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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#Genotype Diversity of Highly Pathogenic Avian #Influenza #H5N1 Clade 2.3.4.4b in #Pennsylvania #Poultry During Disease #Outbreak from April 2022 to March 2023

 

Abstract

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

Source: 

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

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

 

Abstract

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

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

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

European Union Horizon 2023 RIA project LEAPS, 101094685

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

Fonds National de la Recherche Scientifique, F.4515.22

European Union Horizon 2020 project MOOD, 874850

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

Source: 

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

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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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#Genomic similarity to quantitatively evaluate the #reassortment #potential of #H7N9 with other subtypes of avian #influenza viruses

 

Abstract

Introduction: 

The H7N9 influenza virus poses a significant public health threat due to its potential for reassortment and cross-species transmission. This study aims to systematically evaluate the genomic similarity between H7N9 and other influenza A subtypes to identify strains with high reassortment potential and characterize their spatiotemporal and host distribution patterns.

Methods: 

We analyzed nearly 4,000 H7N9 sequences from GISAID and NCBI, alongside representative sequences of other influenza A subtypes. Open reading frames were extracted, and a genomic similarity index was constructed using Euclidean distance, dot product, and cosine similarity measures, with weights optimized via principal component analysis. The index was applied to quantify inter-subtype similarity and predict reassortment-prone strains.

Results: 

High sequence similarity was observed between H7N9 and cognate subtypes (e.g., H7N3, H15N9), with H7N3 exhibiting the highest similarity index (1.00). Validation using known reassortant strains, such as A/Yixing/805/2022 (H3N2), confirmed that strains with high reassortment potential showed significantly elevated similarity scores across all gene segments (p< 0.001). High-similarity outliers analysis identified 581 spillover events, temporally concentrated during 2014–2017, and spatially clustered in regions like the United States, Europe, and Hong Kong. Host analysis highlighted birds—especially chickens, ducks, and turkeys—as key reservoirs for reassortment.

Discussion: 

The genomic similarity index effectively identifies influenza A subtypes with high reassortment potential, supported by retrospective validation and spatiotemporal congruence with documented outbreaks. The concentration of high-similarity strains in specific hosts and regions underscores the role of ecological factors in viral evolution. These findings provide a predictive framework for monitoring emergent reassortants and inform targeted surveillance strategies.

Source: 

Link: https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2026.1777911/full

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Genetic characterization of a novel triple - #reassortant #influenza #H1N2 virus from #pigs, #China, 2021

 

Abstract

Swine influenza virus (SIV) is a highly contagious respiratory pathogen in pigs, with bidirectional transmission posing a potential threat to human health. In this study, nasal swab samples were collected from pigs in Shandong Province, China, and yielded an H1N2 SIV strain, designated A/swine/Shandong/QD726/2021 (H1N2). Whole-genome sequencing was performed for Sw/SD/QD726/2021, and phylogenetic analysis was conducted together with 156 Chinese H1N2 reference sequences obtained from the Global Initiative on Sharing All Influenza Data (GISAID) database and the National Center for Biotechnology Information (NCBI) Influenza Virus Resource database. The results indicated that Sw/QD726/2021 represents a novel reassortant genotype (G21), with the HA gene derived from Eurasian avian-like H1N1 (EA H1N1), the NA and NS genes from triple-reassortant H1N2 (TR H1N2), and the remaining internal genes (PB2, PB1, PA, NP, M) from the 2009 pandemic H1N1 (pdm/09 H1N1). Key amino acid analysis revealed N31 in M2, responsible for adamantane resistance, and S42 in NS1, which influences viral virulence in mouse models. BALB/c mouse experiments demonstrated efficient viral replication in the lungs and nasal turbinates, accompanied by moderate body weight loss and lung lesions, indicating only moderate pathogenicity. These findings underscore the ongoing evolution of H1N2 SIV in pigs and emphasize the importance of enhanced surveillance and preventive strategies to mitigate public health risks.

