Showing posts with label pigs. Show all posts
Showing posts with label pigs. Show all posts

Sunday, June 28, 2026

#Genetic and biological characterization of a #reassortant #H3N2 swine #influenza virus isolated in #China with internal genes from the 2009 pandemic #H1N1

 


Abstract

Swine influenza virus (SIV) not only causes significant losses to the pig industry but also poses a potential threat to human health due to its ability for cross-species transmission and zoonotic characteristics. In this study, 600 nasal swab samples were collected from pigs in Shandong Province and tested for SIV using RT-qPCR. One sample tested positive, and the virus was successfully isolated in 10-day-old specific-pathogen-free (SPF) embryonated chicken eggs. Subtype-specific RT-PCR and sequencing identified the isolate as H3N2, designated A/swine/Shandong/116/2022 (H3N2). Whole-genome sequencing and similarity analysis showed that PB2, PB1, PA, NP, and M genes were most similar to H1N1 viruses (97.71–99.67%), while HA, NA, and NS genes were closest to H3N2 viruses (96.06–97.85%), suggesting this isolate is a reassortant between H1N1 and H3N2 viruses. Phylogenetic analysis indicated that PB2, PB1, PA, NP, and M genes belong to the 2009 pandemic H1N1 (pdm/09 H1N1) lineage, HA and NA genes belong to the human-like H3N2 (HL H3N2) lineage, and the NS gene belongs to the triple-reassortant (TR) H1N2 lineage. Key amino acid analysis showed a monobasic HA cleavage site (PEKQTR/G), consistent with low pathogenicity, and residues 190V, 226I, and 228S, which may affect receptor binding. PB2 residues 271A, 590S, and 591R may influence viral replication and host adaptation. Compared with the human influenza vaccine strain A/Darwin/9/2021 (H3N2), several amino acid changes were found in HA antigenic sites A, B, C, and E, suggesting possible antigenic drift. In addition, clear differences were found in N-linked glycosylation sites between the isolate and vaccine strain, including loss of several glycosylation sites and the appearance of a new site at position 499, which may change virus antigenicity and immune recognition. Functional studies demonstrated that the isolate efficiently infected MDCK cells and replicated in the respiratory tissues of BALB/c mice, causing mild to moderate lung lesions without mortality or significant weight loss. In summary, the isolated is a multi-source reassortant virus with low pathogenicity, providing valuable insights into the genetic characteristics and epidemiology of H3N2 SIV circulating in pigs in China.

Source: 


Link: https://link.springer.com/article/10.1186/s12866-026-05324-w

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Thursday, June 4, 2026

Breeding #pig #transport drives the dispersal of #swine #influenza A virus across #Europe

 


Abstract

Pigs serve as reservoirs of former human influenza A virus (IAV) H1N1 and H3N2 lineages and act as mixing vessels for diverse strains, facilitating the emergence of novel IAVs. Understanding the spread and evolution of swine IAVs (swIAVs) is therefore crucial to assess the risk of strains with zoonotic potential emerging. This study uses a phylogeographic framework to investigate the predictors of swIAV dispersal across Europe. All publicly available swIAV genomic sequences were retrieved and subsampled for the ten largest European pig-producing countries. Discrete phylogeographic reconstructions were conducted for H1, H3, N1, N2 encoding genes and all internal gene segments. Our analyses indicate that viral dispersal predominantly occurred from north-western to southern and eastern Europe, with frequent long-distance transitions between non-adjacent countries. We also extended the discrete phylogeographical analyses with generalized linear models to test the association between viral movement and potential predictors, such as live pig trade, pork trade, pig densities, farm sizes, or the geographic distance between key pig production zones. We find that breeding pig trade is the only consistently well-supported predictor of between-country transition events, whereas pork trade and geographic distance were not supported. This highlights that farms importing breeding pigs from multiple countries could act as hotspots for reassortment of diverse swIAV strains. Strengthening external biosecurity on farms with emphasis on quarantining breeding pigs, limiting long-distance transport, and implementing a One Health surveillance system for earlier detection of emerging strains, could help curb the rapid spread and evolution of swIAV in Europe.


