# H5N1 avian influenza found in a cat and rats on an Illinois farm after a backyard flock die-off

- Published: 2026-11-06 06:31 UTC
- Section: Life & Health › Biology & biochemistry
- Tags: highly pathogenic avian influenza, H5N1 clade 2.3.4.4b, H5N1 in cats, H5N1 in rats, spillover to mammals, PB2 E627K mutation, qRT-PCR, Illinois backyard flock, whole-genome sequencing
- URL: https://realtech.media/news/rt-f98773cf7f3125f6e401d0f3_h5n1_avian_influenza/

**After 100 of 105 backyard birds died in Illinois in 2025, H5N1 was confirmed in a cat and a rat from the same farm. All three animal species carried the PB2 E627K mutation.**

![H5N1 avian influenza found in a cat and rats on an Illinois farm after a backyard flock die-off](https://sgzwpqqelzmajkcubgkl.supabase.co/storage/v1/object/public/rt-media/2026/11/9b644f14dbfe5cd9.jpg)
*Daniel Ramirez from Honolulu, USA, Wikimedia Commons, CC BY 2.0*

In March 2025, highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b killed 100 of 105 birds in a backyard flock on a farm in southern Illinois, USA. The virus was then found in a domestic cat and rats on the same premises, according to a report published on wwwnc.cdc.gov [1]. The farm lies about 2 miles from a 25,000-acre reservoir lake within the Mississippi Flyway [1].

The flock consisted of 80 chickens, 20 Guinea fowl, 4 turkeys and 1 goose. The farm also kept 17 cattle, 15 cats and 2 dogs. On March 12 the farmer brought the remains of six animals to a veterinarian: a chicken, a turkey, a goose, two Guinea fowl and a rat. The samples went to the University of Missouri Veterinary Medical Diagnostic Laboratory. A chicken sample tested presumptive positive by qRT-PCR, and the National Veterinary Services Laboratories confirmed H5N1 clade 2.3.4.4b [1]. Tests for Mycoplasma gallisepticum, M. synoviae and avian paramyxovirus were negative. The Illinois Department of Agriculture and USDA quarantined the farm and monitored it for four months.

## Infection in the cat and rats

On March 16 the veterinarian collected the remains of a 13-year-old domestic shorthaired cat and a second, feral rat. The University of Illinois Veterinary Diagnostic Laboratory received them on March 19. The cat lung was presumptive positive (Ct 21.2). The rat lung was negative at first screening, but tracheal swabs tested at the national laboratory were H5N1-positive [1]. Necropsy showed hepatitis, pulmonary hemorrhage and edema in the poultry, and bronchopneumonia and meningoencephalitis in the first rat.

Follow-up qRT-PCR found influenza A virus in all 12 cat tissue samples (Ct 10.9–31.1) and in 11 of 15 rat samples (Ct 17.1–39.4). Brain tissue held the highest viral load: Ct 10.9 in the cat and 17.1 in the rat. Tracheal and nasal swabs from both animals were positive (Ct 22.1–29.5). Kidney tissue was positive in both (cat Ct 20.9, rat Ct 34.6), as was rat urine (Ct 32.0). Cat feces gave Ct 28.6, while no nucleic acid was detected in rat feces [1].

## Sequencing results

Whole-genome sequencing of three cat samples (brain, heart, nasal swab) and one rat brain sample on a MiSeq platform returned complete sequences for all 8 segments. Phylogenetic analysis placed the chicken, rat and cat strains together with other avian and mammalian viruses. All three species carried the polymerase basic 2 E627K mutation, which is associated with mammalian adaptation. All cat samples shared identical consensus sequences [1].

Leyi Wang, corresponding author from the University of Illinois laboratory, said the cat and rat were most likely infected through contact with dead or dying birds. He said the nearly identical sequences point to a shared source, likely spillover from the poultry. The authors note that small mammals might contribute to H5N1 transmission.

## Sources

1. [wwwnc.cdc.gov](https://wwwnc.cdc.gov/eid/article/32/10/26-0418_article)
2. [EurekAlert](https://www.eurekalert.org/news-releases/1150613)

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Source: RealTech, realtech.media — https://realtech.media/news/rt-f98773cf7f3125f6e401d0f3_h5n1_avian_influenza/