Source: 

Link: https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2026.1779293/full

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#Genomic characterisation of Crimean-Congo haemorrhagic fever virus (#CCHFV) in #Tajikistan identifies a novel reassortant virus

 

Abstract

Crimean-Congo haemorrhagic fever virus (CCHFV) is an important human tick-borne pathogen, able to cause severe haemorrhagic fever. CCHFV is endemic in Tajikistan, which records between 5–38 cases of CCHF a year from southern regions. Molecular surveillance of CCHFV is crucial to implement effective prevention and control strategies, understand viral evolution, study transmission dynamics, and develop effective diagnostics, therapeutics, and vaccines. While the presence of Asia-1 and Asia-2 genotypes has been previously reported, only two historical samples from Tajikistan have been fully sequenced. In this study we developed and applied a genotype IV-specific tiling PCR enrichment approach recovering 52 CCHFV genome segment sequences from clinical and Hyalomma tick samples collected between 2017–2023. Most sequences belonged to the Asia-2 genotype, but one virus exhibited an Asia-1 S segment combined with Asia-2 M and L segments, representing the first evidence of such viral reassortment event in Tajikistan.

Source: 

Link: https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0014204

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

 

Abstract

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

Source: 

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

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The emergence and molecular #evolution of #H5N1 #influenza viruses in #USA dairy #cattle

 

Abstract

Prior to 2024, highly pathogenic avian influenza H5N1 clade 2.3.4.4b viruses circulated predominantly in wild birds and poultry. In 2024 and 2025, 2.3.4.4b genotypes B3.13 and D1.1 were detected in United States dairy cattle. Using whole-genome and segment-specific phylodynamic inference, we estimate that B3.13 and D1.1 spilled over from wild birds into dairy cattle in late 2023 and late 2024, respectively. Spillover occurred shortly after the formation of the reassortant genotypes and was followed by months of cryptic transmission prior to detection. We found that both B3.13 and D1.1 evolved at higher rates in cattle relative to birds, primarily due to relaxed purifying selection. Site-specific analyses identified genomic sites under positive selection in cattle relative to birds, indicating adaptation and likely contributing to improved viral fitness after spillover. Intensified genomic surveillance in dairy cattle is essential as population immunity introduces additional selection pressures, with ever-changing risk for human emergence.

Competing Interest Statement

M.A.S. receives contracts from Johnson & Johnson and Gilead Sciences outside the scope of this work. M.U.G.K. received consulting fees from Takeda, Bavaria Nordic, and Google DeepMind for work unrelated to the manuscript.

Funder Information Declared

Fonds voor Wetenschappelijk Onderzoek - Vlaanderen, G051322N, G051323N

UK Medical Research Council/Department for Environment, Food and Rural Affairs (DEFRA) FluTrailMap-One Health consortium, MR/Y03368X/1

Biotechnology and Biological Sciences Research Council (BBSRC)/DEFRA ‘FluTrailMap’ consortium, BB/Y007298/1

Pirbright Institute’s Strategic Program Grants, BBS/E/PI/230002A, BBS/E/PI/230002B

EMBO Installation Grant, 5305

Academy of Medical Sciences Springboard, 1049

Centers of Excellence for Influenza Research and Response, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Department of Health and Human Services, 75N93021C00015, 75N93021C00014

National Institutes of Health, AI135995, AI153044, AI192139

Rockefeller Foundation, PC-2022-POP-005

Health AI Programme from Google.org

Oxford Martin School Programmes in Pandemic Genomics & Digital Pandemic Preparedness

European Union's Horizon Europe, 874850, 101086640

Wellcome Trust, 303666/Z/23/Z, 226052/Z/22/Z, 228186/Z/23/Z

United Kingdom Research and Innovation, APP8583

Medical Research Foundation, MRF-RG-ICCH-2022-100069

UK International Development, 301542-403

Bill & Melinda Gates Foundation, INV-063472, INV-090281

Novo Nordisk Foundation, NNF24OC0094346

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.03.30.713641v1

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A newly emergent N1 #neuraminidase associated with clade 2.3.4.4b highly pathogenic avian #influenza #H5 viruses in North #America

 

