Avian Influenza A Virus in Wild Birds and Poultry: Etiology, Epidemiology, Clinical Signs, Pathology, Diagnostics, Treatment, and Control

Etiology

Avian influenza A virus (AIV) is an enveloped, negative-sense, single-stranded RNA virus belonging to the family Orthomyxoviridae, genus Influenzavirus A [1]. The viral genome comprises eight segmented RNA segments encoding at least 10 proteins, including the surface glycoproteins hemagglutinin (HA) and neuraminidase (NA) [1]. Subtype classification is based on the antigenic properties of HA (H1 through H16) and NA (N1 through N9) [1, 2]. Highly pathogenic avian influenza (HPAI) viruses are defined by the presence of a multibasic cleavage site (MBCS) in the HA protein, which allows systemic replication in poultry [1, 3]. Low pathogenic avian influenza (LPAI) viruses possess a monobasic cleavage site and typically cause mild or subclinical infections in gallinaceous birds [3]. The molecular basis for the cleavage site motif involves the insertion of basic amino acids (arginine and lysine) at the HA0 cleavage site, rendering the protein susceptible to ubiquitous furin-like proteases [3]. This cleavage is essential for viral entry and fusion with host endosomal membranes [3]. The NA protein facilitates viral release from infected cells by cleaving sialic acid residues and can also recruit plasminogen to enhance HA cleavage in LPAI strains [3]. The internal proteins, including the polymerase basic 2 (PB2), polymerase basic 1 (PB1), polymerase acidic (PA), nucleoprotein (NP), matrix (M1 and M2), and nonstructural (NS1 and NS2) proteins, contribute to host range restriction and virulence [4, 5]. For example, the PB2 E627K mutation is a well-characterized mammalian adaptation marker that enhances viral replication at lower temperatures [5]. The NS1 protein acts as an interferon antagonist, modulating the host innate immune response [4]. Divergent immunometabolic landscapes between species, such as chickens and swan geese, have identified host restriction factors like SERPINF2 that limit AIV replication [4].

Epidemiology

Avian influenza A virus exhibits a complex epidemiological pattern involving wild aquatic birds as the primary natural reservoir [6, 1, 7]. Wild birds, particularly Anseriformes (ducks, geese, swans) and Charadriiformes (gulls, terns), maintain a diverse pool of LPAI viruses [6, 7, 8]. These viruses are transmitted via the fecal-oral route through contaminated water and environmental surfaces [6, 8]. Migratory flyways facilitate the global dissemination of AIV, linking continents and introducing novel subtypes into naive populations [6, 9, 7]. The emergence of HPAI viruses, particularly those of the H5Nx lineage (clade 2.3.4.4b), has resulted in panzootic events affecting wild birds and poultry worldwide [10, 11, 12, 1, 13]. The 2021-2025 H5Nx clade 2.3.4.4b outbreak in North America demonstrated extensive spillover into wild bird populations, including raptors, seabirds, and waterfowl, with subsequent incursions into commercial and backyard poultry [10, 12, 13]. In Europe, mortality surveillance in wild birds from 2016 to 2022 provided critical data on the spatial and temporal distribution of HPAI, revealing seasonal peaks associated with waterfowl aggregation and migration [8]. Similarly, surveillance in South Korea from 2019 to 2025 identified a high prevalence of H5N1 and H5N6 subtypes in migratory wild birds, underscoring the role of East Asian flyways in viral maintenance [7]. In Egypt, molecular surveillance combined with predictive risk modeling identified environmental and anthropogenic factors associated with AIV circulation in wild birds, including proximity to poultry farms and water bodies [6]. The global spread of H7 subtype AIV has been driven by both wild bird migration and poultry trade networks, as demonstrated by phylogeographic analyses [9]. Genotype diversity within the H5N1 clade 2.3.4.4b has been documented in Pennsylvania poultry, with multiple genotypes co-circulating during a single outbreak season [12]. In Bulgaria, molecular characterization of H5N1 viruses during 2024-2025 revealed evidence of hidden circulation and the presence of zoonotic risk markers [14]. The panzootic H5 viruses have also acquired resistance to human head interface antibodies, indicating ongoing antigenic evolution [15]. Spatiotemporal analyses in Ireland from 1983 to 2024 demonstrated a shift in subtype dominance and host species involvement over time [16]. In Namibia, an H5N1 outbreak among common terns (Sterna hirundo) during 2025-2026 highlighted the vulnerability of seabird colonies to HPAI [11]. The global evolutionary landscape of H11 AIV has been characterized, with initial isolates identified in Xinjiang, China, expanding the known host range of this subtype [2]. H3 subtype AIVs have been isolated from wild birds and poultry in Eastern China, with evidence of reassortment and mammalian adaptation markers [17]. H3NX viruses in Guangdong province, China, from 2023 to 2025, were assessed for cross-species transmission potential [18]. H4N6 AIV was first isolated in Iran, providing molecular insights into the diversity of this subtype in the Middle East [19]. H1N1 AIV from wild birds in Shanghai, China, was characterized for its molecular features and genetic evolution [20]. The role of wild boars (Sus scrofa) as sentinels for AIV exposure has been investigated in Spain, with serologic and virologic evidence of H5N1 spillover risk [21]. Mechanistic modeling of HPAI transmission has identified critical gaps in cross-species transmission models, particularly regarding the interface between wild birds, poultry, and mammals [22]. Machine learning-based geospatial risk modeling has been applied to predict global AIV outbreak hotspots, integrating environmental, ecological, and anthropogenic variables [23]. High-resolution digital twin models of interacting livestock, wild birds, and human ecosystems have been developed to simulate multihost epidemic spread [24]. The 2024-2025 HPAI outbreak in the United States was examined using multimodal data approaches, including genomic, epidemiological, and environmental data [10].

