Within- and between-host #dynamics of highly pathogenic avian #influenza in domestic #birds from #Pennsylvania #farms and live bird #markets

 

Abstract

Since late 2021, highly pathogenic avian influenza viruses (HPAI) of the H5 subtype clade 2.3.4.4b have spread across the Americas, devastating wildlife, agricultural animals, and resulting in dozens of human spillovers. National surveillance strategies generally provide only a single representative sequence per poultry outbreak, precluding fine-scale geographic transmission inference or studies of within-outbreak evolution. We produced high-quality deep sequence data from 46 infected Galliformes and Anseriformes sampled from commercial farm and live bird market (LBM) outbreaks in Pennsylvania from 2023-2025. We found that H5N1 viruses were introduced into Pennsylvania at least 68 independent times. We recover independent origins of live bird market outbreaks within the same county 3 weeks apart, and transmission between Pennsylvania LBM and New York commercial birds, suggesting high transmission risk within the Northeast live bird market distribution system. Analyses of within-farm variant populations show frequent variant sharing between samples from the same outbreak, suggesting that variants are propagated among epidemiologically linked infections. We identified 9 known adaptive mutations in these samples, including one instance of PB2 D701N in a LBM chicken sample, suggesting that while rare, concerning mammalian adaptive mutations can be present within these domestic outbreaks. Our data suggest that domestic bird outbreaks support high circulating diversity and wide transmission bottlenecks, increasing the risk of minority variants arising and propagating between infections. These data can help inform targeted biosecurity measures and better quantify the risk of viral adaptation during agricultural outbreaks.

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

NIAID, NIH 75N93021C00015

Pew Charitable Trusts

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.07.17.739193v1

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#Togo - High pathogenicity avian #influenza #H5N1 viruses (Inf. with) (#poultry) - Immediate notification

 

Poultry farms in the Maritime Region.

Source: 

Link: https://wahis.woah.org/#/in-review/7714

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Detection of #H5N1 HPAIV Clade 2.3.4.4b Avian #Influenza Virus in Backyard #Chickens in #CostaRica

 

Abstract

Influenza A virus is a segmented, negative-sense RNA virus. Since the early 2020s, H5 clade 2.3.4.4b viruses have spread widely across Europe, Africa, and Asia, affecting wild birds and poultry. Costa Rica reported its first H5 clade 2.3.4.4b avian influenza virus (AIV) case on 19 January 2023. This study describes an outbreak in backyard chickens and ducks. Initial serum samples collected on 24 January showed three chickens negative for AIV, while one duck tested positive by ELISA and agar gel immunodiffusion (AGID). During a second visit on 27 January, three of four chicken sera collected tested positive by ELISA and AGID. Tissue samples were positive for influenza A by qRT-PCR. Next-generation sequencing recovered five of the eight viral genomic segments, and the hemagglutinin cleavage site sequence (REKRRKR↓G) confirmed a highly pathogenic avian influenza virus (HPAIV) H5 strain. The samples were submitted to the National Veterinary Services Laboratories for confirmation. Serological testing showed reactivity to North American low pathogenic H5 antigens, and qRT-PCR amplified influenza A and N1 genes. Virus isolation and next-generation sequencing (NGS) of all eight viral genome segments were successfully performed at the WHO Collaborating Centre at St. Jude Children’s Research Hospital (SJCRH).

Source: 

Link: https://www.mdpi.com/1999-4915/18/7/799

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Pan-continental #spillover #risk: integrated spatiotemporal, transmissibility and #surveillance analysis of avian #influenza #H5N1 in #Africa

 

Abstract

Background: 

The HPAI H5N1 panzootic represents a critical threat to human health in Africa, where traditional poultry systems and dense human-animal interfaces facilitate frequent zoonotic spillover. While sporadic human cases raise pandemic concerns, continent-wide integration of spatial dynamics, transmissibility indicators, and surveillance performance has been lacking. This study quantifies avian influenza transmission over two decades across Africa, identifies geographical hotspots, and evaluates the responsiveness of current surveillance systems.

