#Virus-host #interactions on #volcanic #ash from Mount #Etna

 

Abstract

Volcanic ash represents an extreme and dynamic habitat, yet it hosts diverse microbial communities with largely unexplored viral diversity. This study investigated bacterial and viral populations in volcanic ash from Mount Etna (Italy) collected during the eruption, focusing on microbial novelty, activity, and virus-host interactions. Taxonomic profiling revealed that Pseudomonas and Telluria were the dominant bacterial genera, both frequently detected in airborne environments. In contrast, enrichment cultures with volcanic ash were dominated by spore-forming members of the phylum Bacillota, highlighting their resilience under harsh conditions. Metagenomic analysis recovered 19 high-quality metagenome-assembled genomes, including four previously undescribed bacterial species. Replication rate estimates showed that certain taxa were metabolically active, particularly at one sampling site. The presence of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) systems with spacers matching viral sequences suggested viral predation pressure on volcanic ash. A total of 1139 viral operational taxonomic units (vOTUs) were identified, of only around half (660 vOTUs) showed similarities to known phages, underscoring the presence of novel viruses. Shared vOTUs across sites revealed the presence of both a core virome and site-specific viral populations. Virus-host predictions indicated frequent interactions with hosts from multiple Gammaproteobacterial genera. Additionally, a 336 kb jumbo phage genome exhibited extensive metabolic capabilities and genetic autonomy. Experimental work identified a unique lytic Bacillus-infecting phage (″Phoenix″) with limited propagation capacity. Furthermore, prophage induction experiments revealed active, morphologically diverse temperate phages across multiple bacterial host strains. Overall, these findings highlight volcanic ash as a reservoir of microbial and viral diversity, shaped by environmental extremes and dynamic ecological interactions.

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

Swedish Research Council, https://ror.org/03zttf063, 2023-03310_VR, 2022-06725

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.06.17.732739v1?rss=1

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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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The #canine respiratory #epithelium is a permissive #ecosystem for #influenza interspecies #transmission and emergence

 

Abstract

The outcome of virus spillover ranges from dead-end infections to pandemics and is underpinned by host-pathogen interactions as well as evolutionary and epidemiological processes. The emergence of novel influenza A viruses (IAVs) has been associated with reassortment events involving multiple species, highlighting the importance of reservoir and intermediate hosts in viral emergence. Highly pathogenic H5N1 IAVs of the 2.3.4.4b genotype have caused a panzootic affecting a broad range of mammals. The role of dogs -arguably the most popular companion animal and a natural host of IAVs- in the ecology of IAVs under this new zooepidemiological scenario is unknown. To address this, we characterised the glycome of the dog respiratory epithelium, infected canine tracheal explants with multiple IAVs (including canine H3N2 and H3N8, equine H3N8, avian H3N8 and H5N1, swine H1N1, human H1N1 and H3N2, and bovine H5N1 viruses), and determined their cellular tropism. We show that the respiratory tract of dogs presents abundant sialylated glycans known to act as IAV receptors. Further, most IAVs (including 2.3.4.4b viruses) infected and replicated in dog tracheas, targeting mainly ciliated cells. Serological testing showed evidence of influenza spillover infections in dogs from the UK. Overall, our results show that the canine respiratory tract can provide a suitable environment for the generation of new IAVs. Given the multi-host contact networks of dogs in nature, they could act as recipients, bridging hosts, and/or mixing vessels for multiple IAV lineages, playing a central role in the ecology of influenza emergence.

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

Medical Research Council, https://ror.org/03x94j517, MR/Y03368X/1, MC_UU_0034/2, MC_UU_0034/3

Biotechnology and Biological Sciences Research Council, BB/Y007093/1, BB/Y007298/1, BBS/E/PI/230001A, BBS/E/PI/230002A, BBS/E/PI/230002B, BBS/E/PI/230001C

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.06.04.730051v1

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Two #epidemics, one #genotype, different outcomes: evolutionary #changes of Avian #Influenza #H5N1, genotype EA-2024-DI

 

