Avian influenza outbreak: Moving from testing birds to testing barns

Farm Forum

Highly pathogenic avian influenza (HPAI) continues to hold its grip on the area’s poultry producers. The Upper Midwest is the worldwide epicenter of the outbreak, with an infected flock count approaching 200. What presumably began as sporadic infections from migrating birds has turned into a regional outbreak, raising the possibility that airborne virus may be responsible for some of the spread.

As such, poultry producers are on high alert. Those finding increased death losses in their flocks then face a critical question: is HPAI the cause? The answer means the difference between business as usual and a quarantine – with euthanasia of all birds on site. Animal health labs such as the South Dakota Animal Disease Research and Diagnostic Laboratory at SDSU are providing these answers for area poultry producers.

The virus detection process begins with collection of swabs from the birds’ throats or vents, which are placed in a test tube preserving the viability of the virus. Detection in any bird is sufficient to call a farm infected, so not every bird has to be sampled. Swabs from several birds can be combined into one test.

Real-time Polymerase Chain Reaction (PCR) is the test used for these samples. RNA (nucleic acid) is chemically extracted from viruses or other material in the sample. The nucleic acid can be considered a unique fingerprint for every strain of virus. This extraction is then treated such that the distinguishing part of this “fingerprint” is duplicated many times. If it all works, an indicator dye attached to the nucleic acid segment will “light up,” alerting scientists that the specific virus was indeed in the sample. For HPAI, these procedures are run step-by-step: generic influenza RNA is detected first, then the specific H5 gene for the HPAI strain of interest.

Enough time has lapsed since the outbreaks that many previously-infected operations can now restock their barns. This could be as soon as three weeks following barn cleaning and disinfection. The last thing these producers want to do is to put birds back into a barn that still contains HPAI virus. For these operations, virus detection now has shifted from the birds to the barn.

PCR testing is used for these environmental samples as well. Compost piles and barns, including walls, fans, floors, feeders, and waterers are tested. A negative (no virus) result provides evidence that cleanup procedures have worked.

However, as is often the case, things aren’t always as easy as they sound. Effectively sampling a 50,000 square foot barn is challenging. PCR tests are not inexpensive, so testing an unlimited number of samples is not feasible. Sampling procedures need to be thorough and representative of the facility.

On the other hand, since PCR tests only detect RNA, a positive test in a barn may not necessarily mean it came from viable HPAI virus. The next step is to try to grow the HPAI virus in a process called virus isolation. A reliable virus isolation test requires the virus to stay alive from sampling time to the time it’s tested. In addition, virus isolation can take a long time: potentially 10 or 14 days before a test can be called negative.

SDSU’s ADRDL has been inundated with HPAI testing requests for the past two months; the test count is well over several thousand now. The lab has gained a reputation for fast, accurate PCR results. As a result, neighboring states have begun to depend on our South Dakota lab. Because of a lack of biosafety level 3 space, however, our lab is not able to perform virus isolation, or to do any further research on the virus. Our role is limited to that of our efficient, accurate PCR testing.

As avian influenza shifts from outbreak to recovery, environmental testing will become more important. In addition, environmental testing of wild bird habitats and areas around poultry barns will help us understand the virus’ spread. The ADRDL is proving its worth as our poultry producers enter recovery mode. Taking care of our state’s animal industries, however, means ensuring that our lab has all the space and tools needed to safely and quickly respond not only to animal health disasters like this one, but also to the next one looming in the future.

Russ Daly, DVM, is the Extension Veterinarian at South Dakota State University. He can be reached via e-mail at or at 605-688-5171.