Clinical Signs

Clinical manifestations of avian influenza A virus infection vary markedly depending on viral pathotype, host species, age, immune status, and concurrent infections [1]. In poultry, HPAI viruses cause severe systemic disease characterized by high morbidity and mortality [1, 13]. Clinical signs include depression, inappetence, decreased egg production, respiratory distress (coughing, sneezing, dyspnea), cyanosis of combs and wattles, edema of the head and neck, hemorrhagic lesions on shanks, and neurological signs such as ataxia, torticollis, and paralysis [1]. Sudden death without premonitory signs is common in highly susceptible species, particularly chickens and turkeys [1]. In contrast, LPAI viruses typically cause mild respiratory disease, decreased egg production, and increased susceptibility to secondary bacterial infections [1]. In wild birds, clinical signs are often absent in natural reservoir hosts such as dabbling ducks, which can shed virus asymptomatically [6, 7]. However, HPAI infection in certain wild bird species, including swans, geese, gulls, and raptors, can result in severe disease and mortality [11, 8]. Neurological signs, including head tremors, circling, and inability to fly, have been observed in HPAI-infected wild birds [11]. In ducks, experimental infection with HPAI H5N1 has been characterized using systems-level analyses integrating transcriptomic, proteomic, and phosphoproteomic data, revealing dysregulation of immune and metabolic pathways [25]. The immunometabolic response to AIV infection differs between chickens and swan geese, with the latter exhibiting a more robust interferon response and upregulation of restriction factors such as SERPINF2 [4].

Pathology

Gross pathological findings in HPAI-infected poultry include severe congestion and edema of the comb and wattles, petechial hemorrhages on serosal surfaces (particularly the proventriculus, gizzard, and heart), multifocal necrotic foci in the liver, spleen, and pancreas, and consolidation of the lungs [1]. Histopathological examination reveals necrotizing pancreatitis, myocarditis, encephalitis, and lymphocytic depletion in lymphoid organs [1]. The presence of viral antigen in endothelial cells and parenchymal tissues confirms systemic dissemination [1]. In ducks, HPAI infection induces a distinct immunometabolic response characterized by activation of interferon signaling pathways and metabolic reprogramming [25]. The HA cleavage site sequence and NA-mediated plasminogen recruitment synergize to enhance virulence in LPAI strains, providing a mechanism for pathotype switching [3]. In wild birds, pathological findings vary by species. In common terns, HPAI H5N1 infection resulted in severe necrotizing hepatitis, splenitis, and encephalitis [11]. In swans and geese, gross lesions included hemorrhagic enteritis and pulmonary edema [8].