Competing Interest Statement

The authors have declared no competing interest.

Source: 


Link: https://www.biorxiv.org/content/10.64898/2026.06.01.729471v1

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Tuesday, May 26, 2026

#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: 


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Thursday, May 14, 2026

Concurrent #Detection of #Swine-Origin #Influenza #H1N1 Virus in #Pigs and #Farmer, #Switzerland

 


Abstract

We report zoonotic transmission of Eurasian avian-like swine influenza A(H1N1) virus from pigs to a farmer. The pigs and farmer experienced influenza-like illness. Whole-genome sequencing revealed >99.9% isolate sequence identity between hosts. Our findings highlight the risk posed by enzootic swine influenza A virus and the need for genomic and epidemiologic surveillance.

Source: 


Link: https://wwwnc.cdc.gov/eid/article/32/6/25-1487_article

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Wednesday, May 13, 2026

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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Saturday, May 9, 2026

#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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Thursday, April 23, 2026

Longitudinal #serum #proteomics analyses reveal #biomarkers for porcine #influenza and #coronavirus infections

 


Abstract

Respiratory virus infections affect both humans and livestock, causing considerable mortality and morbidity. While respiratory pathogens such as swine influenza A virus (pH1N1) and porcine respiratory coronavirus (PRCV) often present with overlapping clinical symptoms, their pathological trajectories and outcomes differ. Given the propensity for pathogen spillover and the use of pigs as a physiologically relevant large-animal translational model, we aimed to characterise host serum protein signatures that detect and differentiate pH1N1 from PRCV, enabling improved disease monitoring and control. Using high-resolution mass spectrometry-based proteomics, we identified 162 serum proteins that were significantly dysregulated across 3 infection timepoints (1, 5, and 12 days post-infection (DPI)), with signatures correlating with viral shedding and lung pathology as early as 1 DPI. Notably, multiplexed targeted analysis of a subset of proteins in an independent cohort from a different breed and geographic location demonstrated detection, femtomole-level targeted quantitation, and validation of SRGN as a diagnostic marker for pH1N1 and PRCV (AUC=0.85). Further, SOD1 was validated as an early marker for PRCV, increasing as early as 1 DPI (AUC= 0.9). Finally, a multi-peptide signature composed of SRGN, SOD1, and RAN demonstrated reasonable predictive power for pH1N1 (AUC=0.75) and PRCV (AUC=0.65) at 1 DPI. Our data validate the proteomic screening, provide insights into the role of early protein markers in distinguishing respiratory viral infections, and pave the way for the development of point-of-care diagnostics and targeted prevention strategies, enhancing preparedness against emerging zoonotic threats.


Competing Interest Statement

The authors have declared no competing interest.


Funder Information Declared

UKRI Biotechnology and Biological Sciences Research Council (BBSRC), BB/X019780/1, BBS/E/PI/230002A, BBS/E/PI/230002B, BBS/E/PI/230002C, BS/E/PI/23NB0004

University of Surrey, https://ror.org/00ks66431

Source: 


Link: https://www.biorxiv.org/content/10.64898/2026.04.21.719833v1

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Monday, April 13, 2026

ONWARD: a #OneHealth, pan - #European multidisciplinary #network advancing #surveillance, #research, clinical management and control of zoonotic #hepeviruses

 