Abstract

We investigated the evolutionary history of the newly emergent neuraminidase (am4N1) associated with the D1.1 and D1.2 genotypes of highly pathogenic avian influenza A(H5N1) viruses in North America. Phylogenetic inference places am4N1 in a sister clade to Eurasian avian, swine, and human A(H1N1)pdm09 viruses and distinct from 1918, pre-2009 human seasonal, and classical swine A(H1N1) lineages. Am4N1 descends from diverse avian N1 genes endemic to the Americas. Phylodynamic analysis indicates a monophyletic am4N1 lineage with numerous introductions of viruses carrying the am4N1 gene likely originating from western Canada into the United States during emergence of the D1.1 and D1.2 genotypes. The lineage has diversified and accumulated deletions in the stalk domain. Despite amino acid divergence, structural modeling shows conserved neuraminidase architecture in the globular head. Given its distinct ancestry and amino acid sequence, further studies are needed to assess cross-reactivity of antibodies from prior human A(H1N1)pdm09 infections.

Competing Interest Statement

The authors have declared no competing interest.

Funding Statement

This study did not receive any external funding.

Source: 

Link: https://www.medrxiv.org/content/10.64898/2026.03.09.26347929v1

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Novel #Reassortant #H5N2 Highly Pathogenic Avian #Influenza Viruses from Backyard #Poultry in #Mexico

 

Abstract

Highly pathogenic influenza A viruses of the H5 subtype continue to diversify worldwide through mutation and genetic reassortment, generating novel variants with unpredictable consequences under the One Health approach. Between 2024 and 2025, five outbreaks of avian influenza A viruses were detected in backyard poultry across Michoacán, Estado de México, and Ciudad de México. We conducted molecular and genetic characterization of five highly pathogenic H5N2 viruses isolated from these events. All cases tested positive for influenza A virus and the H5 hemagglutinin, exhibiting high pathogenicity with intravenous pathogenicity index values ranging from 2.88 to 3.0. Whole-genome sequencing revealed novel reassortants containing hemagglutinin from Eurasian H5N1 clade 2.3.4.4b and neuraminidase from the endemic Mexican H5N2 lineage. The viral genome of the isolate from Michoacán contained six segments derived from Eurasian H5N1 viruses introduced into North America in 2021–2022, while nucleoprotein and neuraminidase originated from Mexican H5N2 viruses. In contrast, viruses from Estado de México and Ciudad de México contained five H5N1-derived segments and incorporated polymerase basic protein 1, nucleoprotein, and neuraminidase from low-pathogenic H5N2 viruses circulating in 2024. Phylogenetic analyses confirmed the emergence of a distinct H5N2 Mexican sublineage, providing evidence of active viral reassortment and local evolutionary processes in Mexico.

Source: 

Link: https://www.mdpi.com/1999-4915/18/3/337

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Characterization of a reassortant #H3N2 swine #influenza virus with 2009 pandemic internal #genes and enhanced potential for zoonotic #risk

 

Highlights

• A swine influenza virus H3N2 subtype was isolated during epidemiological survey.

• It is a complex and novel reassortant, and acquired accumulation of adaptive mutations.

• Both rescue and parent strains demonstrated efficient replication in mammalian cells.

• Key residues of the H3N2 HA collectively enhance the binding preference for human-type receptor.

• The rescued H3N2 cause significant pulmonary pathological damage in mice.

Abstract

Pigs serve as key "mixing vessels" for influenza A viruses, playing a critical role in cross-species transmission, while the H3N2 subtype represents an important lineage within the swine influenza virus (SIV) family. In this study, a novel reassortant H3N2 SIV strain, designated A/Swine/Jiangsu/YZ07/2024, was isolated from pigs exhibiting clinical symptoms in Northern Jiangsu, China during epidemiological survey. Genetic analysis revealed that the virus is a complex reassortant, with the internal genes (M, NP, PB1, PB2, PA) originated from the 2009 pandemic H1N1 lineage, the NS gene exhibiting a North American triple reassortant origin (human-avian-swine origin), and the HA and NA genes belonging to the human-like lineage. Although neither the rescued virus nor its parental strain could replicate effectively in chicken embryos and chicken cells, both demonstrated efficient replication in mammalian cells, reflected by the much higher polymerase activity in mammalian versus chicken cells. The key residues of HA protein (190D, 225D and 228S) collectively enhanced the binding preference for human-type α-2,6-linked sialic acid receptors, which was confirmed by receptor binding assays. Furthermore, mouse infection experiments using the rescued H3N2 demonstrated efficient viral replication in nasal turbinates and lung tissues, accompanied by significant pulmonary pathological damage. These findings indicate that the YZ07 strain, through the vast reassortment and accumulation of adaptive mutations, has acquired potential zoonotic risk, underscoring the importance of surveillance of swine influenza viruses.