Diagnostics

Diagnostic approaches for avian influenza A virus encompass virological, molecular, serological, and pathological methods [1, 26]. Sample types include oropharyngeal and cloacal swabs, tracheal and lung tissue, feces, and environmental samples (water, feces) [6, 8]. Virus isolation in embryonated chicken eggs or cell culture (e.g., MDCK cells) remains a gold standard for virus characterization [1]. Molecular diagnostics, particularly real-time reverse transcription polymerase chain reaction (RT-PCR), are the primary tools for rapid detection and subtyping [12, 14, 26]. RT-PCR assays targeting the matrix (M) gene provide pan-influenza A detection, while HA and NA subtype-specific assays enable differentiation [12, 14]. High-throughput sequencing technologies, including next-generation sequencing (NGS), are increasingly used for whole-genome sequencing and phylogenetic analysis [12, 14]. These methods allow for the identification of genetic markers associated with virulence, mammalian adaptation, and antiviral resistance [5, 14]. Serological diagnostics, including hemagglutination inhibition (HI) and neuraminidase inhibition (NI) assays, as well as commercial enzyme-linked immunosorbent assay (ELISA) kits, are used for surveillance and to differentiate infected from vaccinated animals (DIVA) [1, 27]. The development of DIVA vaccines, such as those using chimeric NA epitopes, enables serological differentiation between vaccinated and naturally infected birds [27]. External quality assessment programs have demonstrated that medical laboratories can efficiently detect animal influenza A viruses using molecular methods [26]. In the context of mixed-species holdings, molecular detection and subtype differentiation are critical for outbreak management. The use of CRISPR-based diagnostics for avian influenza represents an emerging technology with potential for field-deployable testing.

Treatment

Antiviral therapy for avian influenza A virus in poultry is not routinely recommended due to concerns about resistance development and the potential for masking clinical signs [1]. However, experimental studies have evaluated the efficacy of antiviral compounds in avian models. Baloxavir marboxil, a cap-dependent endonuclease inhibitor, demonstrated therapeutic efficacy against HPAI virus infection in a duck model, reducing viral shedding and mortality [28]. In ferrets infected with avian- or bovine-origin H5N1 virus, baloxavir alleviated severe disease and viremia [29]. These findings suggest that baloxavir may have a role in therapeutic intervention in outbreak settings, particularly in valuable genetic stocks or zoological collections [28, 29]. Supportive care, including fluid therapy, nutritional support, and management of secondary bacterial infections, may be considered in individual cases, but is impractical in commercial poultry operations [1]. The use of antiviral drugs in poultry is subject to regulatory restrictions and should be guided by veterinary oversight and antimicrobial stewardship principles.

Control

Control of avian influenza A virus in poultry and wild birds relies on a combination of biosecurity, surveillance, stamping out, and vaccination strategies [1, 13]. Biosecurity measures include preventing contact between domestic poultry and wild birds, implementing strict hygiene protocols (footbaths, dedicated clothing, equipment disinfection), controlling human and vehicle movements, and ensuring proper disposal of carcasses and manure [1]. Surveillance programs, both passive (reporting of sick or dead birds) and active (routine sampling of healthy birds), are essential for early detection and rapid response [6, 7, 8]. In wild birds, mortality surveillance and targeted sampling of migratory populations provide early warning of HPAI incursions [8]. Stamping out policies, involving the culling of infected and exposed flocks, are implemented in many countries to eradicate HPAI outbreaks [1]. Compensation schemes are often used to encourage timely reporting and compliance [1]. Vaccination is a complementary control tool, particularly in endemic settings or when stamping out is not feasible [1, 30]. Inactivated whole-virus vaccines, recombinant vector vaccines (e.g., fowlpox virus-vectored H5), and DIVA vaccines are available [1, 27]. Vaccination of wild king penguins against H5 HPAI resulted in a persistent immune response, suggesting that vaccination could be used to protect endangered wild bird populations [30]. The 2024 avian influenza vaccination campaign in Finland provided lessons on vaccine acceptance and logistical challenges [31]. Vaccination strategies must be carefully designed to avoid masking infection and to enable DIVA surveillance [27]. In the Republic of Korea, preventive responses to human avian influenza infection included enhanced surveillance, culling, and public health measures [32]. The World Organisation for Animal Health (WOAH) provides international standards for AIV surveillance, reporting, and trade restrictions. Control efforts must also consider the role of fomites, vectors, and environmental persistence in viral transmission. The integration of genomic epidemiology, risk modeling, and machine learning can inform targeted surveillance and control interventions [10, 23]. Cross-species transmission models should incorporate wild bird, poultry, and mammalian hosts to predict spillover events [22]. The development of high-resolution digital twins of interacting ecosystems can simulate outbreak scenarios and evaluate control strategies [24]. Ultimately, a One Health approach that integrates veterinary, environmental, and public health sectors is essential for effective AIV control [1, 13].