Highlight

• HEV remains the leading cause of acute viral hepatitis in Europe

• Surveillance and diagnostics for HEV are heterogeneous across EU/EEA

• Zoonotic HEV circulates widely in pigs, wildlife and food chains

• Rat HEV expands the zoonotic spectrum and clinical burden in Europe

• ONWARD integrates One Health surveillance, research and capacity building


Abstract

Zoonotic hepeviruses, particularly hepatitis E virus (HEV, species Paslahepevirus balayani) represent a major yet underestimated public health challenge in Europe. Despite being the leading cause of acute viral hepatitis, surveillance, diagnostic practices and prevention strategies remain heterogeneous across EU/EEA countries, limiting comparability and hindering accurate burden estimates. Underdiagnosis is further compounded by extrahepatic manifestations and the growing impact of chronic HEV infection in immunocompromised patients. At the human–animal–environment interface, zoonotic HEV circulates widely in domestic pigs, wildlife and food products, while coordinated surveillance and control measures remain inconsistently implemented. The recent recognition of ratHEV (species Rocahepevirus ratti) as a cause of acute and chronic hepatitis in Europe further expands the spectrum of zoonotic hepevirus infections and underscores the need for integrated One Health approaches. To address these challenges, the One Health Zoonotic Hepevirus Network (ONWARD; COST Action CA24140) was launched in 2025 as a pan-European, multidisciplinary collaboration uniting experts across human, veterinary, food safety and environmental health sectors. ONWARD aims to harmonise diagnostic tools, strengthen clinical research, integrate multisectoral surveillance, promote capacity building and support evidence-based policy development. By fostering coordination with European stakeholders ONWARD provides a structured framework to strengthen preparedness, surveillance and response to zoonotic hepevirus threats across Europe.

Source: 


Link: https://www.sciencedirect.com/science/article/pii/S1386653226000338?dgcid=rss_sd_all

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Thursday, April 9, 2026

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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Thursday, April 2, 2026

‘Our problem here is the #pig #Ebola’: local accounts of #epizootics preceding Ebola #outbreaks in north-eastern #DRC

 


Abstract

Introduction 

Despite their potential relevance for outbreak understanding, epizootic reports associated with Ebola scarcely appear in biomedical literature. This study examines local accounts of animal deaths preceding the 2012 and the 2017 Ebola outbreaks in the north-eastern Democratic Republic of the Congo (DRC).

Methods 

The analysis is based on retrospective interviews conducted with scientists deployed during these two Ebola outbreaks, as well as testimonies collected in 2022 and 2023 from local residents, clinicians and veterinarians. It also draws on local archives to examine how reports of animal deaths were framed and understood in light of a new epidemic situation.

Results 

Selective pressures that favour certain wild animal species, along with social practices such as bushmeat hunting, contribute to a narrowing of focus during outbreak investigations. This has contributed to overlooking some testimonies from marginalised local actors, which remain unpublished to this day. Animal death reports, however, need to be read in their social context. During the 2017 Ebola outbreak, local breeders framed their concerns about pig mortality into a question to be addressed by global health researchers—even though the deaths were not linked to Ebola but were likely caused by an unrelated pathogen, the African swine fever virus.

Conclusion 

Beyond their biological relevance, epizootics can offer insight into the social contexts in which epidemics are identified. These epizootics can shed light on local experiences of diseases, illustrating local priorities and sense-making processes.


Data availability statement

Data sharing is not applicable as no data sets were generated and/or analysed for this study.

DOI: https://doi.org/10.1136/medhum-2025-013586


Footnotes

Contributors: JV conceptualised the study, conducted the research and wrote the manuscript. JV is the guarantor.

Funding: The author received support from Sciences Po Medialab and IFAS (Institut Français d'Afrique du Sud) for fieldwork in the DRC in 2022 and 2023.

Competing interests: None declared.

Patient and public involvement: Patients and/or the public were involved in the design, or conduct, or reporting, or dissemination plans of this research. Refer to the Methods section for further details.

Provenance and peer review: Not commissioned; externally peer reviewed.

