Mechanistic #modelling of highly pathogenic avian #influenza: A scoping #review revealing critical gaps in cross-species #transmission models

 

Abstract

Background

Highly pathogenic avian influenza (HPAI) viruses, particularly subtypes such as H5N1 and H7N9, have caused widespread outbreaks in wild birds, poultry, livestock and occasionally humans, raising concerns about cross-species transmission and pandemic potential. Effective control and surveillance strategies require a thorough understanding of HPAI transmission dynamics, which can be supported by mathematical modelling.

Objective

This scoping review aimed to identify mechanistic models used to study HPAI transmission. Specifically, we sought to categorize model types, describe their application contexts (e.g., wild birds, poultry, livestock, and humans), and highlight modelling gaps relevant to understanding and mitigating the risks of HPAI spread.

Methods

Following PRISMA guidelines and the PRISMA extension for scoping reviews (PRISMA-ScR), we conducted systematic searches of PubMed and Web of Science to identify peer-reviewed studies employing deterministic and stochastic models to analyze HPAI transmission. Eligible articles published between January 2023 and June 2025 were screened and grouped by model structure, host populations, transmission pathways, and modelling objectives.

Results

After screening, 30 studies published after 2023 were included in this scoping review. Compartmental models were the most common (26 studies), with 16 deterministic and 10 stochastic approaches. These models were primarily used to describe transmission among wild birds, poultry, livestock, and humans and to evaluate interventions such as culling, vaccination, and movement restrictions. Agent-based models (2 studies) captured individual-level interactions and spatial heterogeneity, while network models (2 studies) represented contact structures and transmission pathways between farms or species.

Conclusions

Currently, mechanistic modelling of HPAI is dominated by compartmental approaches, including both deterministic and stochastic formulations, whereas agent-based and network models remain relatively underused. Although most studies focus on transmission in wild birds and poultry, and in some cases spillover infections to humans, few explicitly examine infection dynamics in livestock or in transmission between livestock and humans, despite the importance of livestock (e.g., cattle) as potential intermediaries in human infection. Key gaps persist in the integration of empirical data, representation of multi-host interactions, and evaluation of realistic intervention strategies. Addressing these limitations is essential to improve predictive accuracy and to strengthen the role of modelling in informing HPAI surveillance and control.

Source: 

Link: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0347929

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Highly Pathogenic Avian #Influenza #H5N1 Clade 2.3.4.4b Virus and Mass #Mortality in Eurasian #Cranes, #Germany, 2025

 

Abstract

In autumn 2025, highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus, genotype EA-2024-DI.2.1, caused systemic infections leading to a mass mortality event among the western migrating subpopulation of Eurasian cranes (Grus grus) in Germany. Gregarious behavior at feeding and resting sites likely promoted rapid viral spread within the population.

Source: 

Link: https://wwwnc.cdc.gov/eid/article/32/5/26-0170_article

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#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

 

Abstract

The 2022 highly pathogenic avian influenza (HPAI) outbreak of H5N1 clade 2.3.4.4b was one of the major avian influenza outbreaks, leading to multiple spillover events infecting domestic and wild bird flocks, as well as mammals. The sustained spread was a result of viral circulation in wild birds across migratory flyways in North America. Pennsylvania has a significant poultry population that supports both retail and live bird markets. The state also features migratory bird stopovers on the Atlantic flyway, increasing exposure to HPAI infections. This study investigates clinical presentation and sequence data from H5N1 clade 2.3.4.4b viruses during the 2022 outbreak in Pennsylvania. Eight different H5N1 clade 2.3.4.4b genotypes were detected (A1, B1.1, B1.2, B1.3, B2.2, B3.3, B3.5, and one minor genotype) during the first year. The earliest detection was genotype A1, a fully Eurasian virus, in commercial poultry in April 2022. All other genotypes identified were reassortants of A1 with North American avian influenza gene segments (denoted with “B”). Genotype B3.3 was a rare genotype prior to the initial spillover into the live bird market system, but remained predominant among backyard flocks in Pennsylvania and surrounding states until September 2023. Genotype B3.3 has not been detected in migratory waterfowl since, suggesting the genotype has waned and is no longer in circulation. This study sheds light on the genotype diversity of H5N1 during the 2022 outbreak in Pennsylvania poultry, contributing to the understanding of virus evolution and its potential impacts.