Diagnostic and Control Workflow

flowchart TD
    A[Clinical suspicion or surveillance sampling], > B[Sample collection: oropharyngeal/cloacal swabs, tissues, feces]
    B, > C[Laboratory testing]
    C, > D{Real-time RT-PCR for M gene}
    D, >|Positive| E[Subtype-specific RT-PCR: HA and NA]
    D, >|Negative| F[No AIV detected]
    E, > G{Pathotype determination}
    G, >|MBCS present| H[HPAI confirmed]
    G, >|Monobasic CS| I[LPAI confirmed]
    H, > J[Confirmatory virus isolation and sequencing]
    I, > J
    J, > K[Phylogenetic and genetic marker analysis]
    K, > L[Reporting to veterinary authorities]
    L, > M{Control strategy}
    M, >|Stamping out| N[Culling, disposal, disinfection]
    M, >|Vaccination| O[DIVA vaccine deployment and serological monitoring]
    M, >|Enhanced biosecurity| P[Quarantine, movement restrictions, hygiene]
    N, > Q[Surveillance for recrudescence]
    O, > Q
    P, > Q
    Q, >|Negative surveillance| R[Restore normal status]
    Q, >|Positive surveillance| S[Re-evaluate control measures]
    S, > M

References

[1] Brown IH. The Gordon Memorial Lecture: A paradigm shift in high pathogenicity avian influenza and perspectives for the future. Br Poult Sci. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42145115/

[2] Li Y, Yu Q, Jiang Q et al. Global evolutionary landscape of H11 avian influenza and initial isolates identified in Xinjiang, China. Emerg Microbes Infect. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41770598/

[3] Lee HM, Sutton K, Harvey W et al. Synergy between HA cleavage site sequence and NA-mediated plasminogen recruitment as a virulence mechanism for low-pathogenic avian influenza. mBio. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41744684/

[4] Li F, Ren C, Liu W et al. Divergent immunometabolic landscapes of chicken and swan goose identify SERPINF2 as a novel restriction factor for influenza A virus. Virol J. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42216012/

[5] Zhang X, Chen J, Ge Z et al. Genetic and biological characterization of a duck-origin clade 2.3.4.4b H5N6 avian influenza virus reveals partial mammalian adaptation. Vet Microbiol. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41946007/

[6] Nabil NM, Tawakol MM, Hagag N et al. Molecular surveillance and predictive risk modelling of avian influenza virus in wild birds in Egypt. J Gen Virol. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42301748/

[7] Lee JK, Kim MB, Kim SH et al. Surveillance of avian influenza viruses in migratory wild birds in South Korea, 2019-2025. J Vet Sci. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41947677/

[8] Blin L, Calenge C, Decors A et al. Surveillance of Highly Pathogenic Avian Influenza in Wild Birds in France, 2016-22: What Did We Learn from Mortality Data? J Wildl Dis. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41759901/

[9] Qu R, Yang L, Li S et al. Disentangling the drivers and host-mediated global spread of H7 influenza A virus. Nat Commun. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42091586/

[10] Sopko J, Han AR, Powers J et al. Multimodal Data Approaches for Examining the 2024-2025 Highly Pathogenic Avian Influenza Outbreak in the United States: Descriptive Study. JMIR Public Health Surveill. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42330167/

[11] Hamunyela E, Coetzee L, Marcacci M et al. Highly pathogenic avian influenza H5N1 virus outbreak among common terns (Sterna hirundo) in Namibia, 2025-2026. Vet Ital. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42237945/

[12] Tewari D, Sekhwal MK, Nicholson C et al. Genotype Diversity of Highly Pathogenic Avian Influenza H5N1 Clade 2.3.4.4b in Pennsylvania Poultry During Disease Outbreak from April 2022 to March 2023. Viruses. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42198705/

[13] Giacinti J, Signore A, Torchetti M et al. North American perspective on the highly pathogenic avian influenza H5Nx clade 2.3.4.4b outbreak (November 2021-March 2025). Can J Microbiol. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42114152/

[14] Goujgoulova G, Stoimenov G, Koev K. Molecular Characterization of Highly Pathogenic Avian Influenza H5N1 Viruses Circulating in Bulgaria During 2024-2025: Evidence for Hidden Circulation and Zoonotic Risk Markers. Int J Mol Sci. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41751847/

[15] Graber AL, Simmons HC, McCarthy KR. Panzootic H5 influenza viruses acquired resistance to human head interface antibodies. PLoS Pathog. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41779811/

[16] Farrell ML, McGrath G, Cuartero LG et al. Avian influenza in Ireland: a spatiotemporal, subtype and host-based analysis (1983-2024). J Gen Virol. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41739543/