Methods: 

We analysed 8,037 avian influenza outbreak events and 369 laboratory-confirmed human cases, predominantly caused by HPAI H5N1 (2004–2025), using harmonised data from FAO (EMPRES-i+), WHO, and WOAH. A Bayesian Besag-York-Mollié (BYM) spatiotemporal model estimated residual transmission risks and Incidence Rate Ratios (IRR) by subtype. The basic reproduction number (R₀) was derived via an exponential growth model applied to human outbreak phases across infectious durations of 7–30 days. Surveillance responsiveness was assessed by quantifying notification delays between clinical observation and official reporting.

Results: 

Risk of infection in animals: HPAI H5N1 was the dominant strain, representing 87.8% of animal cases, with Egypt acting as the primary epidemiological epicentre (66% of total records). The spatiotemporal model revealed that H5N1 is associated with a significantly higher risk of animal infection (IRR = 8.37; 95% CI: 6.65–10.53). Although 71% of outbreaks were reported within 5 days of detection, significant delays (≥15 days) occurred in 12% of cases, with notable regional disparities. Risk of infection in human: H5N1 was associated with a 67-fold increase in the incidence of human cases compared to other subtypes (IRR = 66.78; 95% CI: 25.29–176.37). Sensitivity analyses yielded R0 estimates ranging from 1.05 (95% CI: 0.91–1.31) to 1.23 (95% CI: 0.60–2.33), indicating localised epidemic potential.

Conclusion: 

Our findings highlight a persistent and geographically heterogeneous H5N1 reservoir in Africa with high zoonotic affinity. Although sustained human-to-human transmission remains limited, the identification of dual poultry-human hotspots and localised R0 peaks underscores the urgent need for geographically targeted One Health interventions. Strengthening real-time reporting systems and improving biosecurity in high-risk poultry value chains are critical to mitigating future pandemic threats on the continent.

Source: 

Link: https://www.frontiersin.org/journals/epidemiology/articles/10.3389/fepid.2026.1813211/full

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

 

    ° As a result of the strengthened epidemiological surveillance of avian influenza implemented by the National Agri-Food Health and Safety Services (SENASA), a report was received regarding an unusual increase in mortality among backyard birds in a community, associated with contact with wild birds. 

    ° In response, national protocols for addressing suspected cases of high pathogenicity avian influenza (HPAI) were immediately activated, including the conduct of an epidemiological investigation, sample collection, and the implementation of containment measures established in the National Contingency Plan. 

    ° Analyses conducted by the official laboratory confirmed the presence of the high pathogenicity avian influenza virus, prompting the implementation of the corresponding sanitary measures. 

    ° These included the culling of affected birds and susceptible birds (stamping out) on adjacent properties within the risk zone; the safe disposal of products and materials considered to pose a risk; as well as the cleaning and disinfection of the facilities and all potentially contaminated items, with the aim of reducing the risk of the virus spreading. 

    ° Additionally, SENASA has established an outbreak zone, a perifocal zone, and a surveillance zone around the confirmed outbreak, where intensified epidemiological surveillance, sampling of susceptible birds, epidemiological investigations, restriction of bird movement, and risk communication efforts targeting producers and the general public are being carried out; furthermore, the Ministry of Health has been notified to ensure a joint response to the event. 

    ° These activities aim to promptly detect any associated events and verify the effectiveness of the control measures implemented. 

    ° SENASA will continue epidemiological monitoring of the event until the activities established in the National Contingency Plan are completed and the absence of viral circulation in the affected area is demonstrated. 

    ° It will also keep producers, authorities, and the general public informed through periodic updates to the relevant reports.

    ° The affected population consisted of backyard birds, comprising susceptible domestic species raised in family-based production systems. 

    ° These birds were of various age groups and were in frequent contact with the outdoor environment, a condition that facilitates interaction with wild birds and increases the risk of exposure to the high pathogenicity avian influenza virus.

Source: 

Link: https://wahis.woah.org/#/in-review/7710

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#Peru - High pathogenicity avian #influenza #H5N1 viruses (Inf. with) (#poultry) - Immediate notification

 

    ° The National Agricultural Health Service (SENASA) within its epidemiological surveillance responds to reports of suspected animal diseases. 

    ° It has identified an outbreak of highly pathogenic avian influenza in poultry (fighting birds) exhibiting respiratory and neurological signs. 

    ° Real-time PCR confirmed the presence of the H5N1 avian influenza virus, prompting the immediate implementation of quarantine measures and an epidemiological investigation. 