Source: 

Link: https://www.mdpi.com/1999-4915/18/5/502

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Emergence of D1.1 #reassortant #H5N1 avian #influenza viruses in North #America

 

Abstract

Since 2021, highly pathogenic avian influenza viruses (HPAIVs) belonging to H5N1 clade 2.3.4.4b have circulated widely in North American wild birds and repeatedly spilled over into mammals. In 2025, the first H5N1-associated deaths in humans were recorded in the Western hemisphere, raising questions about how the ongoing evolution of the virus in wild birds impacts spillover risk. Here, our analysis of 21,471 H5N1 genomes identified an evolutionary shift in mid-2024, driven by interhemispheric migration from Asia and reassortment with new antigens. The genotypes that dominated the early years of North America's H5N1 epizootic traced their ancestry back to Europe, but Asia was the source of new "D1.1" genotype viruses that (a) spread faster, (b) have higher reassortment potential, (c) a broader host range, (d) repeatedly spill over to bovines, and (e) cause severe disease in humans, including non-farm workers.

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

Research Foundation - Flanders, https://ror.org/03qtxy027, G098321N, G0E1420N

European Union Horizon 2023 RIA project LEAPS, 101094685

DURABLE EU4Health project 02/2023-01/2027, 101102733

Fonds National de la Recherche Scientifique, F.4515.22

European Union Horizon 2020 project MOOD, 874850

Centers of Excellence for Influenza Research and Response, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Department of Health and Human Services, 75N93021C00014

Source: 

Link: https://www.biorxiv.org/content/10.64898/2025.12.19.695329v2

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#Ocular findings in Northern #Gannets following an #outbreak of high pathogenicity avian #influenza #H5N1

 

Abstract

During 2021-2022, high pathogenicity avian influenza (HPAI) caused mass mortality in wild birds across Europe, with Northern Gannets (Morus bassanus) among the most affected. Following the outbreak, unusual alterations in the species' characteristic pale iris were observed in some individuals. Opportunistically captured gannets on Bass Rock (n=52), selected to represent a range of iris pigmentation, were examined. Slit-lamp biomicroscopy, indirect ophthalmoscopy, rebound tonometry and photography were performed. Iris pigmentation was classified as normal, mottled or black. Eleven birds underwent avian influenza virus (AIV) serology. Histopathology was performed on two eyes. Abnormal iris pigmentation was found in 74% of adult and immature gannets, with 61% affected bilaterally. Additional signs consistent with uveitis were present in 77% of affected birds. Iris pigmentation abnormalities were positively associated with AIV H5 seropositivity (Fishers exact test, P=0.018). Histopathology from affected eyes showed increased melanin deposition and disorganisation, including loss of a distinct anterior layer of melanocytic cells and hypertrophy of melanocytes within the iris stroma. Field conditions limited uniform lighting and concurrent serology. Iris pigmentation changes were associated with prior HPAI exposure and frequently accompanied by signs of uveitis, suggesting iris alterations may indicate past infection and potential chronic sequelae.

Competing Interest Statement

The authors have declared no competing interest.

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.04.15.718625v1

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Frequent seasonal #reassortment between high and low path #viruses drives the diversification of #influenza #H5N1

 

Abstract

Since 2021, highly pathogenic (HPAI) H5N1 viruses have spread across the Americas, diversifying via reassortment into new genotypes that have spilled into humans and livestock, raising fears of a new influenza pandemic. Pandemic lineages are typically associated with reassortment, but we currently have limited understanding of where and when reassortment is expected to occur, which limits our ability to assess pandemic risks. Using a dataset of 9,052 full-genome sequences, we show that reassortment and novel genotype formation are associated with seasonal variation in low pathogenicity avian influenza (LPAI) cases and with the spatial and host distributions of viral transmission. We pinpoint ducks, geese, and the Central flyway as frequent sources of new genotypes, and show that reassortment rates vary seasonally, driven by mixing between high- and low-pathogenicity viruses. Cattle spillover genotypes (B3.13 and D1.1) evolved during periods of high reassortment, implicating reassortment as a common occurrence in lineages evolving during particular time periods. Together, these findings reframe reassortment as a predictable ecological process, with direct implications for how surveillance and pandemic risk assessment should be designed.

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

US Centers for Disease Control Insight Net, CDC-RFA-FT-23-0069

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.04.17.719307v1

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#Russia - #Influenza A #H5N1 viruses of high pathogenicity (Inf. with) (non-poultry including wild birds) (2017-) - Immediate notification [FINAL]

Wild Anatidae (unidentified) in the Yevrey Region.