Abstract

Since 2020, high pathogenicity avian influenza H5Nx viruses of clade 2.3.4.4b have become enzootic in Europe, causing recurrent epidemic waves characterized by extensive reassortment events. Here, we describe the emergence of a single high-fitness genotype (EA-2024-DI) that has driven two consecutive waves, evolving into distinct sub-lineages. While its circulation is ongoing, during the 2025-2026 wave it caused an unprecedented number of cases in wild birds. Using phylodynamic analyses of a large dataset of genomic sequences, we compared the spatial diffusion and host transmission pattern of the EA-2024-DI sub-lineages across the three most recent epidemic waves (2023-2024, 2024-2025 and 2025-2026). We show that the genotype has persisted over time and has spread primarily through wild Anseriformes, but with a marked change in the transmission patterns between the different waves and a shift in the epicenter from Eastern to Central Europe, the latter having emerged as an important hub for virus diffusion throughout Europe. Our results reveal a recent increase in the frequency of viruses from wild and domestic mammals carrying mutations enhancing virus replication in mammalian hosts, highlighting the importance of proactive monitoring of this group of hosts to better understand its role in the virus ecology and evolution.

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

Funded by the European Union under grant agreement (101084171) - (Kappa-Flu). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or REA. Neither the European Union nor the granting authority can be held responsible for them

Support for this work was provided by the European Union within the framework of the activities foreseen by the European Union Reference Laboratory for Avian Influenza and Newcastle Disease under grant agreement 101201937

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.05.25.727580v1

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The Q226H #Mutation in #Avian #H5N1 #Hemagglutinin Mediates a Path towards Structural #Adaptation in #Humans

 

Abstract

The global outbreak of highly pathogenic avian influenza (HPAI) A(H5N1) among birds and the spillover to mammals increases the risk for humans. A recent case in British Columbia with a clade 2.3.4.4b H5 virus infection revealed a mixture of 226Q/H in the receptor-binding site of hemagglutinin. While significant changes in pre-existing immunity by H1 or H3 polyclonal sera are not evident, we show that the Q226H mutation enables binding to human-type α2-6 sialic acid receptors. High-resolution cryo-EM structures provide a basis for the alteration in receptor preference and show that a possible path towards human adaptation also requires a conformational change of the bound α2-6-sialylated glycan. Continued surveillance for additional mutations that could enhance this phenotype is warranted.

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

Ministry of Technology and Innovation through Striving for Pandemic Preparedness—The Alberta Research Consortium

Canada Excellence Research Chair Program

Alberta Innovates Graduate Student Scholarship

Canada Biomedical Research Fund grant

Biosciences Research Infrastructure Fund grant

Natural Sciences and Engineering Research Council of Canada Discovery Grant

Natural Sciences and Engineering Research Council of Canada

Canada Foundation for Innovation

Alberta Innovation and Advanced Education Research Capacity Program

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.05.21.726965v1

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#Zoonotic #infections and genomic #evolution associated with novel #reassortants swine-origin #influenza A viruses in #Spain

 

Abstract

Influenza A virus (IAV) circulates widely in European pig populations and continues to diversify through frequent introductions from humans, followed by reassortment within swine. Spain represents a particularly dynamic ecological setting due to the coexistence of intensive white pig production, extensive Iberian pig systems, and abundant wild boar populations. This study provides an integrated analysis of IAV evolution and genomic diversity in swine in Spain between 2019 and 2022, expanding on previous surveillance from 2016 to 2019. Sampling across 24 provinces yielded 66 new whole genome sequences from Iberian and white pigs. We identified 18 genotypes, including 11 novel reassortants not detected in our previous survey. Several genotypes, such as H1huN2 G21 and G22, H3N2 G23, and the unusual H3N1 G12, were exclusive to the country. Some genotypes were detected across white pigs, Iberian pigs, and wild boar in Toledo and Badajoz, suggesting viral flow among swine populations. Phylogenetic analyses revealed ongoing introductions of H1N1pdm09 from humans into pigs, generating at least five reassortant genotypes (G10, G16 to G19). These lineages incorporated pandemic internal cassettes and, in some cases, human seasonal N2 segments, highlighting the continued role of humans as a source of viral incursions. Conversely, four zoonotic infections (H1N1v) detected in Spain between 2022 and 2026 were linked to genotypes circulating in white pigs, underscoring the bidirectional nature of IAV transmission at the human swine interface. Overall, this study demonstrates that Spain provides ecological conditions conducive to IAV diversification, reassortment, and zoonotic risk. The findings reinforce the need for sustained One Health surveillance.

