Assessment of Quantitative #Genetic #Distances Supports the Separation of #H17N10 and #H18N11 Subtypes of #Influenza a Virus into a Distinct Species

 

Abstract

The taxonomic status of the H17N10 and H18N11 influenza A viruses isolated from bats remains unclear due to the absence of quantitative classification criteria at this taxonomic level. A total of 3328 representative IAV genomes, encompassing all eight protein-coding segments, were analysed. Various genetic distance-based metrics were assessed at the pairwise level, including intra- and intergroup nucleotide distances, dN/dS ratios, and transition/transversion ratios, to facilitate the differentiation of the Alphainfluenzavirus genus into distinct taxa. Pairwise distances for seven of the eight segments (PB2, PB1, PA, NP, M, NA, NS) consistently differentiated the H17–H18 group from H1–H16. Across segments, intergroup nucleotide divergence was consistently above a lower bound of ~25%, with segment-specific values extending to higher levels (up to ~40% in PB2 and PA), while intragroup divergence remained substantially lower. The HA segment did not conform to this pattern, which is consistent with the hypothesis of ancient reassortment. The distribution of pairwise dN/dS values for the PB2, PB1, PA, and NP segments is evidently bimodal. Intergroup comparisons were consistently higher across all segments, whereas intragroup values remained lower. A similar lower boundary of approximately 0.12 was observed across segments, while the upper range of intergroup values varied by gene. Overall, the results support a consistent gene-specific separation pattern. Previously demonstrated absence of reassortment compatibility between bat viruses (H17–H18) and canonical influenza A (H1–H16) viruses indicates that these lineages have evolved independently over an extended period. These consistent genomic patterns provide support for the hypothesis that H17N10 and H18N11 viruses may represent a separate species within the genus Alphainfluenzavirus.

Source: 

Link: https://www.mdpi.com/1999-4915/18/8/838

____

#Mutations in severe #human #H5N1 cases facilitate #evasion from human mucus and #antivirals

 

Abstract

In late 2024, two individuals in Canada and the United States were treated in intensive care for acute respiratory distress caused by infection with the avian Influenza A Virus H5N1 2.3.4.4b genotype D1.1. Viral sequence data obtained from sampling these patients indicated mixed alleles at haemagglutinin (HA) positions 190 and 226. Mutations at these positions are key determinants of HA usage of α2,6-linked sialic acids (SA), the most abundant influenza receptors in human upper respiratory tracts. Thus, these mutations raised concerns about human adaptation and pandemic potential of the H5N1 virus. In this study, we investigated the impact of the mutations at residues 190 and 226 in H5 HA. We studied the receptor binding properties, cell entry phenotypes and fitness impacts of the mutations using recombinant proteins, pseudotyped lentiviruses, and in the context of influenza viruses using reverse genetics. The mutations did not confer any detectable α2,6-linked sialic acid receptor usage either alone or in combination. Rather, viruses carrying these mutations exhibit weakened binding towards α2,3-linked sialic acid receptors. This correlated with an enhanced capacity to evade human airway mucus, and a reduced susceptibility to oseltamivir and zanamivir. This research underscores that in addition to the way HA interacts with SA as entry receptors, other factors that impact the HA/NA balance might influence the evolutionary trajectory of a zoonotic virus in the human respiratory tract. This study presents a new paradigm for the evolutionary drivers of HA, where reduced sialic acid binding can serve as an advantage for escape from host barriers and antivirals.

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

Medical Research Council, https://ror.org/03x94j517, MR/Y03368X/1, MR/Y015061/1, CC2127

Biotechnology and Biological Sciences Research Council, BB/Y007298/1, APP104179, BBS/E/PI/23NB000, BBS/E/PI/23NB0003

Wellcome Trust, https://ror.org/029chgv08, CC2127, 218304/Z/19/Z

Department for Environment Food and Rural Affairs, BB/Y007298/1

The Pirbright Institute, BBS/E/PI/230002A, BBS/E/PI/230001C, BBS/E/PI/230002B

Cancer Research UK, CC2127

UK Research and Innovation, https://ror.org/001aqnf71, UKRI3602

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.07.28.740943v1

____

#H5N1 #influenza binding and cell entry via #human class II #MHC, and blocking by cross-reactive #antibodies

 