Source: 

Link: https://wahis.woah.org/#/in-review/7426

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#Sweden - #Influenza A #H5N1 viruses of high pathogenicity (Inf. with) (non-poultry including wild birds) (2017-) - Immediate notification

 

-- In accordance with the WOAH Terrestrial Animal Health Code, Article 10.4.1, point 4, this outbreak does not change the disease-free status of Sweden as these are wild birds or birds kept in a single household, and therefore do not fall within the WOAH definition of poultry.

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-- Tjörn: 

- A Whooper swan was found dead. It was sent to the Swedish Veterinary Agency for laboratory analysis as part of the national surveillance program for avian influenza.

-- Varberg: 

- A Eurasian Buzzard was found dead. It was sent to the Swedish Veterinary Agency for laboratory analysis as part of the national surveillance program for avian influenza.

- A Peregrin falcon was found dead. It was sent to the Swedish Veterinary Agency for laboratory analysis as part of the national surveillance program for avian influenza.

-- Nyköping: 

- An Eurasian buzzard was found dead. It was sent to the Swedish Veterinary Agency for laboratory analysis as part of the national surveillance program for avian influenza.

-- Södertälje: 

- A Eurasian jackdaw was found dead. It was sent to the Swedish Veterinary Agency for laboratory analysis as part of the national surveillance program for avian influenza.

-- Hallstahammar: 

- A Eurasian jackdaw was found dead. It was sent to the Swedish Veterinary Agency for laboratory analysis as part of the national surveillance program for avian influenza.

-- Växjö: 

- A Canada goose and a Greylag goose were found dead and sent to the Swedish Veterinary Agency for laboratory analysis as part of the national surveillance program for avian influenza.

Source: 

Link: https://wahis.woah.org/#/in-review/7452

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Susceptibility of wild and domestic #songbirds to #Usutu virus

Abstract

Usutu virus (USUV) is an emerging mosquito-borne orthoflavivirus that can cause neuroinvasive disease in humans and wild birds. USUV clusters phylogenetically within the Japanese encephalitis virus serocomplex, sharing antigenic and ecological similarity with West Nile virus (WNV). USUV is maintained in an enzootic cycle primarily involving passerine birds and Culex spp. mosquitoes. USUV was first isolated in South Africa in 1959 and has since spread throughout Africa and Europe, causing mortality and disease in several wild bird populations, specifically the Eurasian blackbird (Turdus merula). To understand transmission and pathogenesis of USUV in birds, we sought to develop passerine bird models of infection using wild-caught house finches (Haemorhous mexicanus), wild-caught American robins (Turdus migratorius), domestic canaries (Serinus canaria domestica), and captive-bred zebra finches (Taeniopygia guttata). Birds were inoculated with one or two isolates of USUV and viremia was measured. House finches, American robins, and canaries were susceptible to USUV, with 100% of inoculated birds developing viremia. These avian species reach viremias that have the potential to infect Cx. quinquefasciatus mosquitoes. Clinical disease and histopathological evidence of disease were severe in American robins and moderate to severe in canaries, with limited disease in house finches. However, zebra finches inoculated with one isolate of USUV did not develop detectable viremia. These findings provide additional tools for studying USUV enzootic transmission and pathogenesis in passerine birds.

Source: 

Link: https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0014213

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#Greece - #Influenza A #H5N1 viruses of high pathogenicity (Inf. with) (non-poultry including wild birds) (2017-) - Immediate notification

 

A wild Whooper Swan in Kastoria Region.

Source: 

Link: https://wahis.woah.org/#/in-review/7433

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#Norway - #Influenza A #HxNx viruses of high pathogenicity (Inf. with) (non-poultry including wild birds) (2017-) - Immediate notification

{A Canada Goose}

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{A Greylag Goose}

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A wild Greylag Goose and a wild Canada Goose in Innlandet and Østfold Regions.

Source: 

Link: https://wahis.woah.org/#/in-review/7424

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#Genetic and #biological characterization of a #duck-origin clade 2.3.4.4b #H5N6 avian #influenza virus reveals partial #mammalian #adaptation

 

Highlights

• Duck-origin H5N6 virus A/Duck/Jiangsu/628/2022 shares high homology with the human strain A/Yangzhou/125/2022.

