Detection of highly pathogenic avian influenza A (H5N1) clad 2.3.4.4b genotype D1.2 virus in swine after experimental inoculation

Authors: SEGER, HANNAH - Oak Ridge Institute For Science And Education (ORISE); Baker, Amy; Devries, Alexandra; Anderson, Tavis; Markin, Alexey; CAMPOS, ALESSANDRA - Oak Ridge Institute For Science And Education (ORISE); Caetano Trindade, Bruno; Vincent, Marissa; CIACCI ZANELLA, GIOVANA - Oak Ridge Institute For Science And Education (ORISE); TORCHETTI, MIA - Animal And Plant Health Inspection Service (APHIS); LANTZ, KRISTINA - Animal And Plant Health Inspection Service (APHIS); Arruda, Bailey

Submitted to: Emerging Infectious Diseases
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/22/2026
Publication Date: 7/15/2026
Citation: Seger, H., Baker, A.L., Buckley, A.C., Anderson, T.K., Markin, A., Campos, A., Caetano Trindade, B., Vincent, M.L., Ciacci Zanella, G., Torchetti, M.K., Lantz, K., Arruda, B.L. 2026. Detection of highly pathogenic avian influenza A (H5N1) clad 2.3.4.4b genotype D1.2 virus in swine after experimental inoculation. Emerging Infectious Diseases. https://doi.org/10.3201/eid3208.251765.
DOI: https://doi.org/10.3201/eid3208.251765

Interpretive Summary: Highly pathogenic avian influenza (HPAI) H5NX clade 2.3.4.4b continues to circulate globally and infect mammals. Continued circulation has resulted in numerous different HPAI strains that pose an unknown risk to livestock including pigs. We assessed the risk of one HPAI strain in pigs. We found that this HPAI strain could replicate in the upper respiratory tract of pigs without overt clinical signs. The strain could also be detected in the lower respiratory tract and digestive, lymphatic, musculoskeletal, and nervous system and was isolated from skeletal muscle of pigs indicating the virus could move from the respiratory system to different tissue types. After more than 4 weeks, the virus could still be detected in the brain of an animal with lesions consistent with a virus and within the upper respiratory tract of two animals. These findings support systemic distribution and protracted infection of HPAI H5N1 clade 2.3.4.4b in swine, raising implications for food safety, surveillance, and reassortment.

Technical Abstract: Highly pathogenic avian influenza (HPAI) H5NX clade 2.3.4.4b continues to circulate globally, causing outbreaks in avian and mammal populations. Continued circulation and re-introduction of fully Eurasian lineage viruses into North America and reassortment with North American low pathogenic avian influenza A viruses has resulted in numerous genotypes within clade 2.3.4.4b including D1.2. This genotype was responsible for the first detection of HPAI H5N1 2.3.4.4b in backyard pigs in the United States, despite the absence of known mammalian adaptation markers. An isolate from a peafowl from the same site as the backyard pigs was intranasally inoculated into pigs to assess pathogenicity and cellular tropism. Viral RNA was detected in nasal swabs from all inoculated animals for multiple days. At 5 days post-inoculation (DPI), the virus was detected by PCR in the respiratory, digestive, lymphatic and nervous systems and virus was isolated from meat juice. Immunohistochemistry at 5 DPI demonstrated viral antigen in neurons, leukocytes outside the respiratory tract, skeletal myocytes and adjacent axon, fila olfactoria, and respiratory and olfactory epithelium. At 35 DPI, viral antigen and RNA were detected in the brain of an animal with lesions consistent with a viral etiology and viral antigen was detected in the ethmoid of two animals. Despite consistent viral detection in nasal secretions and systemic spread, neutralizing antibody titers were low at 35 DPI. These findings support systemic distribution and protracted infection of HPAI H5N1 clade 2.3.4.4b genotype D1.2 in swine, raising implications for food safety, surveillance, and reassortment.