Search Results (585)

During the 41st Chinese Antarctic Expedition (2024–2025), fresh faecal samples were collected from sympatric Adélie, chinstrap, and gentoo penguins on Ardley Island. The faecal viromes were systematically profiled via transcriptomic sequencing coupled with viral contig assembly. Thirty-two known viral families were annotated, yet over half of viral reads remained unclassified, indicating substantial uncharacterised viral diversity in Antarctic penguin guts. No significant interspecific differences in viral abundance or alpha-diversity were detected, and host-species exerted only a weak effect on viral community structure. While H5N1 highly pathogenic avian influenza and Newcastle disease virus were absent, several potential pathogens, including deltacoronaviruses, novel astroviruses, and picornaviruses, were recovered. This work establishes baseline virome data for Antarctic pygoscelid penguins and provides valuable insights for long-term pathogen surveillance of polar wildlife and assessments of viral spillover risk. Full article

H3 subtype avian influenza virus (AIV) is one of the most widely distributed and frequently detected low-pathogenicity avian influenza viruses (LPAIVs) in wild birds and poultry worldwide. Wild waterfowl are the natural reservoir of this virus. In recent years, driven by frequent genetic reassortment and continuous evolution, H3 subtype AIV has expanded its host range to include various mammalian species—dogs, cats, horses, seals, pigs (experimental infection), and humans. Among these, the H3N8 subtype shows the broadest cross-species transmissibility, having established sustained transmission lineages in horses and dogs, while also causing sporadic infections in seals and humans. Avian-origin H3N2 canine influenza virus has circulated stably in dog populations across Asia and North America for nearly two decades. Between 2022 and 2023, China reported three human cases of H3N8 subtype AIV infection, one of which was fatal (Guangdong, March 2023), indicating that this virus poses a potential zoonotic transmission risk. Novel triple-reassortant strains, including genotype G25 of H3N8 and H3N3, first detected in chicken flocks in late 2022, have continued to emerge. Their HA genes originate from H3 subtype viruses of wild bird or chicken origin, whereas their internal gene segments are predominantly acquired from H9N2 subtype AIV, resulting in enhanced mammalian adaptability. This review summarizes the global epidemiology of H3 subtype AIV (covering wild birds, poultry, and live poultry markets), its genetic evolution and reassortment patterns, and the molecular mechanisms underlying cross-species transmission. This review particularly highlights the regulatory roles of key amino acid mutations—such as PB2-D701N, M1-M192V, and HA-Q226L/G228S—in receptor binding preference, polymerase activity, and pathogenicity. This review also summarizes recent advances in detection techniques (multiplex RT-PCR, quantum dot-based immunochromatographic strips, RT-RAA, and CRISPR-Cas13a) and vaccine development (inactivated, adenovirus-vectored, and mRNA vaccines). Key prevention and control challenges—including covert circulation, surveillance gaps, and limited subtyping diagnostic capacity at primary laboratories—are also discussed. This review proposes that H3 subtype AIV should be recognized as a potential zoonotic threat warranting continued surveillance, although no evidence of sustained human-to-human transmission has been documented to date. Better understanding of cross-species mechanisms, stronger surveillance and early warning, and evidence-based control strategies are needed to inform future risk assessment. Full article

In the poultry industry, infection with low-pathogenicity avian influenza viruses is often accompanied by atypical clinical manifestations, such as diarrhea, the underlying mechanisms of which are yet to be elucidated. In this study, ten chickens were randomly divided into two groups (n = 5 per group). One group is infected with the H9N2 subtype of avian influenza virus to simulate the clinical infection. Bronchioalveolar lavage fluid (BALF), as well as cecal and colonic contents samples, was collected at 5 days post inoculation (dpi), and 16S rRNA sequencing was employed to analyze the alterations of the pulmonary and intestinal microbiota. Our results showed that H9N2 infection did not significantly alter the alpha or beta diversity of either the gut or lung microbiota. LEfSe analysis revealed that the infected group exhibited enrichment of Oscillospira and Fournierella in the gut and Delftia and Pelomonas in the lung, whereas the control group showed enrichment of Bacteroides, Enorma, Anaerostignum, and Collinsella in the gut and Mycoplasma in the lung. Procrustes analysis showed no significant overall structural association between the two niches, while Spearman correlation analysis identified 54 significant cross-site microbial correlations. BugBase analysis indicated that the lung microbiota in the infected group exhibited significantly enhanced phenotypes related to potential pathogenicity, Gram-negative status, and stress tolerance. Collectively, these findings suggest that H9N2 may reshape the composition, function, and cross-site interaction networks of specific microbial taxa. Viral infection may be associated with cross-site alterations in the gut and lung microbiota via the “gut-lung axis”, with gut microbiota perturbations potentially influencing pulmonary susceptibility to secondary infections. This highlights the gut microbiota as a potential target for modulating respiratory pathogen colonization and reducing antibiotic use, while providing a novel theoretical basis for understanding the gut-lung axis in avian influenza infection in poultry. Full article

