Testing Guidelines for HPAI H5N1

Highly pathogenic avian influenza (HPAI), particularly subtype H5N1, is the current focus of surveillance in the U.S. and has been detected in dairy cattle, felines (domestic and wild), poultry, wild birds, and a variety of other mammals. Humans may also be infected, particularly those who work with infected animals, but currently infection in people has not been severe.

As a level 2 National Animal Health Laboratory Network (NAHLN) facility, our laboratory works closely with state and federal agencies (Illinois Department of Ag, NAHLN, and National Veterinary Services Lab -NSVL) to help address the spread of HPAI by offering testing. Ours is the only lab in Illinois authorized to perform HPAI testing. In 2024, our lab tested 1,027 samples from within and outside the state.

In December 2024 and January 2025, we performed 440+ tests as part of surveillance of flocks identified within the zone of an outbreak. Through our Zoological Pathology Program (ZPP) based in the Chicago area, we also provide HPAI testing for several zoos and federal wildlife agencies.

Acceptable Avian Sample Types

Although we offer a variety of acceptable sample types for birds, optimal tests vary according to species/group. Below is a brief description of the proper sample types validated by NAHLN for testing.

• Gallinaceous poultry: Oropharyngeal swabs
• Domestic waterfowl: Cloacal swabs
• Wild waterfowl: Cloacal and oropharyngeal swab
• Wild or captive bird: Cloacal swab
• Any avian species: Respiratory, enteric, and/or reproductive tissue samples (collect and submit tissues separately by system)

Acceptable Sample Types for Cats and Other Mammals

Dogs and cats can become infected, particularly from the consumption of infected animals, uncooked poultry, eggs, beef, and unpasteurized milk. Cats are particularly susceptible and may show acute respiratory or neurologic signs.

If cats are showing neurological signs, it is recommended that the cat be tested for rabies before testing for H5N1. For cats with respiratory signs but no evidence of exposure, it is recommended to rule out other respiratory diseases before requesting HPAI testing.

Proper sample types for mammals are described below.

• Antemortem: Nasal swab or urine
• Postmortem: Brain swab/brain tissue (for neurologic signs); Lung (for respiratory signs)
• Tissue samples (if multiple tissues are collected, separate by system)

Note: Fecal samples have very little value for Influenza testing.

Acceptable Swabs for Collection

Please use synthetic or semi-synthetic swabs (rayon, nylon, polyester) with plastic handles. AVOID cotton or calcium alginate swabs with wooden handles; these swabs have been shown to inactivate virus and inhibit PCR.

Bovine Milk Samples

In addition, we provide HPAI testing of bovine milk samples. We currently offer testing for lactating dairy cows (individual) for interstate movement, for fairs and exhibitions, and those cattle displaying clinical signs (requires a Foreign Animal Disease Investigation Number). See our post on submitting samples for bovine milk testing.

If a non-negative (virus detected) result is obtained, the samples are forwarded to NVSL for confirmation, and the sample is declared positive. Confirmatory results can take several days depending on the workload at NVSL during peak/outbreak times.

Additional Information

• CDC: https://www.cdc.gov/bird-flu/
• Illinois Department of Agriculture: https://agr.illinois.gov/animals/animalhealth/highly-pathogenic-avian-influenza.html
• Illinois Department of District Wildlife Biologists: https://wildlifeillinois.org/idnr-district-wildlife-biologist/
• Illinois Department of Public Health: https://dph.illinois.gov/topics-services/diseases-and-conditions/respiratory-disease/diseases/influenza/h5n1.html
• USDA
  • General response: https://www.aphis.usda.gov/labs/nahln/response-guidance
  • Livestock: HPAI in Livestock | Animal and Plant Health Inspection Service (usda.gov)
  • Mammals: HPAI Detections in Mammals (usda.gov)