Competing Interest Statement

The A.G.-S. laboratory has received research support from Avimex, Dynavax, Pharmamar, and Accurius, outside of the reported work within the last three years. A.G.-S. has consulting agreements for the following companies involving cash and/or stock within the last three years: Castlevax, Amovir, Vivaldi Biosciences, Contrafect, Avimex, Pagoda, Accurius, Applied Biological Laboratories, Pharmamar, CureLab Oncology, CureLab Veterinary, Virofend and Prosetta, outside of the reported work. A.G.-S. has been an invited speaker in meeting events within the last three years organized by Seqirus, Novavax and Hipra. A.G.-S. is inventor on patents and patent applications on the use of antivirals and vaccines for the treatment and prevention of virus infections and cancer, owned by the Icahn School of Medicine at Mount Sinai, New York, outside of the reported work. The rest of the authors report no conflicts of interest.

Funder Information Declared

Centre for Research on Influenza Pathogenesis and Transmission (CRIPT), one of the National Institute of Allergy and Infectious Diseases (NIAID) funded Centres of Excellence for Influenza Research and Response (CEIRR), contract #75N93021C00014

Intramural Research Program of the National Library of Medicine at the US National Institutes of Health

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.05.22.724525v1

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Clade 2.3.4.4b #H5N1 #HPAIV from Migratory #Birds in Beidaihe #Wetland, North #China

 

Abstract

During 2022–2024, a highly pathogenic avian influenza virus (HPAIV) H5N1 strain, designated A/Seagull/Hebei/qhd6/2024 (H5N1), was isolated from migratory birds in Beidaihe National Wetland Park, North China. Phylogenetic analyses revealed that its hemagglutinin (HA) gene belongs to the 2.3.4.4b clade, while the neuraminidase (NA) gene and internal genes clustered with strains originating from multiple continents, consistent with a transcontinental reassortment event. The virus also exhibited 90.1–98.1% nucleotide homology with human-derived H5N1 isolates. Molecular characterization identified key virulence-associated mutations, including the classic HPAIV HA cleavage site, HA-T160A (associated with enhanced human receptor-binding capacity), and NA-I117T (potentially linked to drug resistance). BALB/c mouse infection experiments confirmed systemic replication and high pathogenicity of strain qhd6, with a 50% lethal dose (LD50) of 0.95 log10EID50/mL. Antigenic analysis revealed good cross-reactivity with the widely used H5-Re14 vaccine strain. This study reports the identification, in Beidaihe National Wetland Park, of an HPAIV H5N1 strain whose genetic characteristics suggest intercontinental reassortment and indicate cross-species transmission risk. It clarifies the genetic characteristics and pathogenicity of this strain, providing an important theoretical and practical basis for precise surveillance, risk early warning, and comprehensive prevention and control of AIV at migratory bird stopover sites in North China.

Source: 

Link: https://www.mdpi.com/1999-4915/18/6/595

____

Understanding the emergence of the #influenza #H3N2 K #subclade in its historical and evolutionary context

Abstract

The emergence in 2025/26 of the influenza A/H3N2 K substrain (H3N2/K) was the cause of significant public health concern. This genetically divergent virus was assessed to have a strongly decreased reactivity to contemporary vaccine strains. Respectively prolonged and early influenza seasons in the Southern and Northern Hemispheres contributed to concerns about vaccine efficacy. Here we retrospectively assessed the genetic and antigenic properties of this virus, combining epidemiological surveillance data, computational antigenic analysis, and serological data using samples from a well-stratified UK cohort. In contrast to initial indications, we found that despite the genetic distinctiveness of H3N2/K the virus had undergone limited antigenic change, suggesting that its emergence was instead the result of selection for non-antigenic properties. We confirmed previous results showing that contemporary vaccines produced an enhanced neutralising response to H3N2/K but, in a stratified serological analysis, showed that responses to the J and K substrains were age-dependent, largely driven by patterns of vaccination. Our results have implications for antigenic surveillance and for public communication strategies in future influenza seasons.

Competing Interest Statement

PRM declares funding by MSD. EH has received an honorarium for advisory board work for Seqirus.