Source: 


Link: https://mh.bmj.com/content/early/2026/04/01/medhum-2025-013586

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Tuesday, March 24, 2026

Porcine #influenza #mAbs to #H3, #H5, and #H7 hemagglutinins recognize H3 egg adapted site and target the HA stem

 


Abstract

Introduction

Monoclonal antibodies (mAbs) are critical tools for elucidating viral evolution, informing vaccine design, and developing antiviral therapeutics. Large-animal models, such as the pig, that closely mirror human immune responses are essential for understanding influenza immunity.

Methods

Pigs were either infected or sequentially immunized with influenza viruses and monoclonal antibodies directed against H3, H5, and H7 influenza virus haemagglutinins were isolated. Antibody specificity, breadth, epitope targeting (head versus stem), neutralizing capacity, and Fc-mediated activity were assessed across influenza subtypes.

Results

Pigs generated both strain-specific and broadly reactive mAbs targeting haemagglutinin head and stem epitopes. An H3-specific mAb (H3–57) selectively recognized the egg-adapted L194P mutation associated with reduced human vaccine effectiveness. H5 and H7 immunization induced neutralizing antibodies, including cross-group stem mAbs reactive with H1, H3, and H5 haemagglutinins. Fc-mediated activity correlated with antibody binding strength rather than epitope location.

Conclusions

These findings demonstrate that pigs mount antibody responses closely resembling those observed in humans, including recognition of conserved stem epitopes and adaptive head mutations. Porcine mAbs represent powerful new tools for dissecting influenza immunity, guiding vaccine design, and enhancing pandemic preparedness using a physiologically relevant large-animal model.

Source: 


Link: https://academic.oup.com/discovimmunology/article/5/1/kyag006/8503709

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Thursday, February 19, 2026

Impact of an #aminoacid #deletion detected in the #hemagglutinin (HA) #antigenic site of swine #influenza A virus field strains on HA antigenicity

 


ABSTRACT

Swine influenza A virus (swIAV) is an important pathogen with regard to both the swine industry and public health. The pandemic A(H1N1) 2009 outbreak was caused by the swine-origin pandemic A(H1N1) 2009 [A(H1N1)pdm09] virus. Several reports have shown that several amino acid substitutions in the hemagglutinin (HA) antigenic sites can alter HA antigenicity. However, the impact of the amino acid deletion at position 155 on HA antigenicity remains unknown. In this study, we have isolated 11 samples of swIAVs from seven pig farms in Japan and found an amino acid deletion at position 155 of the HA region in one of the isolates of the H1N2 subtype. To examine the impact of this amino acid deletion on viral replication and HA antigenicity, we generated recombinant influenza A viruses possessing the H1 HA gene encoding either an artificial insertion or deletion of glycine at position 155. The growth kinetics of these recombinant viruses in two different cell lines demonstrated that the effect of amino acid deletion at position 155 of H1 HA on viral replication is limited. In contrast, microneutralization assay-based neutralization titers revealed that amino acid deletion significantly altered HA antigenicity. These results demonstrate that a naturally occurring amino acid deletion at position 155 in an H1 HA antigenic site can markedly alter HA antigenicity with only a limited impact on replication in vitro, highlighting the need to monitor such variants in swine populations and to assess their zoonotic potential.

Source: 


Link: https://journals.asm.org/doi/full/10.1128/jvi.01820-25?af=R

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Thursday, February 12, 2026

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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Thursday, January 15, 2026

Genetic Characterization and Evolutionary #Insights of Novel #H1N1 Swine #Influenza Viruses Identified from #Pigs in #Shandong Province, #China

 