    ° All birds were culled, and the affected premises were cleaned and disinfected; in addition, surveillance around the outbreak was conducted to detect possible cases.

    ° A premises raising fighting cocks and backyard poultry of various ages

Source: 

Link: https://wahis.woah.org/#/in-review/7700

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Highly Pathogenic Avian #Influenza #H5N1 in South #America, 2022–2025: Spread, Affected Species, and Southward Expansion into the #Antarctic Region

 

Abstract

The H5N1 highly pathogenic avian influenza (HPAI) virus has caused severe global losses, reaching South America in 2022 and Antarctica in 2024. Here, we synthesize outbreak reports submitted to the World Organization for Animal Health by South American countries and overseas territories in this continent, and document the virus’s unprecedented expansion into Antarctica, affecting wild birds, wild mammals, and domestic poultry. Phylogenetic and time-calibrated Bayesian analyses were performed on available genomic sequences. Over 6 million domestic birds were lost, mostly from commercial operations. Of the 11 South American countries and overseas territories that reported H5N1 to WOAH, 10 reported infections in wild birds, spanning 104 species, 59.62% of which are migratory and predominantly non-trans-equatorial. Marine mammal outbreaks followed wild bird detections, with the South American sea lion (Otaria flavescens) being the most reported species. Several Antarctic bird species with migratory behavior were also reported in South America. Genomic analyses revealed multiple introduction events, regional viral diversification, and patterns consistent with repeated cross-species spillover events. These findings highlight H5N1’s extensive ecological reach in the Southern Hemisphere and underscore the urgent need for a One Health approach that strengthens wildlife and backyard-poultry surveillance, alongside coordinated regional action to control and prevent further HPAI spread.

Source: 

Link: https://www.mdpi.com/1999-4915/18/7/764

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#Philippines - High pathogenicity avian #influenza #H5N1 viruses (Inf. with) (#poultry) - Immediate notification

 

    ° A backyard poultry flock in the Oriental Mindoro Region.

Source: 

Link: https://wahis.woah.org/#/in-review/7687

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Characterization of #oseltamivir-resistant #H5N1 clade 2.3.4.4b, genotype #D1.1 #variants identified in #poultry farms of British Columbia, #Canada

 

ABSTRACT

Highly pathogenic avian influenza A(H5N1) viruses of clade 2.3.4.4b, genotype D1.1, are responsible for widespread outbreaks in poultry and continue to cause sporadic, sometimes severe, human infections. Herein, we characterized a wild-type (WT) influenza A(H5N1) D1.1 isolate (BC-H5N1-WT) and its H275Y neuraminidase (NA) variant (BC-H5N1-H275Y), both of which emerged on farms in British Columbia, Canada, during the fall 2024 outbreak. In vitro analysis assessed replication kinetics in MDCK cells, with supernatants collected at different days post-infection (p.i.) and titrated by TCID50 and qRT-PCR. Neuraminidase inhibitor (NAI) susceptibility was determined by NA inhibition assays, whereas susceptibility to baloxavir acid (BXA) was evaluated by plaque reduction assay. In vivo virulence was evaluated in BALB/c mice infected with serial 10-fold dilutions of each virus to monitor weight loss and mortality. Viral titers in lungs, brain, nose, kidney, spleen, and heart were quantified at day 4 p.i. The BC-H5N1-WT virus was susceptible to the four antivirals tested, whereas BC-H5N1-H275Y displayed resistance to oseltamivir and peramivir but remained susceptible to zanamivir and BXA. The BC-H5N1-WT exhibited significantly higher viral replication titers than BC-H5N1-H275Y at all tested time points and showed larger plaque sizes. In mice, BC-H5N1-WT was more virulent with LD50 values of 1.78 × 103 PFUs compared to 8.71 × 104 PFUs for BC-H5N1-H275Y, and produced higher viral titers in lungs and other organs. Despite the reduced fitness of the resistant H5N1 D1.1 variant, its emergence in the absence of viral selection pressure underscores the need for continued surveillance.

Source: 

Link: https://www.tandfonline.com/doi/full/10.1080/22221751.2026.2686474

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

 

    As part of the epidemiological surveillance activities carried out by the Colombian Agricultural Institute, aimed at the early detection of clinical signs consistent with avian influenza, an outbreak of high pathogenicity avian influenza was confirmed in the village of Puerto Murillo, in the municipality of Puerto Carreño, Vichada Department. 