Funder Information Declared

Medical Research Council, MR/Y03368X/1, MC_UU_0034/1, MC_UU_0034/2, MC_UU_0034/3, MC_UU_0034/5, MC_UU_0034/6

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.05.21.726823v1

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A Panel of #Human Monoclonal #Antibodies for Tracking the #Antigenic #Evolution of #Influenza #H5N1 Clade 2.3.4.4b

 

Abstract

The ongoing panzootic of clade 2.3.4.4b H5N1 influenza has resulted in widespread infection of birds, mammals, and livestock, underscoring the need for tools to interpret its real-time evolution. Here, we describe the isolation and characterization of a panel of 19 human monoclonal antibodies that potently neutralize current isolates. Competition immunoassays and cryo-electron microscopy analyses revealed their collective near-complete epitope coverage of the H5-hemagglutinin surface. Neutralization profiling across multiple historical and contemporary H5 viruses defined their epitope-specific patterns of virus neutralization. One cluster of antibodies potently neutralized only clade 2.3.4.4b viruses, while many others exhibited broadly neutralizing activity against diverse H5N1 clades. Application of this structurally calibrated antibody panel to recent North American human isolates revealed genotype-specific antigenic divergence between lineages that have spread among cattle (B3.13) and poultry (D1.1). Together, the findings of this study establish a structurally grounded antibody reference panel spanning major vulnerable sites of H5 hemagglutinin and provide a toolbox for interpreting emergent mutations, monitoring ongoing antigenic drift, and anticipating the evolutionary trajectory of circulating H5N1 influenza viruses.

Competing Interest Statement

H.H., M.W., S.C., J.Y., Y.H., Y.G., and D.D.H. are inventors on the provisional patent application filed by Regeneron for several H5N1 neutralizing antibodies described herein. D.D.H. is a co-founder of TaiMed Biologics and RenBio, consultant to Brii Biosciences, and board director for Vicarious Surgical.

Funder Information Declared

Gates Foundation, INV019355

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.05.14.725215v1

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#Reassortant High Pathogenicity Avian #Influenza #H5N1 Viruses During the Reemergence in #Uruguay Suggest Increasing #Genetic Diversity in South #America

 

Abstract

Highly pathogenic avian influenza (HPAI) H5N1 viruses of the goose/Guangdong (Gs/GD) lineage have driven a global panzootic since 2020, with clade 2.3.4.4b establishing sustained transmission in wild birds. In South America, early outbreaks were largely associated with the North American-derived B3.2 genotype, which showed limited diversification after its introduction. Here, we report the genomic characterization of eight H5N1 viruses detected in Uruguay during the reemergence of avian influenza in February–March 2026. Complete genomes were obtained from wild birds exhibiting neurological signs, predominantly Coscoroba coscoroba. All viruses belong to clade 2.3.4.4b but exhibit a reassortant genomic constellation distinct from B3.2. The HA, NA, and MP segments retain the Eurasian backbone, whereas internal genes derive from both South American and North American low-pathogenicity avian influenza lineages. PB2 variation distinguishes two closely related viral groups differing in PB2 origin, whereas the remaining genomic segments retain a shared background. Sequence variation in the neuraminidase gene reduced the sensitivity of a widely used N1-specific RT-qPCR assay, highlighting limitations of existing diagnostic tools during viral evolution. These findings confirm the presence of reassortant H5N1 viruses in Uruguay and, together with recent reports from Argentina and Brazil, support an emerging pattern of genomic diversification in southern South America.

Source: 

Link: https://www.mdpi.com/1999-4915/18/5/558

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#Outbreak of #H9N2 avian #influenza viruses in lesser #rhea in #Peru, June-July 2025

 

Abstract

Avian influenza viruses (AIVs) are endemic in the Americas and responsible for outbreaks in both domestic and wild birds that occasionally spill over into humans. We report the first known outbreak of AIV H9N2 in lesser rhea (Rhea pennata), also known as Darwin’s rhea, in the region of Puno-Peru. The animals in this study lived in an isolated conservation center located in remote highlands above 4,000 m.a.s.l. Between June and July 2025, a total of 46/92 animals were recorded sick, with symptoms including greenish diarrhea (100%), hyporexia (24%), dyspnea (76%), nasal discharge (42%), drowsiness (18%) and isolation from the flock (73%), and 94% later died. Gross pathology exams revealed septicemia characterized by severe hepatitis, pneumonia, tracheitis, enteritis, and encephalitis. Swab and necropsy samples tested positive for Influenza A by PCR and were later identified as H9N2 through whole genome sequencing. We generated complete H9N2 genomes for two individuals. No additional pathogens were found. Phylogenetic analysis across all eight segments revealed that the viruses were low pathogenicity H9N2 AIV strains of North American origin, which indicated this outbreak was a new introduction of the virus into South America. We also performed a comparative mutational analysis and identified multiple mutations previously associated with mammalian host adaptation, increased virulence, increased pathogenicity, and increased virus binding to α2-6 receptors, which may explain the high mortality rates observed despite the supposedly low pathogenicity of the strain. We also identified novel mutations specific to rhea viruses that will need to be experimentally validated. This is the first report of a natural H9N2 systemic infection in an avian host, highlighting a need for increased surveillance efforts for zoonotic influenza viruses with pandemic potential.