Abstract

Influenza A viruses exhibit broad host tropism, infecting multiple species including humans, avian species, and swine. Swine influenza virus (SIV), while primarily circulating in porcine populations, demonstrates zoonotic potential with sporadic human infections. In this investigation, we identified two H1N1 subtype swine influenza A virus strains designated A/swine/China/SD6591/2019(H1N1) (abbreviated SD6591) and A/swine/China/SD6592/2019(H1N1) (abbreviated SD6592) in Shandong Province, China. The GenBank accession numbers of the SD6591 viral gene segments are PV464931-PV464938, and the GenBank accession numbers corresponding to each of the eight SD6592 viral gene segments are PV464939-PV464946. Phylogenetic and recombination analyses suggest potential evolutionary differences between the isolates. SD6591 displayed a unique triple-reassortant genotype: comparative nucleotide homology assessments demonstrated that the PB2, PB1, NP, NA, HA, and NEP genes shared the highest similarity with classical swine-origin H1N1 viruses. In contrast, SD6592 maintained genomic conservation with previously characterized H1N1 swine strains, although neither of these two isolates exhibited significant intrasegmental recombination events. Through comprehensive sequence analysis of these H1N1 SIVs, this study provides preliminary insights into their evolutionary history and underscores the persistent risk of cross-species transmission at the human–swine interface. These findings establish an essential foundation for enhancing national SIV surveillance programs and informing evidence-based prevention strategies against emerging influenza threats.

Source: 


Link: https://www.mdpi.com/1999-4915/18/1/117

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Monday, December 22, 2025

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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#Influenza at the #human - #animal #interface - Summary and #risk #assessment, from 6 November to 19 December 2025 (#WHO, edited)

 


Influenza at the human-animal interface 

Summary and risk assessment, from 6 November to 19 December 2025 {1}


-- New human cases {1,2}: 

- From 6 November to 19 December 2025, based on reporting date, the detection of influenza A(H5N1) in one human, A(H5N5) in one human, A(H9N2) in seven humans, and an influenza A(H1N1) variant virus in one human were reported officially. 

- In addition, one human case of infection with an influenza A(H1N2) variant virus was detected. 


-- Circulation of influenza viruses with zoonotic potential in animals

- High pathogenicity avian influenza (HPAI) events in poultry and non-poultry animal species continue to be reported to the World Organisation for Animal Health (WOAH).{3} 

- The Food and Agriculture Organization of the United Nations (FAO) also provides a global update on avian influenza viruses with pandemic potential.{4} 

- Additionally, low pathogenicity avian influenza viruses as well as swine influenza viruses continue to circulate in animal populations. 


-- Risk assessment {5}: 

- Sustained human to human transmission has not been reported associated with the above-mentioned human infection events. 

- Based on information available at the time of this risk assessment update, the overall public health risk from currently known influenza A viruses detected at the human-animal interface has not changed and remains low

- The occurrence of sustained human-to-human transmission of these viruses is currently considered unlikely

- Although human infections with viruses of animal origin are infrequent, they are not unexpected at the human-animal interface.  


-- IHR compliance {6}: 

- This includes any influenza A virus that has demonstrated the capacity to infect a human and its haemagglutinin (HA) gene (or protein) is not a mutated form of those, i.e. A(H1) or A(H3), circulating widely in the human population. 

- Information from these notifications is critical to inform risk assessments for influenza at the human-animal interface.  


Avian influenza viruses in humans 

-- Current situation:  

- Since the last risk assessment of 5 November 2025, one laboratory-confirmed human case of A(H5N1) infection was detected in Cambodia, and one laboratory-confirmed human case of A(H5N5) virus infection was detected in the United States of America


A(H5N1), Cambodia 

- On 16 November 2025, Cambodia notified WHO of a confirmed human infection with avian influenza A(H5N1) in a 22-year-old male from Phnom Penh

- The case developed symptoms on 10 November 2025, sought medical care at a clinic, and was diagnosed with pneumonia. 

- He was subsequently admitted to the national hospital in Phnom Penh on 13 November. 

- Samples were collected on the same day and tested positive for avian influenza A(H5N1) on 15 November. 

- His condition deteriorated rapidly, and he died the same day.   

- Investigations conducted in the case's hometown in Kampong Cham Province, which he visited between 4 and 6 November, revealed that the case had apparently healthy domestic birds (chickens and ducks) in his house. 