Avian influenza viruses (AIVs) circulate widely among migratory birds, where frequent reassortment drives the emergence of novel genomic constellations. However, the evolutionary pathways underlying these events remain poorly understood in South America due to historically limited genomic surveillance. Here, we report the detection and evolutionary reconstruction of a low pathogenic avian influenza virus (LPAI) subtype H1N8 isolated from a White-rumped Sandpiper (Calidris fuscicollis) sampled at Lagoa do Peixe National Park (PNLP), southern Brazil, an important migratory stopover along the Atlantic Flyway. Between 2023 and 2025, 1787 samples were collected from wild birds, resulting in six AIV-positive detections during April 2024, from which one H1N8 isolate was successfully recovered and whole-genome sequenced. Genomic analyses identified a reassortant virus sharing five internal gene segments (PB2, PB1, PA, NP, and MP) with a previously described H11N2 virus detected at the same site and host species, whereas the HA, NA, and NS segments belonged to distinct South American lineages. Bayesian temporal reconstruction, discrete phylogeographic analyses, ancestral-state reconstruction, and reassortment inference consistently supported the persistence of a shared North American-derived genomic backbone followed by the acquisition of locally circulating South American gene segments. Although based on a single isolate, these findings provide an evolutionary snapshot of a reassortment event in South American migratory birds and reinforce PNLP as a key site for long-term avian influenza virus surveillance. Full article

In June 2023, Poland experienced an unprecedented outbreak of highly pathogenic avian influenza (HPAI) H5N1 virus infections in cats, raising concerns about the role of cats in HPAI H5N1 virus ecology and potential public health implications. We describe the clinical course and molecular findings in a cat designated as cat No. 14 during this outbreak, with emphasis on the viral load detected in various organs and tissues. The cat was initially examined for recurrent dermatological problems, although the owner also reported reduced activity. Over the following five days, the disease rapidly progressed, with systemic and neurological signs unresponsive to treatment. Blood analyses revealed no major haematological abnormalities, whereas serial serum biochemistry showed progressive abnormalities. Due to the poor prognosis, the cat was humanely euthanized five days after the initial veterinary examination. Tissue samples from major internal organs and lymph nodes, together with tracheal and rectal swabs and bile, were collected for real-time RT-PCR. Viral RNA was detected in all analysed samples except the intestines, mesenteric lymph nodes, rectal swab, and bile, with the highest viral loads observed in the cerebellum and brain. This case provides molecular evidence of widespread HPAI H5N1 viral RNA distribution across tissues, complemented by detailed haematological and biochemical findings, further characterizing the systemic nature of infection. Full article

Highly pathogenic avian influenza (HPAI) represents an enormous pandemic risk amid the ongoing H5N1 panzootic. HPAI, defined by its high lethality in domestic poultry, includes the influenza A virus (IAV) H5N1 and H7N9 subtypes and has a 40–50% case fatality rate in humans. To facilitate the development of efficacious HPAI vaccination regimens and isolation of HPAI-neutralizing monoclonal antibodies (nmAbs) for prophylactic and therapeutic use, we performed a proof-of-concept pilot study wherein we developed an array of mRNA and adenovirus-vectored vaccines encoding HPAI hemagglutinins (HAs) and then assessed their immunogenicity in IAV-naïve Indian rhesus macaques (RMs). All RMs developed binding IgG recognizing both HPAI HAs. HPAI-nAbs were detected in RMs vaccinated with full-length HAs, but not in RMs vaccinated with HA stems alone. Potent HPAI neutralization activity was observed in two animals with serum ID₅₀ titers of ~1:100,000 against H5N1 and ~1:50,000 against H7N9. Most RMs developed cross-reactive IgG recognizing the HAs of additional IAV subtypes, and HA-specific B cells were readily identifiable in vaccinee PBMCs by flow cytometric analysis. The results of our pilot study suggest that elicitation of potent HPAI-nAb responses is enhanced by vaccination with the HA head domain and that vaccination with the HA stem alone tends to elicit binding non-nAbs. Furthermore, use of our fluorophore-conjugated HA probes to identify HA-specific B cells could enable HPAI-nmAb isolation. Collectively, our findings could facilitate the development of novel vaccines and nmAb therapeutics leveraging the superior neutralization potency of HA head-specific Abs to prevent and treat HPAI infections in humans. Full article