Competing Interest Statement

The authors have declared no competing interest.

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.05.08.723762v1

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G4 #Eurasian avian-like #H1N1 swine #influenza viruses exhibit enhanced #pathogenicity potential in mice and #pigs

 

Abstract

Currently circulating swine influenza viruses (SIVs) mainly include H1N1, H1N2, and H3N2 subtypes. In this study, two G4 genotype Eurasian avian-like (EA) H1N1 SIVs were isolated from 556 samples collected between 2023 and 2026. A systematic analysis was conducted on the two EA H1N1 isolates (FYD30 and YZF69) to assess their pandemic potential. The hemagglutinin (HA) proteins of both H1N1 viruses possessed residues 225E and 228S, indicating enhanced affinity for human-like alpha-2,6-linked sialic acid receptors, which was confirmed by receptor-binding assays. Polymerase activity tests demonstrated that the two SIVs exhibited significantly higher activity in mammalian cells, relative to avian cells, which is consistent with the efficient replication in mammalian cells. Challenge experiments revealed that both H1N1 caused significant pathogenicity in mice and pigs, with YZF69 exhibited higher virulence than FYD30. The higher virulence of YZF69 may be attributed to its molecular features, including the NP Q357K mutation, and an additional glycosylation site in HA. In conclusion, currently circulating EA H1N1 SIVs have acquired key molecular signatures of mammalian adaptation, exhibit enhanced virulence in mammals, and continue to undergo extensive reassortment driven by international swine trade. These findings highlight the potential pandemic risk of SIVs and underscore the urgent need for strengthened surveillance.

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.05.12.724537v1

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A single PA-X #mutation in #bovine-origin #H5N1 #influenza virus reduces #pathogenicity in mice

 

Abstract

Dairy cows have emerged as a reservoir for human infection with highly pathogenic avian influenza (HPAI) H5N1. At the bovine-human interface, H5N1 strains may acquire adaptive mutations that influence their zoonotic potential. Sequence analysis identified a K142E substitution (bovine to human) in the PA and PA-X proteins, with the potential to affect both polymerase activity and host shutoff. Here, we used a loss-of-function approach to investigate how the bovine substitution (E142K) in PA/PA-X impacts viral replication, host shutoff activity, and pathogenicity in the human H5N1 background. Viral growth kinetics demonstrated that the virus containing the E142K substitution is attenuated, with reduced replication compared to wild-type (WT) virus. Consistently, PA-X-mediated host shutoff activity was reduced, resulting in increased induction of interferon (IFN) responses relative to WT. In vivo, mice infected with the E142K mutant virus survived, whereas infection with the WT virus was uniformly lethal. Despite comparable viral titers and inflammation score in mouse lungs, cytokine and chemokine profiling revealed distinct immune responses, with reduced CCL2 and increased CCL5 and IFN-γ in mice infected with the E142K mutant virus compared to mice infected with the WT virus. These findings indicate that increased virulence of the human-adapted strain is driven by a PA-X mutation that modulates inflammatory responses, producing distinct immune signatures linked to host survival or viral lethality rather than changes in polymerase activity by PA. Collectively, these results highlight PA-X as a key determinant of pathogenicity of H5N1 and a potential target for the rational design of antiviral strategies.

Competing Interest Statement

The authors have declared no competing interest.

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.05.09.724031v1

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#Genetic and #biological characterization of #H9N2 avian #influenza viruses isolated from #swine in #China

 

Abstract

Background

H9N2 avian influenza virus (AIV) has been circulating in poultry in China for decades and are undergoing adaptation to mammals, posing potential pandemic risks. To investigate the prevalence of H9N2 AIVs in swine, we conducted surveillance in Shandong Province from 2021 to 2023.

