#19,340
Today we've a dispatch, published yesterday in the CDC's EID Journal, which describes the findings of HPAI H5N1 in a cat and a rat from an Illinois farm which experienced a bird flu outbreak in March of 2025.
While it is not exactly `news' that both species are susceptible to H5N1 infection (see below), our understanding of how HPAI may spread among peridomestic animals on farms remains limited.EID Journal Dispatch: Seroprevalence of Influenza A(H5N1) Virus in Domestic Cats at Epicenter of Dairy Cattle Outbreaks, California, USA, 2024–2026
MMWR: Serologic Evidence of HPAI A(H5N1) Virus Infection in a Veterinary Professional Exposed to an Infected Domestic Cat
Experimental Infection of Rats with Influenza A Viruses: Implications for Murine Rodents in Influenza A Virus Ecology
Emer. Microbe & Inf.: HPAI Virus H5N1 clade 2.3.4.4b in Wild Rats in Egypt during 2023
According to this report, a farmer brought the remains of six animals (a chicken, a turkey, a goose, 2 Guinea fowl, and a rat (Rattus norvegicus)) to his veterinarian after nearly all of his chickens died. Suspecting H5N1, the vet sent the remains to the University of Missouri Veterinary Medical Diagnostic Laboratory (VMDL; Columbia, MO, USA) for postmortem examination.
Four days after the first report, the local vet visited the farm and collected the remains of a 13-year-old cat and a second feral rat from the farm. They were then sent to the University of Illinois Veterinary Diagnostic Laboratory (VDL) for necropsy and additional testing.VMDL ran a qRT-PCR on 1 chicken sample, which came back presumptive positive for H5, and forwarded tissue samples to NVSL in Ames, IA for confirmatory testing (which verified HPAIV H5N1 clade 2.3.4.4b virus).
According to this report, state and local authorities were notified, and the Illinois Department of Agriculture and USDA quarantined the farm and monitored it for 4 months.
Today's report is primarily an analysis of the extensive infection of both the cat and the rat submitted to VDL. Sadly, while the first rat underwent necropsy, it was never tested for H5N1, so all we have is a sample of one.
That said, this is a fascinating report that strongly suggests that an H5N1 farm outbreak should be viewed as a whole-premises event. Animals living around infected livestock - including cats and rats - may also be infected, and contribute to the evolution and further spread of the virus.This seems like it was a great opportunity to explore the potential spread of HPAI among peridomestic animals on an infected poultry farm. But there is no indication that any attempts were made to collect and test additional samples.
Another finding of this dispatch is that all 3 animal species tested (cat, rat, and chicken) carried the PB2 E627K mutation which is generally considered a mammalian adaptation. While not unheard of, reports of this mutation in birds are rare.
Since only 1 chicken was tested, we've no idea of the frequency of this mutation in the rest of the flock.
I've only posted the Abstract and some excerpts from the dispatch, so follow the link to read it in its entirety. I'll have a postscript after the break.
Detection of Highly Pathogenic Avian Influenza A(H5N1) Virus in Cat and Rats during Outbreak in Backyard Poultry, United States, 2025
Suzanna M. Storms, Jade Rathmann, Lynette Hemker, Miranda Vieson, and Leyi Wang
Abstract
In 2025, highly pathogenic avian influenza A(H5N1) virus was detected in a poultry flock in Illinois, USA. Quantitative reverse transcription PCR, sequencing, and histopathology on cat and rat samples from the farm showed multiple positive tissues and high sequence identity to an avian isolate. Small mammals might contribute to H5N1 transmission.
The Study
On March 12, 2025, a farmer in southern Illinois with a small backyard poultry flock brought remains of 6 animals to their primary veterinarian for a necropsy workup after acute illness and near-complete mortality (100/105 birds) of the flock. The farm, ≈2 miles from a 25,000-acre reservoir lake within the Mississippi Flyway, housed 4 turkeys (Meleagris gallopavo), 1 goose (Anser sp.), 20 Guinea fowl (Numida spp.), 80 chickens (Gallus gallus domesticus), 17 cattle, 15 cats, and 2 dogs. Because HPAI virus (HPAIV) was suspected, the 6 animals, a chicken, a turkey, a goose, 2 Guinea fowl, and a rat (Rattus norvegicus), were sent to the University of Missouri Veterinary Medical Diagnostic Laboratory (VMDL; Columbia, MO, USA) for postmortem examination.
