virus. All of those birds had to be killed as well to try to stop the spread. In total, almost 50 million chickens and turkeys were killed. This was really devastating to poultry farmers in affected areas.

These, however, were only the immediate costs of losing the chickens. It doesn’t tell the full story. There are also the costs of downstream effects on trade and cost of agricultural products. What happens internationally, under the World Organisation for Animal Health’s regulations, is that countries can refuse to buy poultry from affected areas. Many countries shut down trade with us. Economy-wide losses are estimated at 3.3 billion USD based on the official Congressional Research Service report.

In addition, because so many chickens were infected and had to be killed, the wholesale price of eggs more than doubled in June 2015 from 1.20 USD to 2.50 USD per dozen. That put a lot of pressure on the consumer as well.

Disease biologist Todd Felix releasing mallard. Credit: U.S. Fish and Wildlife Service
Disease biologist Todd Felix releasing mallard. Credit: U.S. Fish and Wildlife Service

RG: How do you track the outbreak and spread of avian influenza? 

Deliberto: Our efforts are led by the Interagency Steering Committee for Surveillance for HPAI in Wild Birds.  This committee is comprised of experts from United States Department of Agriculture (USDA) Animal and Plant Health Inspection Service (APHIS), the Department of the Interior’s US Geological Survey and US Fish and Wildlife Service, the US Department of Health and Human Services’ Centers for Disease Control and Prevention (CDC) and States’ Departments of Natural Resources represented by the National Flyway Council and the Association of Fish and Wildlife Agencies.

The Steering Committee’s history dates back to 2006, when the Asian H5N1 virus emerged as a global pathogen out of Asia. Our charge is to coordinate all the surveillance and laboratory testing for influenza in wild birds. This is a big charge because it goes from Alaska to Florida, from Maine to Hawaii and even the US Territories. This very large surveillance network takes a collaborative approach. We all use very similar sampling and testing protocols to try and assimilate all data that is collected and understand what patterns there are, develop risk assessments for poultry and if necessary for human health and safety as well.

RG: What does this look like on the ground?

Deliberto: We test wild birds in primarily four ways. We go out during the hunting season when hunters go and shoot waterfowl. That’s where we meet them and ask whether we can swab their birds. We use what looks like a normal cotton swab with a long handle. We sample the cloaca of the animal by rubbing the swab inside on the mucosal lining. We also swab the inside of the oral cavity. We take these swabs, put them in a tube with media – a liquid that preserves the virus and helps it to stay alive. Then we take the tubes and ship them to the diagnostic lab. That’s the main way we get most of our samples.

We also go out into the field for testing with researchers who conduct bird-banding activities. Here the live birds are caught with nets. In this case we sample the live bird, swab it, band it and release it. Another way to get data is mortality surveillance. When we know wild birds are sick or die, we try to go out and sample those birds. We use the same sampling techniques. Finally, we also sample the droppings of birds on the ground.

Since July 2015, we’ve tested 45,455 birds in total.  Beginning this July through next June, we will sample another 30,000-35,000 wild birds.

If there are presumptive positive test results we send them to our National Veterinary Services Laboratory in Ames, Iowa. They confirm whether it’s high path, or a virus of no concern. This information is made available to the public on the USDA website and flows into the posts in the project on ResearchGate. The public can go and track our surveillance efforts and see how many birds we’ve tested in each state. We update that every week. They can see what the prevalence of the wild birds we find viruses in and you can follow the chart for that. We also have a table where we list all high path findings and post that as well.

Avian influenza sampling. Credit: USDA Wildlife Services
Avian influenza sampling. Credit: USDA Wildlife Services

RG: What do you do to stop viruses from spreading?

Deliberto: Preventing the spread of avian influenza viruses in the wild bird reservoirs and the natural environment is currently not possible. However, we can take precautions to minimize the risks for farms to become infected with a virus, and to minimize the risks of the virus spreading if a farm becomes infected.  For example, we encourage producers to prevent wild birds and other wildlife from coming into direct contact with their poultry, as well as wild bird fecal material and secretions from being accidentally transported on boots, equipment, and food to their birds. When a high path virus is detected on a farm, State Agricultural Agencies implement a quarantine zone around the farm, preventing the movement of poultry out of the area.  On-farm biosecurity measures are also critical for not only preventing a farm from becoming infected, but also in preventing a high path virus from leaving an infected farm.

RG: How do you test whether a virus is also dangerous for humans?

Deliberto: If our colleagues in USDA’s Veterinary Services Program and States’ Departments of Agriculture get indication that there is a positive case, they check how likely the virus is to spread in mammals and humans by working with Departments of Health and the CDC. They do that by taking a sample and incubating it in chicken eggs. If a virus grows and rapidly kills the embryos in the eggs, that tells them it’s likely highly pathogenic. They can then remove the material from the egg and take that isolate and conduct whole genome sequencing to determine its genetic sequence. The nice thing – if there is a nice thing about avian influenza – is that, unlike other more complex organisms such as humans and animals, avian influenza viruses are pretty simple structures that only have eight strands of RNA, which code for at least 11 proteins. It’s relatively easy to sequence these genes, especially with the technology we have now. Once you have the sequence, we can compare it to influenza types that are known to have previously infected humans and evaluate the chance of the one at hand being infectious to people as well.

RG: What’s the likelihood of the current virus being contagious in humans?

Deliberto: The high-path viruses H5N2 and H5N8 did not show any particular indication as of yet that they are capable of infecting humans. It really depends on the genetic make-up of the virus. In this case, the viruses’ genetic sequences are different than what we’ve seen in other viruses that have infected mammals. These viruses can mix, however. That’s why it’s important we keep looking and conducting our surveillance because we need to continually monitor what these viruses are evolving into. We don’t want to be blindsided if viruses evolve to infect poultry or people.

Feature image: Anna Martin on flickr