Abstract

Highly pathogenic avian influenza H5N1 clade 2.3.4.4b viruses are currently responsible for a multi-species outbreak affecting wild birds, poultry, numerous mammalian species, and humans. Influenza A viruses typically initiate infection through binding to sialic acid, although select bat and human influenza viruses can also exploit class II major histocompatibility complex (MHC–II) molecules for cell entry. Here we show that emerging H5N1 clade 2.3.4.4b viruses, but not historical H5 lineages, bind human MHC–II HLA-DR and mediate sialic acid-independent cell entry. Hemagglutinin binding to primary human immune cells varies with MHC–II expression and is further shaped by HLA–DR allelic variation, identifying host genetic determinants that may influence susceptibility to infection. Mammalian-adaptive substitutions within the hemagglutinin sialic acid receptor-binding domain reduce MHC–II binding, suggesting this interaction is remodeled during clade 2.3.4.4b H5 adaptation to a human host. Lastly, cross-reactive monoclonal antibodies isolated from clade 2.3.4.4b H5–naive humans can block the hemagglutinin–MHC–II interaction. These findings identify a previously unrecognized receptor pathway in contemporary H5N1 viruses and reveal that both human genetic variation and pre-existing humoral immunity can modulate this interaction, with implications for host range, cellular tropism, spillover risk, and therapeutic intervention.

Competing Interest Statement

S.D.B. has consulted for Regeneron, Sanofi, Novartis, Genentech, Pfizer, Visterra, and Otsuka on topics unrelated to the research presented here; owns stock in AbCellera Biologics; and is a scientific cofounder of Immunera, Inc.; S.E.H reports receiving consulting fees from Sanofi, Pfizer, Lumen, Novavax, and Merck.

Funder Information Declared

NIH/NIAID CEIRR contract, 75N93021C00015

NIH, 1U54CA260517

HIPC, U19AI057266

P01 grant, 5P01AI153559

David Crown Foundation endowment

Early Postdoc Mobility Fellowship Stipend from the Swiss

National Institutes of Health NRSA T32, T32OD011121

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.07.22.739677v1

____

Evolving #dynamics of #H5Nx avian #influenza in #China revealed by long-term wild bird #surveillance

 

Abstract

H5Nx highly pathogenic avian influenza viruses pose persistent threats to poultry, wildlife, and public health. Over the past two decades, their geographic and host ranges have expanded across migratory networks whose epidemiological connectivity has become increasingly apparent through recent surveillance and genomic analyses. To elucidate these dynamics, we conduct long-term nationwide wild-bird surveillance in China, integrating active and passive monitoring. Our analyses reveal the maintenance, reassortment, and transmission of H5Nx viruses in wild birds, highlighting the value of sustained surveillance in capturing viral evolution. We identify distinct ecological patterns among major clades, with 2.3.4.4b showing the widest distribution and acting as the main lineage mediating intercontinental spread. Since 2020, most 2.3.4.4b viruses detected in wild birds in China have clustered with lineages originating outside China, consistent with repeated reintroduction rather than sustained local circulation. This shift underscores the growing role of migratory connectivity in shaping global viral exchange and the need for coordinated international active surveillance.

Source: 

Link: https://www.nature.com/articles/s41467-026-76039-9

____

Characterization and evolutionary history of novel #SARS-CoV-2-related viruses in #bats from #Cambodia

 

Abstract

Circulating bat coronaviruses present a significant pandemic threat, yet our understanding of their genetic diversity and evolutionary dynamics remains limited. Over 3 years, we sampled 1,462 bats in Cambodia’s Steung Treng province, identifying extensive and diverse coronaviruses co-circulation. Using metatranscriptomic and amplicon sequencing, we generated 33 complete sarbecovirus genomes sequences, revealing novel lineages that cluster into four distinct groups, each associated with different Rhinolophus bat species. Our analysis highlights rapid migration and recombination of sarbecovirus lineages over short distances and timescales. Of note, the receptor-binding domains of two novel viral groups exhibit high similarity to SARS-CoV-2, and pseudovirus assays confirmed the ability of this spike protein to mediate entry into cells expressing human ACE2, suggesting a potential zoonotic risk. The observed genetic diversity underscores the urgent need for continuous surveillance to identify high-risk animal-to-human interfaces and inform pandemic preparedness.