VMDL collected and evaluated fresh and formalin-fixed tissues and performed influenza A virus (IAV) quantitative reverse transcription PCR (qRT-PCR) on 1 chicken sample, according to guidelines from the US Department of Agriculture (USDA) National Animal Health Laboratory Network (NAHLN; https://www.aphis.usda.gov/labs/nahln). The sample tested presumptive positive per NAHLN guidelines, and VDML subtyped it as H5 influenza. VDML then forwarded the sample to the National Veterinary Services Laboratories (NVSL; Ames, IA, USA) for confirmatory testing, which verified HPAIV H5N1 clade 2.3.4.4b virus.
Further PCR testing of the avian species for Mycoplasma gallisepticum, M. synoviae, and avian paramyxovirus were all negative. The necropsy findings reported hepatitis, pulmonary hemorrhage, and pulmonary edema in the poultry species and bronchopneumonia and meningoencephalitis in the rat. No additional testing was performed on the rat or other bird species.
Upon report of HPAIV on the farm, state and federal agencies were notified. The Illinois Department of Agriculture and USDA quarantined the farm and monitored it for 4 months.
On March 16, 2025, the primary veterinarian collected the remains of a 13-year-old domestic shorthaired cat and a second feral rat from the farm. In conjunction with Illinois Department of Agriculture and USDA, the cat and rat specimens were sent to the University of Illinois Veterinary Diagnostic Laboratory (VDL; Urbana, IL, USA) on March 19. VDL performed gross necropsy and collected fresh and formalin-fixed tissues. VDL screened lung tissues from the cat and rat for IAV by qRT-PCR, following NAHLN guidelines. The cat lung tested presumptive positive (cycle threshold [Ct] value 21.2), subtyped as H5; NVSL confirmed H5N1 clade 2.3.4.4b virus. The rat lung tissue was negative upon initial screening, but NVSL conducted follow-up testing on tracheal swab samples, which were H5N1-positive.
Quantitative reverse transcription PCR results from HPAIV A(H5N1) in cat and rats during outbreak in backyard poultry, United States, 2025. Specimens obtained from a cat (A) and a rat (B) found dead on farm where the outbreak occurred were confirmed to be positive for H5N1 clade 2.3.4.4b, genotype D1.1 virus.
(SNIP)
Conclusions
We describe a strain of H5N1 that resulted in high mortality in a poultry flock and fatal illness in small mammals on a backyard farm in Illinois, USA. Our results show that extensive systemic H5N1 virus spread occurred in both cat and rat tissues after natural infection. Rat nasal turbinates and trachea preferentially expressed α2,3-linked sialic acid receptors relative to lung, likely explaining the lower Ct values in upper respiratory tissues and presence of bacterial bronchopneumonia, potentially leading to increased viral shedding (10).
Cat feces and urine have previously been shown to harbor H5N1 virus (11,12), which our results corroborate. Rats have previously been reported to harbor HPAIV in agricultural settings and have been detected in the current epizootic (13,14). Detection of HPAIV in rat urine and kidney tissue suggests that rodent urine could be a potential transmission medium and warrants further investigation.
Rats reside on many farms, can predate birds, and might serve as an intermediate step between infected avian species and susceptible mammalian hosts (15). That coexistence is particularly threatening for commercial poultry and swine confinement farms, which frequently harbor rodent populations despite strict biosecurity efforts. A limitation of our study was that no virus isolation was performed on tissues or urine due to biosafety constraints.
Although cats have been shown to participate in HPAIV transmission, our findings indicate that further investigation is needed to clarify the role of rodents. This study raises awareness of small mammals at the wildlife–livestock interface and highlights the potential role of rats in influenza transmission to commercial livestock production.
Dr. Storms is a veterinarian-scientist at Texas A&M Veterinary Medical Diagnostic Laboratory, College Station, Texas, USA. Her research interests center around influenza virus transmission and diagnostic development.
Our continued reliance on passive surveillance severely limits our ability to understand the ecology and threat of HPAI H5.
Because of the limited sampling on this farm, we can't say whether the PB2-E627K mutation was `fixed' in the poultry flock, or whether rat-to-rat transmission occurred, or whether any other species in and around the farm were affected.
And we saw last year, in Nature: Lengthy Delays in H5N1 Genome Submissions to GISAID, the median delay in submitting sequences to GISAID was 7 months (228 days), with some countries taking nearly 2 years.
Despite the mounting evidence of the susceptibility of cattle, sheep, goats, pigs, cats, and rats (ad nauseam) to HPAI H5 - and the continued calls from the scientific community for more aggressive surveillance and testing of livestock (see here, here, here, here, and here) - the world seems content to don blinders and hope for the best.