    The outbreak affects non-poultry birds in a backyard, in which digestive symptoms and mortalities were observed. 

    The National Veterinary Authority initiated screening and epidemiological monitoring efforts in the area of origin of the affected birds. 

    As a control measure, all the birds in the epidemiological unit were culled, and, in addition, epidemiological surveillance in the surrounding area was strengthened to identify other possible cases and prevent the spread of the outbreak.

    The animal health event occurred on a family subsistence farm (backyard) and affected only a flock of birds that, according to the definitions in the WOAH Terrestrial Animal Health Code, are not considered poultry, as they are intended solely for the household consumption without commercial purposes or links to livestock production chains. 

    The reported clinical picture was characterized by weakening, anorexia, profuse diarrhea, and high mortality following epidemiological contact with migratory wild birds.

Source: WOAH, https://wahis.woah.org/#/home

Link: https://wahis.woah.org/#/in-review/7674

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

Laying hens and ducks in the Niedersachsen Region.

Source: WOAH, https://wahis.woah.org/#/home

Link: https://wahis.woah.org/#/in-review/7679

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Avian #influenza #overview March–May 2026 (ECDC, Summary, June 26 '26)

26 June 2026

Publication series: Avian influenza overview

    

    Between 28 February and 4 June 2026, 949 highly pathogenic avian influenza (HPAI) A(H5) virus detections were reported in domestic (186) and wild (763) birds in 30 countries in Europe.

Abstract

    The downward trend in the number of detections observed at the end of the previous reporting period continued and is expected to persist throughout the summer. 

    While the number of HPAI A(H5N1) outbreaks in domestic birds remained at a low level, except in a few countries, A(H9N2) virus of clade G5.5 was detected in poultry in Europe for the first time. 

    Following the intense circulation of HPAI viruses in waterfowl in recent months, sporadic detections were reported in mammals, particularly in wild carnivores, including the detection of A(H5N5) virus in a polar bear and a walrus in Norway. 

    Outside Europe, the focus of HPAI virus detections shifted from North to South America, where a large number of outbreaks and mortality events in swans were reported. 

    Between 28 February and 4 June 2026, 19 cases of avian influenza virus infection were publicly reported in humans (including three fatal cases) in six countries and territories: Bangladesh (two cases with A(H5N1), one fatal), Cambodia (three cases with A(H5N1), one fatal), India (one case with A(H5N1)), Italy (one imported case with A(H9N2)), China (10 A(H9N2) cases and one fatal A(H5N6) case), and Taiwan (one A(H7N7) case). 

    Most human cases reported exposure to poultry or a poultry environment prior to detection or onset of illness. 

    Human infections with avian influenza viruses remain rare and no sustained human-to-human transmission has been documented. 

    The risk posed by avian influenza A(H5N1) clade 2.3.4.4b viruses currently circulating in Europe remains low for the general public in the European Union/European Economic Area (EU/EEA) and low-to-moderate for those occupationally or otherwise exposed to infected animals or contaminated environments.

Source: 

Link: https://www.ecdc.europa.eu/en/publications-data/avian-influenza-overview-march-may-2026

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#Honduras - High pathogenicity avian #influenza viruses (Inf. with) (#poultry) - Immediate notification

 

    As a result of the ongoing operation of the epidemiological surveillance system, which actively promotes the detection and reporting of events, the Official Veterinary Services of Honduras (of the National Agri-Food Health and Safety Services, SENASA) received a report of a sudden high mortality rate at a breeding farm. 

    Upon receiving the notification, health authorities responded immediately to conduct an epidemiological investigation, collect samples, and place the premises under quarantine. 

    Following subsequent laboratory confirmation of high pathogenicity avian influenza (HPAI), SENASA proceeded to implement the protocols established in the National Plan for the Prevention, Early Detection, Control, and Eradication of Avian Influenza. 

    The control health measures included the culling of all breeding birds. 

    Likewise, at the hatchery that received batches of fertile eggs from that farm, 89,900 chicks and 315,979 incubated eggs were disposed of, following strict biosecurity protocols to ensure proper disposal. 

    Currently, the cleaning and disinfection of the facilities are underway. 