Source: 

Link: https://www.sciencedirect.com/science/article/abs/pii/S0378113526000684?via%3Dihub

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Digest: #Reassortment-based #evolution of #H1N1 subtype Swine #Influenza Virus in #China

 

Abstract

In a new study, Zhao et al. (2025) obtain 959 whole genome sequences of H1N1 subtype swine influenza virus (SIV) isolated from China. Their analysis of the sequences, isolated between 1977 and 2020, reveals how H1N1 lineages have co-evolved and contributed to instances of zoonotic transmission within the region. This study’s findings characterize the long-term evolutionary effects of frequent viral reassortment in SIV and highlight its potential to drive future pandemics.

Source: 

Link: https://academic.oup.com/evolut/advance-article/doi/10.1093/evolut/qpaf262/8400336

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Novel Highly Pathogenic Avian #Influenza #H5N1 Virus, #Argentina, 2025

 

Abstract

Genomic sequencing of reemerging highly pathogenic avian influenza A(H5N1) virus detected in Argentina in February 2025 revealed novel triple-reassortant viruses containing gene segments from Eurasian H5N1 and low pathogenicity viruses from South and North American lineages. Our findings highlight continued evolution and diversification of clade 2.3.4.4b H5N1 in the Americas.

Source: 

Link: https://wwwnc.cdc.gov/eid/article/31/12/25-0783_article

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Emergence of a novel #reassorted high pathogenicity avian #influenza #H5N2 virus associated with severe #pneumonia in a young #adult

 

Abstract

Background 

Infection of backyard and poultry with low pathogenicity avian influenza LPAI A(H5N2) viruses has occurred in Mexico since 1994, and the first human infection caused by this influenza virus was detected in 2024. Since its emergence in the Americas, frequent reassortments between high pathogenicity avian influenza HPAI A(H5N1) and LPAI viruses has occurred. In September 2025, the Instituto Nacional de Enfermedades Respiratorias of Mexico City identified an unsubtypeable influenza A virus infection in a young adult patient later determined to be a reassortant HPAI (H5N2) virus with a clade 2.3.4.4b HA. 

Methods 

We analyzed clinical and epidemiologic data from this patient. Respiratory samples were tested for influenza RT-qPCR assays. Genomic sequence and phylogenetics analyses were performed to provisionally assign a new genotype to the novel HPAI A(H5N2) reassortant virus. 

Results 

The patient presented with fever and tachypnea, later developed hemoptysis and thoracic pain, with oxygen saturation decreasing to 70%. CT scan showed bilateral ground-glass opacities consistent with diffuse alveolar hemorrhage and zones consistent with consolidation. Clinical improvement was observed and the patient was discharged. Through viral complete genome analysis, we identified an HPAI A(H5N2) virus with genes from both clade 2.3.4.4b A(H5N1) viruses similar to those detected in North America during 2022-2023 and genes from the LPAI A(H5N2) viruses detected in Mexico during 2024. 

Conclusions 

This is the first ever laboratory-confirmed human infection caused by an HPAI A(H5N2) virus infection, suggesting a new genotype provisionally classified as B3.14. The relationship of the virus with the severity of illness remains unknown.

Competing Interest Statement

Conflicts of Interest: The authors declare that they have no competing interests. The sponsors had no role in the design, execution, interpretation, or writing of the study. The findings and conclusions in this report are those of the authors and do not necessarily represent the views of the Centers for Disease Control and Prevention or the Agency for Toxic Substances and Disease Registry.

Funding Statement

Funding: This work was financially supported by Secretaria de Ciencia, Humanidades, Tecnologia e Innovacion (SECIHTI), Grant CBF-2025-I-3693 to J.A.V.-P.

