---
title: "HPAI A(H5N1) Detected in Cat and Rats During Backyard Poultry Outbreak, Illinois 2025"
id: "cdc-emerging-infectious-diseases-journal-2-detection-of-highly-pathogenic-avian-influenza-a-h5n1-virus-in-cat-and-rats"
canonical_url: "https://medichelpline.com/clinical-feed/cdc-emerging-infectious-diseases-journal-2-detection-of-highly-pathogenic-avian-influenza-a-h5n1-virus-in-cat-and-rats"
content_type: "clinical_feed_article"
specialty: "Infectious Disease"
source_name: "CDC Emerging Infectious Diseases Journal"
source_url: "https://wwwnc.cdc.gov/eid/article/32/10/26-0418_article"
published_at: "2026-09-18T04:00:00.000Z"
evidence_level: "Agency Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# HPAI A(H5N1) Detected in Cat and Rats During Backyard Poultry Outbreak, Illinois 2025
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/cdc-emerging-infectious-diseases-journal-2-detection-of-highly-pathogenic-avian-influenza-a-h5n1-virus-in-cat-and-rats
- **Specialty:** [Infectious Disease](https://medichelpline.com/clinical-feed/infectious-disease.md)
- **Primary Source:** CDC Emerging Infectious Diseases Journal
- **Source URL:** [Original Journal Publication](https://wwwnc.cdc.gov/eid/article/32/10/26-0418_article)
- **Published At:** 2026-09-18T04:00:00.000Z
- **Evidence Rating:** Agency Feed
## Executive GIST (TL;DR)
- In 2025, an outbreak of highly pathogenic avian influenza (**HPAI H5N1**, clade 2.3.4.4b) occurred in a backyard poultry flock in southern Illinois, with near-complete flock mortality (100/105 birds). - Initial testing of a chicken was presumptive positive by **qRT-PCR** and confirmed as HPAI H5N1 by National Veterinary Services Laboratories (NVSL). - Domestic and wild mammals on the premises were subsequently tested: a domestic cat and two rats were found dead and sampled. One rat initially screened negative in lung but later had tracheal swabs positive for H5N1; the cat lung screened presumptive positive (Ct 21.2) and was confirmed by NVSL. - Follow-up qRT-PCR on multiple tissues showed widespread viral RNA: all 12 cat tissues tested positive (Ct 10.9–31.1) and 11/15 rat tissues were positive (Ct 17.1–39.4), with highest viral loads in brain tissue. - Nasal and tracheal swabs from both mammals were IAV-positive; viral RNA was also detected in kidney and urine samples and in cat feces. - Whole-genome sequencing produced complete 8-segment genomes from multiple cat tissues and a rat brain; sequences clustered with avian and mammalian HPAIV and shared high sequence identity with the chicken isolate from the farm. - All three animal species’ viruses contained the **polymerase basic 2 E627K** mutation associated with mammalian adaptation; additional amino acid changes (neuraminidase G392D, nucleoprotein K372E) were present in cat and rat but not in chicken. - Histopathology and immunohistochemistry documented bronchointerstitial pneumonia and nonsuppurative meningoencephalitis in the cat and encephalitic lesions in the rat, with influenza immunoreactivity in brain and lung tissues. - State and federal agencies quarantined and monitored the farm for 4 months; the findings suggest small mammals may play a role in H5N1 transmission on affected premises. - Details such as specific management measures beyond quarantine, broader surveillance outcomes, and any human exposures or clinical cases were not reported in the source article.