• The 628 strain shows mammalian adaptation markers: HA mutations enhance human receptors affinity and NA mutations reduce sensitivity to neuraminidase inhibitors.

• Limited airborne transmission but detectable droplet-mediated spread suggests increased mammalian transmission risk.

Abstract

Clade 2.3.4.4b H5Nx highly pathogenic avian influenza viruses (HPAIVs) have caused extensive outbreaks in poultry worldwide. H5 HPAIVs have caused sporadic but severe human infections in China, representing a persistent zoonotic threat. Here, we identified a duck-origin H5N6 HPAIV (A/Duck/Jiangsu/628/2022) through routine surveillance and assessed its biological characteristics and mammalian pathogenesis. Phylogenetic analysis revealed > 98% nucleotide identity between strain 628 and the concurrent human H5N6 strain A/Yangzhou/125/2022. Molecular characterization identified multiple mammalian adaptation markers: hemagglutinin substitutions (S137A, T160A, T192I) associated with enhanced human receptor binding; neuraminidase mutations (I117T, D198N) linked to reduced neuraminidase inhibitor susceptibility; and polymerase complex changes (PB1-D622G, PA-K142Q) conferring increased mammalian cell replication. In vitro studies demonstrated that 628 virus replicated more efficiently in mammalian than in avian cells and exhibited dual receptor-binding specificity. Mouse pathogenicity assays revealed moderate virulence with progressive lung pathology. Critically, transmission experiments confirmed both direct contact and airborne transmission capabilities of 628 in guinea pigs. These findings demonstrate that circulating H5N6 viruses have acquired partial mammalian adaptation while retaining avian fitness, significantly elevating pandemic potential. Enhanced surveillance of wild bird populations, poultry farms, and live poultry markets is urgently needed to develop effective prevention and control strategies.

Source: 

Link: https://www.sciencedirect.com/science/article/abs/pii/S037811352600146X?via%3Dihub

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#Russia - #Influenza A #H5N1 viruses of high pathogenicity (Inf. with) (non-poultry including wild birds) (2017-) - Immediate notification [FINAL]

 

A wild Greylag Goose in Kalmyk Region.

Source: 

Link: https://wahis.woah.org/#/in-review/7410

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#Genomic analysis of high pathogenicity avian #influenza viruses from #Antarctica reveals multiple introductions from South #America

 

Abstract

The spread of high pathogenic avian influenza virus (HPAIV) H5N1 clade 2.3.4.4b into Antarctica poses a major threat to polar wildlife. We report the detection of H5N1 in carcasses of eight species during the 2023-2024 and 2024-2025 austral summers in the South Shetland Islands: Antarctic shag, Antarctic tern, kelp gull, pintado petrel, Antarctic petrel, skuas, Antarctic fur seal, and southern elephant seal. Whole-genome sequencing, mutational profiling, and phylogenetic reconstruction revealed that the viruses detected in these hosts descended from distinct introduction events. One group of strains including complete and partial viral genomes from a gull, skuas, fur seals, an Antarctic tern, and a southern elephant seal clustered with H5N1 strains previously detected in marine mammals in South America and formed a polyphyletic lineage consistent with at least two independent introductions into Antarctica. A second group of strains including complete and partial viral genomes from petrels, shags, and skuas clustered with H5N1 strains previously detected in seabirds and marine mammals in South Georgia and with a previously reported HPAIV detection from Torgersen Island, Antarctic Peninsula. These findings reveal extensive epidemiological connectivity between South America and Antarctica, with South Georgia serving as a “stepping stone” for virus spread in the region.

Source: 

Link: https://www.nature.com/articles/s41467-026-71544-3

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Divergent avian #strains drive an off-season #influenza A #peak in municipal #wastewater

 

Abstract

Wastewater sequencing is an increasingly valuable tool in tracking the spread of infectious disease agents across space and time in areas of dense human settlement. Among pathogens that can be readily detected by this approach is influenza A, which follows predictable patterns of prevalence through the winter months in North America. Here, we leverage routine surveillance of a municipal wastewater treatment plant in Northern California to describe an atypical, off-season spike in influenza A concentrations that rivals that of the winter respiratory virus season. Drawing upon metagenomic data generated through hybrid-capture sequencing, we assemble and subsequently characterize fragments of divergent influenza genomes that appear to derive predominantly from the avian H16 clade. These strains exhibit close evolutionary relationships to influenza isolated from migratory shorebirds, hinting at potential host species and mechanisms of geographic spread. Analysis of read abundances suggest that these avian strains dominate the pool of influenza circulating during the summer months, when typical human-infecting strains are essentially absent. Together, our results expand the value of wastewater sequencing to encompass sensitive tracking of outbreaks within animals in interface regions where human settlement abuts wildlands, increasing overall pandemic preparedness.