    For its part, SENASA maintains active surveillance of backyard birds through community-based epidemiological surveys, of wild birds by promoting reporting, and of production farms by strengthening biosecurity and targeted sampling. 

    To this end, communication processes and mandatory reporting have been strengthened, working jointly with the country’s poultry industry, other government institutions, and cooperation agencies to enhance surveillance and early detection of the disease. 

    Furthermore, through a communication and awareness campaign, biosecurity measures are being promoted in both commercial establishments and backyards. SENASA has already formally notified its trading partners of the event, and updates will be provided in future reports.

Source: 

Link: https://wahis.woah.org/#/in-review/7652

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Epidemiological and Virological Characteristics of #H9N2 Avian #Influenza Virus in #Jiangsu Province, #China, 2024

 

Abstract

H9N2 avian influenza viruses inherently carry cross-species transmission potential, making continuous surveillance critical for pandemic prevention. This study focused on monitoring the 2024 H9N2 epidemic in Jiangsu Province’s external environment, analyzing its molecular evolution and receptor binding properties, assessing cross-species transmission and pandemic risks, and investigating serological antibody levels across different human populations. Environmental samples were collected from live poultry markets, farms, slaughterhouses, and bird habitats across Jiangsu, screened via quantitative PCR (qPCR), with positive samples used for virus isolation and whole-genome sequencing. Receptor binding properties were tested by hemagglutination assay, and H9N2 antibody levels were measured in 370 occupationally exposed individuals and 240 non-exposed individuals using hemagglutination inhibition (HI) assays. Among the 5779 collected samples, 6.89% tested H9N2-positive, and 12 strains belonging to the Eurasian lineage Y280-like clade G57 genotype were successfully isolated. All strains carried the HA-Q226L mutation, with 11 showing preferential binding to human α-2,6 receptors and one strain possessing dual receptor binding capability. Internal genes harbored mammalian adaptation mutations, and M2 proteins contained mutations conferring complete resistance to amantadine-class antiviral drugs. Serological tests revealed antibody positive rates of 4.05% in exposed populations and 2.5% in non-exposed populations, with no statistically significant difference between groups. These findings confirm that Jiangsu’s circulating H9N2 viruses have acquired human receptor preference and mammalian adaptation, posing silent infection and pandemic risks. Enhanced surveillance and the development of candidate vaccine stockpiles are strongly recommended.

Source: 

Link: https://www.mdpi.com/1999-4915/18/6/687

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The Winners Take It All? #Global Evolutionary #Success of #H5Nx #Reassortants in the 2020–2024 #Panzootic

 

Abstract

Avian influenza viruses undergo frequent genetic reassortment, which can coincide with phenotypic changes in transmission, pathogenicity, and host species niche. Since 2020, clade 2.3.4.4b H5 high pathogenicity avian influenza viruses (HPAIVs) have driven a global panzootic, causing mass mortality in wild birds, poultry, and, for the first time, repeated spillover infections in a variety of mammalian species. This worldwide resurgence of H5 HPAIV has coincided with a dramatic increase in the number of circulating reassortant strains; however, the scale, impact and drivers of these reassortants remain unclear. Here, we combined statistical and phylodynamic modelling to reconstruct the global evolutionary dynamics of H5Nx viruses across four epizootic seasons (2020-2024). We identified 209 genetically distinct reassortants, stratified into three transmission categories based on their phylogenetic and epidemiological profiles. Accounting for sampling depth and HPAIV incidence, we estimated that reassortants emerged most frequently from Asia, but `major' reassortants associated with increased host range, inter-seasonal persistence, and long-range dissemination, more frequently emerged from Europe. Altogether, reassortant emergence followed an episodic pattern in which most reassortants were transient, but 2% seeded large clusters of secondary reassortants soon after their own emergence. Statistical modelling revealed that reassortant success was strongly shaped by ecological factors, including sustained circulation in specific wild bird orders and detection across a wider range of host niches. Collectively, our findings uncover global reassortment dynamics in H5 HPAIVs and identify key virological and ecological drivers underpinning the emergence and spread of successful reassortants. These insights support the importance of enhanced surveillance to track evolution of H5 HPAIV and identify traits relevant for consideration in pandemic risk assessment.