Source: 

Link: https://www.nature.com/articles/s41467-026-75954-1

____

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

____

Highly Pathogenic Avian #Influenza #H5N5 in a Polar #Bear and Atlantic #Walrus, #Svalbard, 2026, with Widespread Seroconversion in Polar Bears

 

Abstract

Highly pathogenic avian influenza virus (HPAIV) subtype H5N5 was detected in a one-year-old polar bear (Ursus maritimus) and an adjacent adult Atlantic walrus (Odobenus rosmarus rosmarus), both found deceased in Raudfjorden, Svalbard. This represents the first confirmed case of HPAI in a European polar bear and the second in an Atlantic walrus. Viral genomes were nearly identical and harbored PB2-E627V, a marker associated with mammalian adaptation. Several polar bears, including the deceased individual, had previously been observed feeding on the walrus carcass. Antibodies against H5 were detected in 75% of polar bears in 2023 (n=36) and 97% in 2024-2025 (n=65), suggesting extensive circulation of HPAIV in the population following the first detections in birds in Svalbard in 2022, whereas no antibodies were detected in samples from 2014-2022 (n=243).

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

Project OH4Surveillance, funded by the European Union, Grant Agreement No 101132473

Morris Animal Foundation, Grant ID# D25ZO-430; KJB

Norwegian Veterinary Institute, 12311 SvalVilt

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.07.20.739480v1

____

#Genomic Characterization of #SARS-CoV-2 #NB.1.8.1 and #PQ.2 from the #Infants and Young #Children with #Gastrointestinal Symptoms

 

Abstract

Purpose: 

This study investigated the viral genomic characteristics of infants and young children who presented to our hospital with gastrointestinal symptoms during a local COVID-19 epidemic and were confirmed to have SARS-CoV-2 infection.

Patients and methods: 

Between May and August 2025, pharyngeal swab samples were collected from four infants and young children who presented to the outpatient department of Meizhou People’s Hospital in Meizhou, with gastrointestinal symptoms. Nucleic acid testing and whole-genome sequencing were performed. The viral mutation profile was analyzed, and the potential impact of mutations on protein function was predicted.

Results: 

Pangolin typing identified the NB.1.8.1 variant in three patients and the PQ.2 variant in one patient. Genome sequences from three of the four viral variants displayed varying degrees of mutation. The nonsynonymous mutations for both variants were concentrated in the spike protein. A comparison with the parental XDV.1.5.1 lineage revealed 14 specific mutations, with 7 nonsynonymous sites conserved across all gene sequences. Five of these mutation sites, NSP12: D284Y, ORF3a: L46F, ORF3a: F207C, N: Q9H, and N: Q384H, were predicted to be functionally deleterious and structurally destabilizing.

Conclusion: 

SARS-CoV-2 variants from specimens obtained from four infants and young children exhibited varying degrees of mutation, providing evidence for the ongoing evolution of emerging variants in pediatric patients. However, monitoring genomic changes of circulating variants requires further clinical specimens, which contributes to understanding the dynamic changes at mutation sites, thereby supporting epidemic prevention and control.

Source: 

Link: https://www.dovepress.com/genomic-characterization-of-sars-cov-2-nb181-and-pq2-from-the-infants--peer-reviewed-fulltext-article-IDR

____

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

____

Isolation and characterization of a clade 2.3.4.4b genotype #D1.1 #H5N1 virus from dairy #cattle in #Wisconsin

 

ABSTRACT

Highly pathogenic avian influenza A(H5N1) (HPAI H5N1) viruses of clade 2.3.4.4b have recently been detected in U.S. dairy cattle following multiple spillover events from avian reservoirs. In December 2025, HPAI H5N1 virus was identified in a dairy herd in Wisconsin through the National Milk Testing Strategy. Here, we report the isolation of a clade 2.3.4.4b, genotype D1.1 H5N1 virus, A/dairy cow/Wisconsin/25G05743-001/2025 (WI5743-H5N1), from bulk milk associated with the affected herd, describe its phylogenetic relationships, and assess its pathogenicity in mice. Infectious virus was recovered following blind passage in embryonated chicken eggs. Phylogenetic analysis demonstrated that WI5743-H5N1 is distinct from previously reported D1.1 viruses detected in dairy cattle in Nevada and Arizona, supporting an independent introduction into cattle, and indicating a likely local avian source. Compared with closely related avian viruses, WI5743-H5N1 encoded the mammalian-adapting substitution PB2-E627K and additional amino acid differences in HA, PB1-F2, and NS1. In mice, WI5743-H5N1 replicated efficiently in respiratory tissues and was detectable in the brain but exhibited lower lethality relative to other recent clade 2.3.4.4b, genotype B3.13 viruses. Together, these findings highlight the genetic and phenotypic diversity of HPAI H5N1 viruses infecting dairy cattle and underscore the importance of continued surveillance and functional characterization of emerging strains.