Competing Interest Statement

The authors have declared no competing interest.

Funding Statement

This project was supported by a gift from the Sergey Brin Family Foundation to A.B.B.

Source: 

Link: https://www.medrxiv.org/content/10.64898/2026.04.02.26350079v1

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#Surveillance and cross-species #transmission #assessment of #H3NX avian #influenza viruses isolated in #Guangdong province, #China from 2023 to 2025

 

Abstract

Continued influenza surveillance remains important, especially given that the emergence of novel subtypes or reassorted influenza viruses with pandemic potential continues to be a worldwide threat. In particular, virus circulating in birds can facilitate interspecies transmission to humans. In this study, we conducted systematic surveillance of H3 subtype avian influenza virus (AIVs) in domestic poultry and wild birds throughout Guangdong Province from 2023 to 2025. A total of 21 strains of H3 subtype AIVs were isolated, and phylogenetic analyses and risk assessment of their internal gene segments revealed genetic evidence of reassortment events, indicating a close genetic relationship with highly pathogenic avian influenza viruses (HPAIVs). ZJ1722, ZJ1542 and SZ837 showed dual-receptor binding ability and robust replication in mammalian cells, which coincided with amino acid mutations in the HA protein associated with human receptor binding. Although the H3NX viruses isolated in this study failed to cause lethality in mice, they efficiently replicated in the nasal turbinate and lungs of mice without prior adaptation. This study highlights the paramount importance of sustained, subtype-specific surveillance targeting H3NX avian influenza viruses coupled with timely risk characterization and assessment. Proactive containment of H3NX avian influenza virus (AIV) transmission has vital implications for safeguarding the sustainability of the poultry industry and protecting global human public health, given the inherent zoonotic potential and evolutionary plasticity of this H3 subtype, which could drive future spillover events.

Source: 

Link: https://www.sciencedirect.com/science/article/pii/S0032579126004918?via%3Dihub

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Predicting highly pathogenic avian #influenza #H5N1 #outbreak #risk using extreme #weather and bird #migration data in machine learning models

 

Abstract

Background. 

Climate change is intensifying extreme weather events (EWEs) with potentially profound consequences for zoonotic disease dynamics, yet the mechanisms linking EWEs to highly pathogenic avian influenza (HPAI) H5N1 outbreaks remain poorly characterized. The ongoing H5N1 panzootic, responsible for infection in over 500 avian and mammalian species, as well as nearly 1000 human cases and 477 deaths worldwide, provides a critical opportunity to evaluate how climate conditions shape spillover risk at landscape scales. 

Methods. 

We compiled a county-month dataset of confirmed H5N1 detections across the contiguous United States from 2022 to 2024 and integrated it with satellite-derived climate metrics, storm event data, and wild bird activity data. We trained and validated a gradient boosting machine classifier to predict outbreak risk and characterize predictor relationships. 

Results. 

Our model achieved strong discriminative performance (AUC-ROC = 0.856; AUC-PR = 0.237, representing a 7-fold improvement over chance) and high recall (0.726), supporting its utility as an early warning tool. Human population and temperature-related variables were the most influential predictors: cold temperature shocks and prolonged low temperatures were consistently associated with elevated outbreak risk, likely through enhanced environmental viral persistence, wild bird habitat compression, and allostatic stress-driven immunosuppression in reservoir hosts. Among storm variables, high wind coverage elevated risk, potentially via aerosol dispersal of contaminated particulates, while tornado activity showed an inverse relationship, consistent with documented avoidant behavior in migratory birds. Wild bird reservoir density showed a strong positive monotonic relationship with outbreak risk. 

Conclusions. 

Our analyses demonstrate that routinely available environmental and infection data can be used to predict HPAI outbreak risk at fine spatiotemporal scales. These findings demonstrate the divergent roles of short- versus long-term environmental exposures in HPAI spillover dynamics, as well as the potential for machine learning-based surveillance tools to inform targeted biosecurity interventions and early warning systems.