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

Biotechnology and Biological Sciences Research Council, BB/V011286/1, BB/X006204/1, BB/X006166/1, BB/Y007271/1, BB/Y007298/1

Biotechnology and Biological Sciences Research Council - Institute Strategic Grants, BBS/E/RL/230002C, BBS/E/RL/230002D

Medical Research Council, MR/Y015045/1, MR/Y03368X/1

National Natural Science Foundation of China, https://ror.org/01h0zpd94, 32061123001, 32425053, 32200416

National Key Research and Development Program of China, 2023YFC2307500, 2024YFE0106000

European Union, 727922, 874850, 101094685, 101084171, 874735

Fonds National de la Recherche Scientifique, F.4515.22

Fonds voor Wetenschappelijk Onderzoek — Vlaanderen, G098321N

Source: 

Link: https://www.biorxiv.org/content/10.1101/2025.07.19.665680v2

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#Bhutan - High pathogenicity avian #influenza #H5N1 viruses (Inf. with) (#poultry) - Immediate notification

 

A poultry farm in Samdrupjongkhar Region.

Source: 

Link: https://wahis.woah.org/#/in-review/7623

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#Sweden - High pathogenicity avian #influenza #H5N1 viruses (Inf. with) (#poultry) - Immediate notification

{Helsingborg Region} This is a farm with mallards for restocking for game and breeding for this purpose. The mallards showed an increse in mortality. Euthanasia is ongoing. 

Source: 

Link: https://wahis.woah.org/#/in-review/7622

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

 

A flock of backyard laying hens in Bayern Region.

Source: 

Link: https://wahis.woah.org/#/in-review/7616

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#Senegal - High pathogenicity avian #influenza #H5N1 viruses (Inf. with) (#poultry) - Immediate notification

 

The farm is part of mixed-species premises with several types of animals, including ducks, broiler chickens, Goliath chickens, and rabbits. Two male breeding ducks were purchased at the Passy market on May 8, 2026, in the department of Foundiougne, located in the Fatick region, to restock the flock and ensure mating with the females. One of the newly introduced adult males died from the disease, while the other survived. The quarantine period for the two new ducks was not applied properly. The first symptoms appeared on May 11, 2026, and the first deaths occurred on May 12, 2026. In total, among the ducks, 29 deaths were recorded out of a flock of 50, representing a mortality rate of 58%. As for the Goliath chickens, out of a flock of 11, 4 deaths were recorded, representing a mortality rate of 36.36%. Additionally, 7 other birds were culled by the manager following the appearance of clinical signs.

Source: 

Link: https://wahis.woah.org/#/in-review/7593

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Predicting #Influenza Virus #Host #Tropism and Zoonotic #Spillover #Risk from #Protein Sequences

 

Abstract

Novel infectious diseases, predominantly originating from non-human animals, pose a significant threat to global public health and economic stability. Avian influenza virus presents an especially significant challenge due to its high mortality rates and spillover capability into new host species. Recent H5N1 spillover events into poultry and cattle resulted in massive economic burden and increased human health risk. Traditional methods of disease surveillance rely on reactive case detection and pathogen characterization, providing insufficient lead time for effective intervention. Computational tools that allow efficient and proactive prediction of zoonotic potential are critical in mitigation of influenza outbreaks and identification of strains with human spillover risk. Existing models predicting influenza virus subtypes or host have been developed; however, the complexity of spillover events, including the non-binary nature of zoonotic potential, limits the capabilities of these models. In the approach reported here, rich protein language model embeddings were generated from ESM-2 for each protein in influenza virus strains and used to predict the protein host tropism probabilities across nine animal families. The protein host tropism model achieved weighted precision and recall scores of 0.95 and 0.95, respectively. We then constructed a zoonotic risk prediction model using the outputs from the protein host tropism prediction model to classify the strains into six classifications: avian, mammal, human, avian-to-human zoonotic, avian-to-mammal zoonotic, or mammal-to-human zoonotic. The average weighted precision and recall scores for this model were 0.90 and 0.90, respectively. This framework advances the prediction of influenza zoonotic risk by being agnostic to influenza subtype, incorporating non-human mammals and mammal zoonotic spillover classifications, and using the full influenza proteome to capture the complexity of spillover dynamics.

Competing Interest Statement

The authors have declared no competing interest.

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.05.21.726772v1

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