IMPORTANCE

Highly pathogenic avian influenza A(H5N1) viruses have recently entered U.S. dairy cattle through multiple spillover events from avian reservoirs, creating new opportunities for viral adaptation in mammals. Here, we describe the isolation and characterization of a clade 2.3.4.4b, genotype D1.1 H5N1 virus from bulk milk collected during a spillover event in Wisconsin in December 2025. Phylogenetic analyses demonstrated that this virus represents an independent introduction into dairy cattle distinct from previously reported D1.1 viruses identified in Nevada and Arizona. Although the virus encoded the mammalian-adapting PB2-E627K substitution, it exhibited comparatively low lethality in mice, highlighting the complexity of mammalian adaptation and pathogenicity in H5N1 viruses. These findings expand current understanding of the genetic and phenotypic diversity of H5N1 viruses infecting dairy cattle and emphasize the importance of continued surveillance and functional characterization of emerging strains.

Source: 

Link: https://journals.asm.org/doi/10.1128/jvi.00761-26

____

Evaluation of a proposed #link between the #SARS-CoV-2 #furin #cleavage site and mouse-adapted #MERS-coronavirus MA30

 

Significance

This study formally evaluates a hypothesis that has been advanced by some scientists and public commentators in support of a nonnatural origin of SARS-CoV-2. The hypothesis proposes that the unique polybasic furin cleavage motif of SARS-CoV-2 may be technically or evolutionarily derived from a mouse-adapted laboratory strain of MERS-coronavirus (MA30). While the World Health Organization’s Scientific Advisory Group on the Origins of Novel Pathogens (SAGO) concluded that the available evidence was insufficient to support the proposed link, the underlying scientific rationale for this conclusion has not been published. We systematically assessed the evidence from genomic surveillance and conducted additional experimental studies. Together, these data do not support an evolutionary or genetic relationship.

Abstract

The origin of the polybasic furin cleavage site (FCS) of SARS-CoV-2 remains a central question in debates on the emergence of COVID-19. One hypothesis proposes a genetic relationship between the SARS-CoV-2 S1/S2 motif RRAR and the RRVR sequence found in the mouse-adapted MERS-CoV strain MERS-MA30. Here, we combined large-scale bioinformatic analysis with experimental virology to evaluate this scenario. Analysis of over 17 million SARS-CoV-2 genomes revealed that the S:684V substitution corresponding to RRVR occurred repeatedly but only sporadically, never became phylogenetically basal, and showed limited geographic and temporal spread. Using reverse genetics, we generated SARS-CoV-2 variants encoding RRVR and demonstrated that S:684V consistently reduced viral entry efficiency and competitive fitness in multiple cell systems, including human respiratory epithelial cultures. RRVR variants did not evolve toward RRAR but instead accumulated alternative substitutions. These findings do not support an evolutionary relationship between MERS-MA30 and the SARS-CoV-2 FCS.

Source: 

Link: https://www.pnas.org/doi/abs/10.1073/pnas.2601806123?af=R

____

Deep #mutational #scanning of recent #SARS-CoV-2 #variants highlights changing amino acid preferences within epistatic hotspot residues

 

Abstract

Deep mutational scans across receptor-binding domains (RBDs) of diverging SARS-CoV-2 variants reveal ongoing changes to the effects of mutations, a phenomenon known as epistasis. Careful accounting for these altered mutational effects is important in viral surveillance and forecasting, and more broadly, for understanding the impacts of epistasis on real-world viral evolutionary trajectories. Using a yeast-display RBD deep mutational scanning (DMS) platform, we measure the impacts of virtually all single amino acid mutations and single-residue deletions in the Omicron KP.3.1.1 and LP.8.1 RBDs on folded RBD expression and binding affinity for the human ACE2 receptor. Our comprehensive maps reveal patterns of evolutionary accessibility and constraint at single-residue resolution and, when compared to prior datasets, highlight sites whose amino acid preferences continue to change across viral variants. Notably, sites 455, 456, and 493 – which have exhibited repeated substitutions and epistatic dependencies across Omicron subvariants going back to BA.1 – again demonstrate altered patterns of mutational accessibility and constraint. Therefore, it appears that these hotspots of repeated RBD evolution have not yet converged on fixed amino acid solutions but instead remain sites of ongoing epistatic reconfiguration. We compare our measurements of direct RBD:ACE2 affinity with recently published measurements of mutation impacts on ACE2 binding in the full quaternary spike context, which also integrates the effects of spike conformational dynamics; our analysis uncovers mutations like H505W that could favor adoption of the down/closed RBD conformation as a viral strategy for future antigenic evolution.

Source: 

Link: https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014074

____

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

____

#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

____

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

____

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

____

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

____

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

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