The H9N2 avian influenza virus (AIV) is currently widespread globally and poses a serious threat to the poultry industry and public health; however, its global epidemiological characteristics and key molecular mutation patterns have not yet been systematically elucidated. Based on the NCBI Influenza Virus Resource Database, this study collected relevant data on the H9N2 AIV from around the world between 1966 and 2023. It conducted a comprehensive analysis of the geographic distribution of 11,933 strains, the temporal distribution of 11,824 strains, the host sources of 11,756 strains, and the genetic polymorphisms at key functional sites. The results showed that 90.14% of H9N2 AIV sequences in the dataset originated from Asia, with China contributing the largest number of sequences. The global sequence availability pattern underwent four phases: sporadic sequence availability, gradual increase, high sequence availability, and subsequent decline, with 2007–2018 representing a period of relatively high availability of publicly accessible sequences. Host analysis indicated that H9N2 AIV sequences were predominantly derived from poultry-related hosts, with chickens being the main host source in the dataset, and available sequences have also been reported from various mammals, including pigs and humans, as well as environmental media. Molecular analysis revealed that receptor-binding-related sites in the HA protein, such as Q226L and I155T, have become dominant variants, while mammalian-adaptive mutations such as PB2 E627K and D701N remain at low frequencies; M2 S31N is widely prevalent, whereas the detection rate of NA drug-resistance-associated mutations is low. This study systematically reveals the global distribution patterns of available H9N2 AIV sequences, host distribution characteristics, and key molecular mutation patterns of the H9N2 AIV, providing a scientific basis for cross-host transmission risk assessment, molecular surveillance, and targeted prevention and control. Full article

Background/Objectives: Humans are primarily infected by two distinct seasonal influenza A virus (IAV) subtypes, A(H1N1)pdm09 and A(H3N2). Because IAV mutates rapidly, it continuously escapes existing protective antibodies. However, repeated exposure to these evolving strains increases the diversity of virus-specific memory B cell (MBC) population. To investigate the extent of this diversity and cross-reactivity of IAV- specific immunity in adults, and its possible impact on emerging strains, we analyzed the hemagglutinin (HA)-specific MBC repertoire of an adult frequently immunized with seasonal vaccines. Methods: High-throughput single-cell sequencing of HA probe-positive MBCs collected from an individual with repeated seasonal influenza vaccination was performed. Monoclonal antibodies (mAbs) from multicell clonotypes were tested for HA binding and influenza virus neutralization. Results: Two clonotypes were identified that bound to both A(H1) and A(H3) HAs from strains circulating before and after the season of blood collection. Both clonotypes neutralized A(H3N2) strains, while one also neutralized A(H1N1)pdm09 strains. Notably, these cross-group binders showed affinity for A(H5), A(H7) and A(H9) avian influenza HAs and neutralized bovine A(H5N1) IAV. Conclusions: Our findings suggest that seasonal vaccination can support pre-existing cross-reactive B-cell immunity in some individuals. This underscores the importance of studying influenza-specific MBC repertoires across diverse populations to better understand immune dynamics and improve vaccine design. Full article

Highly pathogenic avian influenza H5N1 virus (H5N1 HPAIV) has long circulated in wild waterfowl and poultry and continues to cross species barriers, posing sustained threats to livestock productivity and public health. The 2024 outbreak of H5N1 HPAIV in dairy cattle across multiple U.S. states represents the first recognized large-scale transmission event of this virus in ruminants, reshaping our understanding of its host range and transmission ecology. This review summarizes recent advances in the epidemiology, virological characteristics, transmission, pathogenesis, surveillance, and control of dairy cattle-associated H5N1. The initial multistate outbreak was dominated by clade 2.3.4.4b genotype B3.13, whereas subsequent independent introductions of genotype D1.1 demonstrated that repeated avian-to-cattle spillover also contributes to the evolving outbreak ecology. A defining feature is efficient replication in bovine mammary epithelial cells, resulting in high viral titers in milk, supporting milk-associated exposure and milking-related contamination as plausible components of transmission, although the relative contribution of different routes remains unresolved. Infected cattle typically show reduced feed intake, a marked decline in milk production, abnormal milk, and mild systemic signs, whereas severe respiratory disease and mortality are uncommon. Mutations such as PB2-M631L, PA-K497R, and changes in NP and NS1 may promote replication and immune evasion in bovine cells, while genotype-specific PB2 adaptations highlight the potential for further mammalian adaptation. Human infections reported to date have been predominantly mild and associated with occupational exposure, with no evidence of sustained human-to-human transmission. Experimental vaccine studies have begun to demonstrate immunogenicity in cattle, although protection against mammary infection, viral shedding, and transmission remains to be established. Future priorities include clarifying mammary tropism and transmission dynamics, while strengthening diagnostics, farm biosecurity, vaccination, evaluating cattle vaccination strategies, and integrated One Health surveillance. Full article