Results

Two H9N2 influenza virus strains, A/swine/Shandong/417/2021(Sw/SD/417/21) and A/swine/Shandong/662/2022 (Sw/SD/662/22), were successfully isolated from swine and genetically characterized. Phylogenetic analyses showed that both isolates were reassortants containing gene segments from multiple H9N2 AIV lineages and closely related to currently circulating H9N2 AIV. Key molecular marker analysis revealed that both isolates carried mammalian-adaptive residues in the HA receptor-binding sites (183 N, 190 V, 226 L), a novel HA cleavage site variant (PSKSSRGL), PB2 mutations (A588V, E627V), and the M2 S31N substitution, suggesting potential adaptation to mammalian hosts and resistance to adamantane antivirals. Mice infection experiments demonstrated efficient viral replication in the respiratory tract, particularly in the lungs, but only mild histopathological changes were observed, with no significant weight loss or mortality, indicating low pathogenicity in mice. Serological surveillance of 3,172 swine serum samples showed a low prevalence of H9N2 influenza virus infection (0.44%), with positive samples sporadically distributed across regions and years.

Conclusion

In summary, although H9N2 AIV infection in swine is rare and generally mild, the presence of mammalian-adaptive markers and reassortant genomes highlights the potential risk of cross-species transmission and subclinical adaptation. Continuous avian–swine–human influenza surveillance is therefore essential to mitigate the potential threat posed by H9N2 AIV.

Source: 

Link: https://link.springer.com/article/10.1186/s12917-026-05501-z

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Emergence and #Evolution of Triple #Reassortant Highly Pathogenic Avian #Influenza #H5N1 Virus, #Argentina, 2025

 

Abstract

The H5N1 subtype of highly pathogenic avian influenza (HPAI) poses a major zoonotic threat due to its high fatality rate and capacity for cross species transmission. In early 2025, Argentina detected a novel triple reassortant A(H5N1) virus in Chaco Province, combining Eurasian, North American, and South American lineage segments. Genomic analyses of subsequent outbreaks in Buenos Aires and Entre Ríos confirmed persistence of this reassortant and additional HA substitutions (T204K, P251S) potentially linked to increased mammalian receptor affinity. Although PB2 sequences lacked canonical mammalian-adaptive markers (E627K, Q591K, D701N), all contained I292M, a mutation associated with human adaptation. Phylogenetic analyses revealed distinct genotypes and increasing divergence. These findings indicate ongoing viral evolution and adaptation within Argentina, emphasizing the urgent need for sustained genomic surveillance, timely data sharing, and integrated One Health strategies to mitigate zoonotic and socioeconomic risks associated with H5N1 spread in South America.

Source: 

Link: https://www.mdpi.com/1999-4915/18/5/525

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An #NS1-F161L #Substitution Determines #Host-Driven #Virulence Enhancement of #H5N6 Avian #Influenza Virus in #Ducks

 

Abstract

H5 subtype avian influenza virus (AIV) can infect both chickens and ducks, leading to substantial economic losses. Nevertheless, certain strains cause silent infections in ducks. In this study, a goose-origin clade 2.3.4.4h H5N6 AIV was isolated, which caused high mortality in mixed-gender white leghorn chickens but no deaths in mixed-gender mallard ducks. After independent serial in vitro passage in duck embryo fibroblasts (DEFs) and in vivo passage in specific-pathogen-free (SPF) ducks, the DEF-passage 10 (P10) virus induced markedly higher mortality rates and viral loads in SPF ducks compared to the DEF-P1 virus and the original parental virus prior to passage. Similarly, the in vivo-passaged P3 and P4 viruses exhibited significantly higher mortality rates than the P1 virus in SPF ducks, with 100% mortality and markedly increased viral titers in the organs. A whole-genome SNP analysis identified seven high-frequency mutations in the M1, NA and NS1 proteins. The NS1-F161L substitution virus exhibited significantly increased mortality rates, viral loads in multiple tissues, and a robustly induced innate immune response in ducks. Furthermore, dynamic evolutionary variations in the NS1 protein among global H5 avian influenza viruses revealed that the NS1-F161L substitution became dominant in clade 2.3.4.4b viruses in 2021 and subsequent years. Collectively, our findings demonstrate that host-driven adaptation can rapidly increase the pathogenicity of H5N6 AIVs in ducks and identify NS1-F161L as a critical virulence marker. These results offer novel insights relevant to the molecular surveillance, virulence prediction, and risk assessment of circulating H5 AIVs in waterfowl.