## Clinical Analysis & Structured Key Points
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[EID Journal](https://wwwnc.cdc.gov/eid/) 2. [Volume 32](https://wwwnc.cdc.gov/eid/early-release) 3. [Early Release](https://wwwnc.cdc.gov/eid/early-release#issue-1346) 4. [Main Article](https://wwwnc.cdc.gov/eid/article/32/10/26-0418_article) * [Facebook](https://www.facebook.com/sharer/sharer.php?u=%2Feid%2Farticle%2F32%2F10%2F26-0418_article "Share to Facebook") * [Twitter](http://twitter.com/share?url=%2Feid%2Farticle%2F32%2F10%2F26-0418_article&text= "Share to Twitter") * [LinkedIn](https://www.linkedin.com/shareArticle?url=%2Feid%2Farticle%2F32%2F10%2F26-0418_article&title= "Share to LinkedIn") * [Syndicate](https://tools.cdc.gov/medialibrary/index.aspx#/sharecontent//eid/article/32/10/26-0418_article "Embed this Page") [ Emerging Infectious Disease journal ISSN: 1080-6059 ](https://wwwnc.cdc.gov/eid/) _Disclaimer: Early release articles are not considered as final versions. Any changes will be reflected in the online version in the month the article is officially released._ #### Volume 32, Number 10—October 2026 ##### _Dispatch_ ### Detection of Highly Pathogenic Avian Influenza A(H5N1) Virus in Cat and Rats during Outbreak in Backyard Poultry, United States, 2025 On This Page [The Study](https://wwwnc.cdc.gov/eid/article/32/10/26-0418_article) * * * [Conclusions](https://wwwnc.cdc.gov/eid/article/32/10/26-0418_article) * * * [Suggested Citation](https://wwwnc.cdc.gov/eid/article/32/10/26-0418_article) Figures [Figure 1](https://wwwnc.cdc.gov/eid/article/32/10/26-0418-f1) * * * [Figure 2](https://wwwnc.cdc.gov/eid/article/32/10/26-0418-f2) * * * [Figure 3](https://wwwnc.cdc.gov/eid/article/32/10/26-0418-f3) Downloads [Appendix ](https://wwwnc.cdc.gov/eid/article/32/10/26-0418-app1.pdf) * * * [RIS [TXT - 2 KB] ](https://wwwnc.cdc.gov/eid/article/32/10/26-0418.ris) Article Metrics [Metric Details](https://wwwnc.cdc.gov/eid/article/32/10/26-0418_article) Related Articles [The Enduring Influence of Nancy J. Cox (1948–2026)](https://wwwnc.cdc.gov/eid/article/32/10/26-0830_article) * * * [Divergent HPAI H5N1 Clade 2.3.4.4b Virus, Brazil](https://wwwnc.cdc.gov/eid/article/32/10/26-0723_article) * * * [HPAI Clade 2.3.4.4b Virus Infection in Alpacas](https://wwwnc.cdc.gov/eid/article/32/10/26-0491_article) * * * [More articles on Influenza](https://wwwnc.cdc.gov/eid/spotlight/influenza) Suzanna M. Storms, Jade Rathmann, Lynette Hemker, Miranda Vieson, and Leyi Wang[![Comments to Author](https://wwwnc.cdc.gov/eid/content/images/icon/email.gif)](https://wwwnc.cdc.gov/eid/article/32/10/26-0418_article#comment) Author affiliation: Texas A&M Veterinary Medical Diagnostic Laboratory, College Station, Texas, USA (S.M. Storms); University of Illinois College of Veterinary Medicine, Urbana, Illinois, USA (S.M. Storms, M. Vieson, L. Wang); Greenville Veterinary Clinic, Ltd, Greenville, Illinois, USA (J. Rathmann, L. Hemker) [Suggested citation for this article](https://wwwnc.cdc.gov/eid/article/32/10/26-0418_article#suggestedcitation) ### 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 current panzootic of highly pathogenic avian influenza (HPAI) A(H5N1) clade 2.3.4.4b virus emerged in Europe in 2020 and by 2022 had spread throughout Europe, Africa, and North America ([_1_](https://wwwnc.cdc.gov/eid/article/32/10/26-0418_article#r1 "1")–[ _4_](https://wwwnc.cdc.gov/eid/article/32/10/26-0418_article#r4 "4")). Trans-Atlantic introduction into North America was first documented in December 2021 and has since persisted in wild and domestic birds, has been detected in dairy cattle, and has been reported sporadically in other mammals ([_5_](https://wwwnc.cdc.gov/eid/article/32/10/26-0418_article#r5 "5")). Waterfowl have played an equal role to seabirds in virus spread, which is concerning given their higher likelihood of overlapping ranges with poultry farms ([_2_](https://wwwnc.cdc.gov/eid/article/32/10/26-0418_article#r2 "2"),[_6_](https://wwwnc.cdc.gov/eid/article/32/10/26-0418_article#r6 "6")). We describe an HPAI H5N1 outbreak in a backyard poultry flock in Illinois, USA, with subsequent spillover into domestic and wild mammals on the premises. ### 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; [External Link](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. Figure 1 ![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. Graphic shows HPAIV-positive tissues and corresponding Ct values. A\) For the cat, Ct values are shown for mesenteric and peripheral lymph nodes; urine, stomach content, and small intestine were not tested. B\) For the rat, Ct values for peripheral lymph node only are shown; no mesenteric lymph node was tested. Also, rat feces, bone marrow, and testis were tested, but HPAIV was not detected in those organs. Figure created with BioRender \(https://www.biorender.com\). Ct, cycle threshold; HPAIV, highly pathogenic avian influenza virus.](https://wwwnc.cdc.gov/eid/images/26-0418-F1-tn.jpg) [Figure 1](https://wwwnc.cdc.gov/eid/article/32/10/26-0418-f1 "Figure 1"). 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)... In addition, we performed follow-up IAV qRT-PCR testing on 12 tissue samples from the cat and 15 tissue samples from the rat and considered Ct values [External Link](https://www.illumina.com)). We used the Galaxy platform ([_7_](https://wwwnc.cdc.gov/eid/article/32/10/26-0418_article#r7 "7")) for sequence assembly. All samples returned complete sequences for 8 segments (GenBank accession nos. PX687012–27) ([Appendix](https://wwwnc.cdc.gov/eid/article/32/10/26-0418-app1.pdf) Table). In addition, we included sequence data of the HPAIV H5N1 strain 25-009367-001 (GenBank accession nos. PV616546–53) from the chicken sample submitted by VDML to NVSL in the analysis. Phylogenetic tree analysis revealed that the chicken, rat, and cat strains clustered together with other avian and mammal HPAIV ([Figure 2](https://wwwnc.cdc.gov/eid/article/32/10/26-0418-f2); [Appendix](https://wwwnc.cdc.gov/eid/article/32/10/26-0418-app1.pdf) Figures 1–8). All 3 animal species from the outbreak contained the polymerase basic 2 E627K mutation that is associated with mammalian adaptation ([_8_](https://wwwnc.cdc.gov/eid/article/32/10/26-0418_article#r8 "8")). All cat samples shared identical consensus sequences. We found 2 amino acid mutations, neuraminidase G392D and nucleoprotein K372E, in the cat and rat samples but not in the IAV strain from the chicken. In addition, we noted 1 synonymous polymerase basic 2 C1552T mutation in the rat strain that we did not see in cat and chicken strains. The genotype of the outbreak virus was D1.1 ([_9_](https://wwwnc.cdc.gov/eid/article/32/10/26-0418_article#r9 "9")) ([Appendix](https://wwwnc.cdc.gov/eid/article/32/10/26-0418-app1.pdf)). Figure 3 ![Histopathology and immunohistochemistry of lesions in a cat and rat infected with highly pathogenic avian influenza A\(H5N1\) virus during outbreak in backyard poultry, United States, 2025. The cat and rat were found dead on a farm in Illinois where the outbreak occurred. A–C\) Cat lung \(A\) and brain \(B, C\) tissue samples showing substantial histopathology lesions likely related to HPAIV infection. A\) Hematoxylin and eosin \(H&E\) stain of lung tissue shows bronchointerstitial pneumonia; original magnification ×10. Inset shows immunohistochemical \(IHC\) stain of lung demonstrates light influenza immunoreactivity in distal airway epithelium \(arrow\). Scale bar indicates 20 µm. B\) H&E stain of brain tissue shows nonsuppurative meningoencephalitis \(arrows\). Scale bar indicates 100 µm. C\) IHC stain of brain shows influenza immunoreactivity in cerebrocortical glial cells and neurons. Scale bar indicates 100 µm. D–F\) Rat lung \(D\) and brain \(E, F\) tissue samples. D\) H&E stain of rat lung tissue shows background alveolitis. Original magnification ×20. E\) H&E stain of brain tissue shows nonsuppurative periventricular encephalitis \(arrows\). Scale bar indicates 50 µm. F\) IHC of brain tissue
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