H9N2 avian influenza viruses pose a persistent zoonotic risk owing to their broad host adaptability. Between 2024 and 2025, two H9N2 isolates (ZHY1022B2 and ZHY0417A11) were recovered from quail flocks in Hebei, China. Phylogenetic analysis clustered their HA genes within the dominant B4.7.2 subclade, but diverged into two subgroups (B4.7.2.2 and B4.7.2.1). Of particular interest was ZHY0417A11, which displayed a multigenic reassortment pattern—its PB1 originated from an H3N8 virus, PA and PB2 from H3N3, NS from H10N3, and the M gene was nearly identical (99.32%) to a human H3N8 isolate, whereas the remaining HA, NA and NP segments maintained the H9N2 backbone. Despite the presence of the HA mammalian-adaptive markers (H191N, A198V and Q234L), both strains showed marked antigenic drift from the vaccine strain SS (BJ/94-like; R < 0.5), while retaining reactivity with currently circulating field strains. These findings argue for heightened vigilance in quail populations, given their role as mixing vessels, and highlight the limitations of current vaccine matching in light of ongoing H9N2 evolution. Full article

Highly pathogenic avian influenza (HPAI) virus H5N1of clade 2.3.4.4b has emerged as the predominant lineage circulating in poultry flocks worldwide, raising concerns regarding the protective efficacy of currently available commercial vaccines, particularly in domestic ducks, which play an important role in virus maintenance and transmission. Thus, this study evaluated the immunogenicity along with the protective efficacy of four inactivated H5 vaccines against a recently isolated local HPAI-H5N1 (Newvalley-3-H5N1-2024, clade 2.3.4.4b) strain in Pekin ducks in Egypt. A total of 150 seronegative ducks were divided into vaccinated and control groups (10 groups) and vaccinated at 10 days of age. At 31 days of age, the vaccinated and positive control groups were challenged using 10^6.5 EID₅₀/0.5 mL/duck with the local isolate (Newvalley-3-H5N1-2024) via the oculo-nasal route. The vaccine efficacy was assessed through clinical signs, survival rate, hemagglutination inhibition (HI) antibody titer, tracheal and cloacal viral shedding quantified by real-time RT-PCR, and histopathological examination of trachea, lung, pancreas, and brain tissues. Generally, all ducks vaccinated with the ValleyVac Avian Flu H5 plus and MEFLUVAC^TM H5 PLUS 8 showed a significantly higher survival rate (100%) at 10 days post-vaccination (DPV) than those in the positive control (66.7% mortality rate). In contrast, ducks exhibited mortality rates ranging from 6.7% in the SERVAC Flu H5N1 group to 13.4% in the Sinder Fluvac group. The ValleyVac Avian Flu H5 plus and MEFLUVAC™ H5 PLUS 8 vaccines induced the highest HI antibody titers at 7, 14, 21, and 28 DPV in both homologous and heterologous AIV antigens, resulting in a significant reduction in viral load among all vaccinated duck groups (p-value < 0.05) comparable to the positive control group. Conversely, the SERVAC Flu H5N1 and Sinder Fluvac vaccines provided partial protection, suboptimal immunogenicity at different time points, and elevated viral shedding. Histopathological findings in ValleyVac Avian Flu H5 plus and MEFLUVAC™ H5 PLUS 8 vaccines exhibited mild tissue alterations following AIV challenge. Marked pathological lesions were observed in the SERVAC Flu H5N1 and Sinder Fluvac vaccinated groups. Among tested vaccines, both ValleyVac Avian Flu H5 plus and MEFLUVAC^TM H5 PLUS 8 showed the highest level of protective efficacy against the circulating AIV strain compared with other commercial vaccines. This study highlights the need for continuous molecular surveillance, antigenic matching, and regular updating of vaccine seed strains to ensure efficient HPAI control in Egypt. Full article