Source: 

Link: https://www.mdpi.com/1999-4915/18/5/488

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A natural five-amino-acid insert at the S2’ #cleavage site of #MERS-CoV #spike enhances viral membrane fusion

 

Highlights

• A novel 5-aa insert, TSGVF, is present at the S2’ cleavage site of the spike protein of MERS-CoV from dromedary camels.

• Pseudovirus-based entry assays showed that the TSGVF insert increases viral entry efficiency in different human cells.

• Pseudovirus with TSGVF insert at the S2’ cleavage site showed strong resistance to TMPRSS2 inhibitor.

• The natural occurrence of TSGVF insert at the spike S2’ cleavage site enhances viral membrane fusion and syncytia formation.

Source: 

Link: https://www.sciencedirect.com/science/article/pii/S1995820X26000611?via%3Dihub

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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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#Infection of the #bovine mammary #gland by avian #H5N1 subclade 2.3.4.4b #influenza viruses

 

Abstract

The emergence of the panzootic clade of highly pathogenic avian influenza H5N1 (2.3.4.4b) in 2020 marked a major expansion in the host range of influenza A viruses (IAVs), raising concerns about further cross‑species transmission events and zoonotic spillover. Introduction of 2.3.4.4b viruses into U.S. dairy herds has resulted in widespread circulation, accompanied by reduced milk yield, mastitis, and high viral loads in milk. Notably, virus circulation in dairy cattle represents a novel route for mammalian adaptation and transmission that has already led to more than 40 human cases in the U.S. since 2024. Here, we investigated whether avian clade 2.3.4.4b viruses could infect mammary tissue from Aberdeen Angus, Holstein Friesian, and Limousin cattle, three breeds commonly farmed in Europe, the Americas, and Oceania. Using mammary gland explants, we inoculated tissues with attenuated reassortant viruses expressing the haemagglutinin and neuraminidase glycoproteins of three 2.3.4.4b viruses that predated the emergence of H5N1 in US cattle: A/chicken/England/053052/2021 (AIV07), A/chicken/Scotland/054477/2021 (AIV09), and A/chicken/England/085598/2022 (AIV48). Infected epithelial cells were identified using immunohistochemistry in explants from both the teat and gland cistern for all three breeds following infection with AIV09 and AIV48, indicating that mammary tissue from each of the three tested cattle breeds cattle is permissive to H5N1 infection. Lectin staining showed expression of both α2,3‑linked and α2,6‑linked sialic acids in the mammary tissue of all donors showing that all three breeds have the potential to support infection with both avian-adapted and mammalian adapted IAVs. Together, these findings demonstrate that mammary glands from both beef and dairy cattle breeds are permissive to infection with avian‑adapted and mammalian-adapted H5N1 viruses and highlight the potential for this tissue to act as a mixing vessel for IAV reassortment, underscoring the need to include cattle in ongoing H5N1 surveillance and risk‑assessment frameworks.

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

Medical Research Council, https://ror.org/03x94j517, MR/Y03368X/1, MR/Y03368X/1, MC_UU_0034/2, MC_UU_0034/3, MC_UU_0034/1

Biotechnology and Biological Sciences Research Council, https://ror.org/00cwqg982, BB/V004697/1

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.04.16.718897v1

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Acquisition of specific #human respiratory tract binding of 2.3.4.4b #H5N1 #hemagglutinins requires multiple #mutations

 

Abstract

It has been suggested that the hemagglutinin of the human-infecting cattle-derived 2.3.4.4b virus A/Texas/34 (H5TX) requires only one mutation, namely Q226L, to switch from binding avian-type to human-type receptor preference. In this study, we examined the binding of H5TX Q226L, along with other key mutations, to sections of human trachea. We conclude that, while H5TX Q226L can bind human-type receptors, more than a single mutation is required for this protein to bind to human respiratory tract tissue. We also report changes in receptor-binding specificity of another 2.3.4.4b HA mutant, H5FR Q226L, associated with the presence of a multibasic cleavage site. This study offers insight into the determinants of evolution towards human-type receptor binding in currently circulating H5Nx viruses. It also emphasizes the importance of testing individual strains using additional methods, including tissue-based approaches, alongside synthetic glycans.

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

NWO, OCENW.M20.106

Horizon, 862605

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.04.16.718875v1

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