H5N1 detected in a cat and rats during a backyard poultry outbreak in Illinois

A highly pathogenic avian influenza A(H5N1) outbreak that killed almost an entire backyard poultry flock in Illinois was accompanied by fatal infections in a domestic cat and rats living on the same premises. Genomic analysis showed that the viruses from the chicken, cat and rat were closely related, raising further questions about the role of small mammals at the poultry–mammal interface.

The outbreak occurred in March 2025 on a small farm in southern Illinois, around two miles from a large reservoir along the Mississippi Flyway. The premises housed 105 birds as well as cattle, 15 cats and two dogs. Within a short period, 100 of the 105 birds died. Testing confirmed highly pathogenic H5N1 clade 2.3.4.4b.

Virus found throughout the cat and rat

A 13-year-old domestic shorthair cat and a feral rat were subsequently found dead on the farm. H5N1 was detected in both animals. Follow-up PCR testing showed particularly extensive systemic infection: all 12 tissues tested from the cat were positive, while 11 of 15 tissues from the rat contained influenza A viral RNA. The highest viral loads in both species were found in the brain.

Nasal and tracheal samples were also positive in both animals. Viral RNA was detected in the cat’s faeces and in the rat’s urine, kidney and several other tissues. The detection of H5N1 in rat urine is notable because it raises the possibility that contaminated urine could contribute to environmental transmission, although the study did not demonstrate that this route actually occurred.

Neurological infection confirmed

Histopathology showed bronchointerstitial pneumonia and nonsuppurative meningoencephalitis in the cat. Influenza viral antigen was detected in airway epithelial cells and strongly in neurons and glial cells of the brain. The rat also had encephalitis, myocarditis and viral antigen in neurons, although severe bacterial bronchopneumonia was also present.

These findings confirm that the infections were not incidental detections: the virus had disseminated systemically and invaded the central nervous system.

Poultry, cat and rat viruses were almost identical

Whole-genome sequencing showed that the viruses from the chicken, cat and rat clustered closely together and belonged to genotype D1.1. All three carried the PB2 E627K mutation, a change associated with improved replication of influenza viruses in mammalian hosts. Two additional amino acid substitutions were found in the cat and rat viruses but not in the chicken isolate.

The genetic similarity is consistent with local cross-species spillover during the outbreak, although the precise transmission route cannot be reconstructed from the available data.

Rats may represent an overlooked link in H5N1 ecology

The study is particularly important for farm biosecurity. Rats are common around poultry and livestock facilities, prey on birds and have frequent contact with contaminated feed, bedding and carcasses. The authors suggest that rodents could potentially act as an intermediate host between infected birds and other susceptible mammals. That possibility is especially relevant for intensive poultry and pig production, where rodent populations may persist despite control measures.

The study does not demonstrate sustained rat-to-rat transmission or prove that rodents are an important reservoir of H5N1. But it does show that naturally infected rats can develop widespread infection and potentially shed viral material.

The findings add another small-mammal component to the expanding ecology of clade 2.3.4.4b H5N1 and reinforce the need to include cats and rodents in investigations of poultry outbreaks where unexplained mammalian illness or mortality occurs.

Study: Storms SM, Rathmann J, Hemker L, Vieson M, Wang L. Detection of Highly Pathogenic Avian Influenza A(H5N1) Virus in Cat and Rats during Outbreak in Backyard Poultry, United States, 2025. Emerging Infectious Diseases. 2026;32(10). DOI: 10.3201/eid3210.260418.