Competing Interest Statement

The authors have declared no competing interest.

Funding Statement

This research was supported by a subaward agreement between prime award recipient Boston University (PI: Gregory Wellenius) and the subaward recipient Regents of the University of Colorado (PI: Elise Grover) under the National Institute of Environmental Health Sciences of the National Institutes of Health, Award Number U24ES035309 -01. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Source: 

Link: https://www.medrxiv.org/content/10.64898/2026.03.30.26349797v1

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Brown and Lesser #noddies as epidemiological #reservoirs and #sentinels of avian #influenza virus in the South-western Indian #Ocean

 

Abstract

Avian influenza virus (AIV) epidemiology is well documented in temperate regions but remains poorly understood in isolated ecosystems like tropical oceanic islands. On these islands, seabirds nest in dense interspecific colonies where the role of different species as reservoirs and dispersers of AIV may vary greatly. Here, we examine the role of noddies (Anous spp.) as potential reservoirs for low pathogenic AIV and evaluate their potential as sentinel species for highly pathogenic AIV introduction on tropical oceanic islands. We analyzed blood samples from 11 seabird species across eight islands in the southwestern Indian Ocean (2015 to 2020). Noddies exhibited high, stable seroprevalence (30 to 45%), comparable to reservoir host species in temperate regions. The detection of two N7 positive noddies, sampled the same year on two distinct islands, provided direct molecular evidence that AIV actively circulates on these island colonies. While most other species showed low exposure, Bridled Terns (Onychoprion anaethetus) had exceptionally high seroprevalence (80%), though their reservoir status requires further investigation due to limited sampling. Given noddies consistent exposure and regional distribution, we recommend prioritizing islands with large noddy populations for AIV surveillance. Continued investigation of viral dynamics within and among islands is now called for to elucidate the ecological drivers of AIV maintenance and transmission.

Competing Interest Statement

The authors have declared no competing interest.

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.03.31.715511v1

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#Finland - #Influenza A #H5N1 viruses of high pathogenicity (Inf. with) (non-poultry including wild birds) (2017-) - Immediate notification

 

Two wild Canada Geese in the Lounais-Suomen aluehallintovirasto Region.

Source: 

Link: https://wahis.woah.org/#/in-review/7401

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Rapid GeneXpert #surveillance of #influenza A virus in #seabirds and the #environment provides early warning for #wildlife health in #Aotearoa New Zealand

 

Abstract

The global expansion of highly pathogenic avian influenza (HPAI) virus A(H5N1) underscores the need for rapid surveillance at high-risk wildlife interfaces. Taiaroa Head (45.7828 S, 170.7333 E) in the South Island of Aotearoa New Zealand hosts a plethora of aquatic wildlife including a large red-billed gull (Chroicocephalus novaehollandiae scopulinus) colony as well as the only mainland breeding colony of northern royal albatross (Diomedea sanfordi). The Royal Albatross Centre is also a major nature tourism destination, attracting tens of thousands of visitors annually, thereby creating a dense ecological and human-wildlife interface vulnerable to viral incursion. We evaluated the GeneXpert II platform using the Xpert Xpress Flu/RSV cartridge as a field-deployable tool for avian influenza virus detection in environmental and wildlife-associated samples. The assay detected synthetic influenza A viral RNA and multiple endemic low pathogenic avian influenza virus subtypes (A(H3N8), A(H1N9), A(H5N2) and A(H7N7)) circulating in New Zealand birds. Influenza A virus was reliably identified in spiked environmental water samples with no consistent PCR inhibition as well as naturally occurring avian influenza virus in duck pond water. Field deployment demonstrated that the system could be operated by non-laboratory personnel with minimal training in a non-clinical setting. This study establishes the feasibility of near-real-time environmental monitoring. Repurposing clinical cartridge-based point-of-care diagnostics offers a practical early warning approach for avian influenza virus surveillance at ecologically and economically significant locations.

Competing Interest Statement

Steven G Badman is employed by Cepheid who supplied the Xpert Flu/RSV kits for free. Jo-Ann Stanton is the owner of JStanton Consulting Ltd who contributed in kind resources to the project. JLS has received support from Cepheid and Roche to attend scientific meetings.

Funder Information Declared

Te Niwha, TN/SWC/24/UoOJG

Rutherford Discovery Fellowship, RDF-20-UOO-007

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.03.23.713605v1

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