[17] Miao X, Zhao X, Zhang N et al. Surveillance and biological characterization of H3 subtype avian influenza viruses in Eastern China. Virulence. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42154626/

[18] Liu J, Xiang HY, Liu J et al. Surveillance and cross-species transmission assessment of H3NX avian influenza viruses isolated in Guangdong province, China from 2023 to 2025. Poult Sci. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41931871/

[19] Bashashati M, Fallah Mehrabadi MH, Moradi Haghgou L et al. H4N6 avian influenza virus in Iran: first isolation and molecular insights. Virus Genes. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41632339/ *** Disclaimer: This article is for educational and informational purposes only. It is not intended to substitute for professional veterinary advice, diagnosis, treatment, or regulatory guidance. Always consult a licensed veterinarian or qualified specialist regarding animal health, disease diagnosis, and therapeutic decisions.

[20] Tang L, Wang R, He G. Research note: Molecular characteristics and genetic evolution of H1N1 avian influenza virus from wild birds in Shanghai, China. Poult Sci. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41653626/

[21] Encinas P, Nogales A, Escribano-Romero E et al. Longitudinal Surveillance of Influenza A Virus Exposure in Wild Boars (Sus scrofa) in Spain (2015-2023): Serologic and Virologic Evidence of Subtype Infections and H5N1 Spillover Risk. Zoonoses Public Health. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41668256/

[22] Wang M, Laison EKE, Philippsen T et al. Mechanistic modelling of highly pathogenic avian influenza: A scoping review revealing critical gaps in cross-species transmission models. PLoS One. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42060628/

[23] Jindal M, Lim S, MacIntyre CR. Machine Learning-Based Geospatial Risk Modeling of Global Avian Influenza Outbreaks. Transbound Emerg Dis. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42022449/

[24] Adiga A, Chopra A, Wilson ML et al. A high-resolution, US-scale digital similar of interacting livestock, wild birds, and human ecosystems for multihost epidemic spread. Proc Natl Acad Sci U S A. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42207910/

[25] Vijayakumar P, Mishra A, Rajamanickam K et al. Systems-Level Analysis of HPAI H5N1 Infection in Ducks: Integrating Transcriptomic, Proteomic, and Phosphoproteomic Data. Int J Mol Sci. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41898742/

[26] Zoomer S, Goderski G, van den Brink S et al. Zoonotic influenza preparedness: Dutch medical labs efficiently detect animal influenza A viruses - External Quality Assessment, 2023. J Clin Virol. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41734493/

[27] Zhang J, Fan Z, Pan Q et al. Development of an inactivated H9N2 subtype avian influenza serological DIVA vaccine using the chimeric A/B NA epitope approach. Vet Microbiol. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41653783/

[28] Shimazu Y, Isoda N, Hiono T et al. Evaluation of therapeutic efficacy of baloxavir marboxil against high pathogenicity avian influenza virus infection in duck model. PLoS One. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41984915/

[29] Jones JC, Andreev K, Sheth V et al. Baloxavir alleviates severe disease and viremia in ferrets infected with avian- or bovine-origin influenza A(H5N1) virus. Sci Transl Med. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41706870/

[30] Lejeune M, Tornos J, Bralet T et al. Vaccination against H5 HP avian influenza virus leads to persistent immune response in wild king penguins. Nat Commun. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41663358/

[31] Härmä V, Palsola M, Kuusipalo A et al. Lessons from the 2024 avian influenza vaccination campaign in Finland: a qualitative inquiry. Vaccine. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42167136/

[32] Lee SH, Yeo SG, Lee S et al. Preventive Responses to Human Avian Influenza Infection in the Republic of Korea, 2023-2024. Public Health Wkly Rep. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42238665/

[33] Kibiger L, Oltean HN, Leitz L et al. Fatal Human Case of Highly Pathogenic Avian Influenza A(H5N5) in a Backyard Flock Owner - Washington, November 2025. MMWR Morb Mortal Wkly Rep. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42096351/

[34] Vaughan A, Joyce A, Traub E et al. Serologic Evidence of Highly Pathogenic Avian Influenza A(H5N1) Virus Infection in a Veterinary Professional Exposed to an Infected Domestic Cat - Los Angeles County, California, December 2024-January 2025. MMWR Morb Mortal Wkly Rep. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42096344/

[35] Wu W, Liu Y, Zhang J et al. Evolutionary lineage and host origin influence virulence and mammalian adaptation of H7N9 avian influenza viruses. Poult Sci. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41747464/