Source: 

Link: https://www.medrxiv.org/content/10.1101/2025.11.21.25340167v1

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#USA, #Washington State: #H5N5 Avian #influenza confirmed in Grays Harbor County resident (DoH, Nov. 15 '25)

 

For immediate release: November 14, 2025   (25-138)

First detection of this strain in a human, risk to the public remains low

Contact: DOH Communications

A Grays Harbor resident who was hospitalized with influenza symptoms in early November has been confirmed to have influenza A H5, a type of avian influenza. 

Additional testing shows the virus to be H5N5, an avian influenza virus that has previously been reported in animals but never before in humans. 

The Centers for Disease Control and Prevention (CDC) and DOH currently consider the risk to the public from avian influenza to be low.

The person is an older adult with underlying health conditions and remains hospitalized. 

The affected person has a mixed backyard flock of domestic poultry at home that had exposure to wild birds. 

The domestic poultry or wild birds are the most likely source of virus exposure; however, public health investigation is ongoing. 

The Washington State Department of Health is working with the local health department and the Washington State Department of Agriculture to complete exposure and animal health investigations.  

Public health disease experts have not identified any increased risk to the public.  

(...)

Source: Department of Health, State of Washington, https://doh.wa.gov/newsroom/h5n5-avian-influenza-confirmed-grays-harbor-county-resident

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Phylogenetic and Molecular Characterization of a Novel #Reassortant High-Pathogenicity Avian #Influenza #H7N6 Virus Detected in #NZ #Poultry

 

Abstract

H7 high-pathogenicity avian influenza (HPAI) virus outbreaks can cause high rates of morbidity and mortality in poultry flocks, leading to devastating impacts on poultry industries. In December 2024, an HPAI virus was detected on a poultry farm in New Zealand, being the first time a case of HPAI was reported in the country. Whole-genome sequencing, subtyping, phylogenetic, and mutation analyses were performed to characterize the virus. Results indicated a novel high-pathogenicity H7N6 avian influenza virus arose through a reassortment event between endemic low-pathogenicity H4N6 and H7 viruses, followed by two mutations at the H7 gene cleavage site. Mutation analysis suggests the novel H7N6 virus exhibits increased risk of host specificity shift, but further work is required to fully understand the functional impacts of the detected mutational events. In this instance, a timely biosecurity response was effective in eliminating the virus and preventing its transmission to secondary poultry flocks in New Zealand. However, the event underscores the critical importance of continued surveillance of commercial poultry and other potential avian carriers to facilitate early detection of low-pathogenicity avian influenza viruses, which may undergo reassortment or de novo mutation into high-pathogenicity variants.

Source: International Journal of Infectious Diseases, https://www.mdpi.com/1422-0067/26/21/10623

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Preplanned Studies: #Phylogenetic and #Molecular Characteristics of An #H3N8 Avian #Influenza Virus Detected in Wild #Birds — #Beijing, #China, September 2024

 

Summary

-- What is already known about this topic?

- The H3N8 avian influenza virus (AIV) demonstrates considerable capacity for interspecies transmission and has been documented in multiple mammalian hosts, including equine and canine species. During 2022–2023, three laboratory-confirmed human infections with H3N8 were reported in China, heightening public health concerns about the zoonotic spillover potential of H3 subtype AIVs.

-- What is added by this report?

- This study reports the isolation of a genetically reassorted, low-pathogenicity H3N8 avian influenza virus (AIV) from an islet in Niukouyu Wetland Park, Beijing Municipality — the first detection of this viral strain in a wild environment within the city. Throat swabs collected from park staff tested negative for influenza viruses. Phylogenetic analysis demonstrated that the viral hemagglutinin gene originated from the Eurasian lineage, while the neuraminidase gene was derived from the North American lineage. Although no direct evidence of human infection has been documented, multiple mutations identified in the virus’s internal genes are associated with enhanced replication capacity, increased virulence, and improved adaptation to mammalian hosts. These molecular features indicate a potential risk for cross-species transmission to humans.

-- What are the implications for public health practice?

- Given the potential threat that H3N8 AIVs pose to mammalian species, including humans, this study emphasizes the critical need to strengthen influenza surveillance networks and broaden monitoring efforts specifically targeting H3 subtype AIVs.