Background/objectives: The emergence of highly pathogenic avian influenza A (H5N1) virus infections in dairy cattle in the United States revealed a novel mammalian host and a potential transmission pathway involving raw milk and dairy production systems. Sustained circulation of H5N1 in dairy herds is of concern because ongoing viral adaptation in mammals may increase the risk of efficient mammalian transmission and subsequent zoonotic spread. In response to this emerging threat, we developed a chimpanzee adenovirus (ChAd)-vectored vaccine expressing the haemagglutinin 5 antigen (H5HA) from the dairy cattle isolate A/dairy cattle/Texas. Methods: Lactating dairy cows were vaccinated by either intramuscular (N = 3) or intranasal administration (N = 3). H5HA clade 2.3.4.4b antibodies in cow’s milk and sera were evaluated by ELISA. Hemagglutination and neutralisation capacity were also evaluated. Results: IgG and IgA H5HA-specific antibodies were detected in serum and milk from parenterally vaccinated animals, demonstrating the induction of a systemic immune response. The neutralising antibody responses elicited were only detected in serum of cows vaccinated via the intramuscular route. Conclusions: These preliminary findings support the feasibility of ChAd-vectored vaccination as a strategy to induce humoral immunity in cattle against emerging H5N1 influenza A viruses. Cross-reactive antibody responses against both A/dairy cattle/Texas/24-008749_001/2024 and A/Ibis/Egypt/RLQP-229S/2022 support the capacity of the vaccine to recognise antigenically related H5N1 clade 2.3.4.4b viruses circulating in mammalian and avian reservoirs. Further studies of vaccine efficacy and the immunological mechanism of protection should now be undertaken with the aim of reducing viral transmission and milk-associated shedding in dairy herds. Full article

H7N9 avian influenza virus (AIV) poses a persistent threat to poultry and public health. Despite widespread vaccination in China, rapid antigenic drift and reassortment necessitate frequent updates of vaccine strains. Phylogenetic analysis of isolates from Chinese provinces (from 2019 to 2023) showed that while surface genes diversified, the internal gene cassette remained conserved yet actively reassorted with other subtypes, suggesting internal gene compatibility may influence vaccine performance. We selected the H7N9 strain A/chicken/Northeast China/19854-6/2019 (E2), which harbors a polybasic Hemagglutinin (HA) cleavage site and predicted dual receptor-binding affinity. To enable safe vaccine development, we modified the HA cleavage site to generate a low-pathogenicity strain (E2-Δ). Using reverse genetics, we constructed three recombinant viruses: E2-Δ (retaining contemporary internal genes), CVI-E2, and CVII-E2 (containing internal genes from commercially used donor strains CVI and CVII, respectively). Inactivated vaccines were evaluated in specific-pathogen-free (SPF) chickens. E2-Δ induced HI antibody titers comparable to those of CVI-E2 and significantly higher than those of CVII-E2, and showed modestly higher cross-reactive HI titers against some recent H7N9 variants in exploratory analyses. All vaccines provided complete homologous protection with reduced viral shedding and no clinical signs in challenge trials. Our findings suggest that internal gene backbone compatibility may influence vaccine immunogenicity. While E2-Δ outperformed CVII-E2, it was comparable to CVI-E2, indicating that certain traditional backbones may still be suitable for H7N9 vaccine development. This approach warrants further validation to support a refined vaccine design strategy for H7N9 and potentially other avian influenza subtypes. Full article

Background: The simultaneous circulation of highly pathogenic avian influenza (HPAI) H5N8 (clade 2.3.4.4b) and virulent Newcastle disease virus (NDV) genotype VII creates a cumulative risk for the poultry industry, rendering monovalent vaccination insufficient. This study aimed to develop and evaluate a combined inactivated vaccine against AIV H5N8 and NDV genotype VII based on local endemic strains. Methods: The vaccine was formulated as a water-in-oil emulsion (30:70) using Montanide™ ISA 78 VG. Evaluation included physicochemical characterization, safety assessment in chickens, immunogenicity evaluation via the hemagglutination inhibition (HI) test, and protective efficacy following challenge with virulent isolates. Results: The formulation demonstrated high stability and complete safety without adverse reactions. By 28 days post-immunization, the vaccine induced a robust, balanced humoral response with antibody titers reaching 9.10 ± 0.23 log₂ against NDV and 9.00 ± 0.26 log₂ against AIV, indicating no antigenic interference. Upon challenge, the vaccinated group exhibited 100% clinical protection and survival, compared to 100% mortality in controls. Furthermore, vaccination significantly reduced viral shedding, limiting horizontal spread. Conclusions: The developed combined inactivated vaccine demonstrates high safety, stability, and protective efficacy. It represents a promising candidate for comprehensive specific prophylaxis in endemic regions, effectively limiting horizontal pathogen transmission and mitigating economic losses in poultry production. Full article