ABSTRACT

Introduction: 

The H3N8 avian influenza virus (AIV) is recognized for its capacity for interspecies transmission and has been detected in multiple mammalian hosts. Between 2022 and 2023, three human infections with H3N8 were documented in China, raising significant concerns about its zoonotic spillover potential. In this study, we characterized an H3N8 isolate from Niukouyu Wetland Park in Beijing Municipality to elucidate the genetic variability and evolutionary dynamics of this AIV subtype.

Methods: 

The virus underwent whole-genome sequencing followed by comprehensive molecular and phylogenetic characterization.

Results: 

We identified a genetically reassorted, low-pathogenicity H3N8 AIV, marking the first detection of this subtype in a wild environment in Beijing. Throat swabs from the park staff tested negative for influenza viruses. Phylogenetic analyses demonstrated that the viral hemagglutinin and neuraminidase genes originated from Eurasian and North American lineages, respectively. Nucleotide sequence comparisons revealed 97.57%–99.06% similarity between the eight gene segments of this virus and those of reference strains. Multiple internal gene mutations were identified, including PB2-K318R and PB1-F2-N66S, which are associated with enhanced polymerase activity, increased virulence, and improved mammalian adaptation.

Conclusions: 

The molecular characteristics of this H3N8 virus indicate a potential risk for cross-species transmission to humans, emphasizing the critical need to strengthen influenza surveillance networks and expand monitoring efforts targeting H3 subtype AIVs.

Source: China Centre for Disease Control and Prevention, Weekly Update, https://weekly.chinacdc.cn/en/article/doi/10.46234/ccdcw2025.233

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Overview of high pathogenicity avian #influenza #H5N1 clade 2.3.4.4b in #wildlife from Central and South #America, October 2022 - September 2025

 

Abstract

Between 2022 and 2025, high pathogenicity avian influenza (HPAI) H5N1 clade 2.3.4.4b was detected in poultry and wildlife across most countries in Central and South America. The epizootic peaked in 2023, subsided in 2024, and resurged in 2025. In Central America, outbreaks in wildlife were few and small, and mostly affected pelicans. In contrast, South America experienced unprecedented mass mortality in colonial seabirds and pinnipeds, including endangered and endemic species. Notably, viral adaptation enabled mammal-to-mammal transmission in pinnipeds and rapid viral spread across multiple countries along the Pacific and Atlantic coasts. Subsequent introductions to subantarctic islands and Antarctica stemmed from South American viruses. In February 2025, a novel reassortant virus emerged, recombining HPAI H5N1 B3.2 genotype with South American low pathogenicity avian influenza viruses. In May 2025, HPAI H5N1 viruses re-emerged in Brazil, causing a series of outbreaks in poultry and wild birds. The ongoing circulation and evolution of HPAI H5N1 in this region underscores the need for strengthened surveillance, expanded genomic monitoring, and enhanced integration of wildlife conservation and environmental sectors in regional response frameworks.

Source: Canadian Journal of Microbiology, https://cdnsciencepub.com/doi/10.1139/cjm-2025-0189

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#Zoonotic Implications of the Co-Circulation of Clade 2.3.4.4b and 2.3.2.1a #H5N1 Avian #Influenza Viruses in #Nepal in 2023

 

Abstract

Samples collected from two avian influenza outbreaks in Bagmati Province in central Nepal between January and March 2023 were positive for H5N1. Full genomes were generated for both viruses, which revealed that one of the viruses was very similar to clade 2.3.4.4b H5N1 identified in Bangladesh in 2021/2022. The second virus was a reassortant H5N1 virus consisting of four genes (HA, NA, NP, and M) originating from a clade 2.3.2.1a H5N1 and the remaining four genes (NS, PB1, PB2, and PA) originating from a 2.3.4.4b H5N1. Notably, this second virus had a high identity with 2.3.2.1a clade viruses identified in humans and cats in India in 2024–2025. These are the first full genome sequences of H5N1 avian influenza viruses from Nepal and given the recent human infections by 2.3.2.1a H5N1 viruses in the region, these data will be of interest to both public health and veterinary authorities.

Source: Viruses, https://www.mdpi.com/1999-4915/17/11/1481

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