- However, sick and dead poultry had been reported in the village since 15 October

- Samples collected from two ducks and one chicken in the village tested positive for influenza A(H5N1). 

- Enhanced public health surveillance was implemented. 

- Among the case’s contacts, one was symptomatic, and all contacts tested negative for influenza A(H5N1).  

- Eighteen human infections with A(H5N1) viruses have been confirmed in Cambodia in 2025 and nine of these have been fatal

- All these cases in 2025 had exposure to domestic birds or their environments. 

- In some cases, domestic birds were reported to be sick or dead. 

- Where the information is available, the genetic sequence data from the viruses from the human cases closely matches that from recent local animal viruses and are identified as clade 2.3.2.1e viruses

- From the information available thus far on these recent human cases, there is no indication of human-tohuman transmission of the A(H5N1) viruses.  


A(H5N5), United States of America 

- On 15 November 2025, the United States of America (US) notified WHO of a confirmed human infection with influenza A(H5). 

- The patient was an adult with underlying medical conditions residing in Washington State

- The patient developed symptoms including fever during the week ending 25 October 2025. 

- During the week ending 8 November 2025, the patient was hospitalized with a serious illness and subsequently died on 21 November.  

- Respiratory specimens collected at the healthcare facility tested positive for influenza A virus by reverse-transcription-polymerase chain reaction (RT-PCR) and were presumptive positive for influenza A(H5) at the laboratory at the University of Washington. 

- The specimens were sent to the Washington State Public Health Laboratory, where influenza A(H5) was confirmed with the US Centers for Disease Control and Prevention (CDC) influenza A(H5) assay. 

- The sample was received at the CDC on 19 November. Sequencing conducted at the University of Washington and at the CDC indicated this was an influenza A(H5N5) virus belonging to the H5 haemagglutinin (HA) clade 2.3.4.4b.  

- Public health investigation revealed that the patient kept backyard poultry and domestic birds. 

- Additional epidemiological investigations were under way at the time of notification and included active monitoring of anyone who was in close contact with the patient.{7,8} 

- This is the first human case of this subtype reported globally. 

- Human infections with A(H5N1), A(H5N2), A(H5N6) and A(H5N8) have been reported previously. 

- A(H5N5) virus infections in animals have been detected and reported. 

- HPAI A(H5) clade 2.3.4.4b A(H5N5) viruses have been detected in North America in wild birds and wild mammals since at least 2023.{9} 

- According to reports received by WOAH, various influenza A(H5) subtypes continue to be detected in wild and domestic birds in Africa, the Americas, Asia and Europe

- Infections in non-human mammals are also reported, including in marine and land mammals.{10} 

- A list of bird and mammalian species affected by HPAI A(H5) viruses is maintained by FAO.{11}


-- Risk Assessment for avian influenza A(H5) viruses:  

1. What is the current global public health risk of additional human cases of infection with avian influenza A(H5) viruses?  

- Most human infections so far have been reported in people exposed to A(H5) viruses, for example, through contact with infected poultry or contaminated environments, including live poultry markets, and occasionally infected mammals and contaminated environments. 

- As long as the viruses continue to be detected in animals and related environments humans are exposed to, further human cases associated with such exposures are expected but remain unusual. 

- The impact for public health if additional sporadic cases are detected is minimal

- The current overall global public health risk of additional sporadic human cases is low


2. What is the likelihood of sustained human-to-human transmission of avian influenza A(H5) viruses related to the events above?  

- No sustained human-to-human transmission has been identified associated with the recent reported human infections with avian influenza A(H5) viruses. 

- There has been no reported human-to-human transmission of A(H5N1) viruses since 2007, although there may be gaps in investigations. 

- In 2007 and the years prior, small clusters of A(H5) virus infections in humans were reported, including some involving health care workers, where limited human-to-human transmission could not be excluded; however, sustained human-to-human transmission was not reported.  

- Current evidence suggests that influenza A(H5) viruses related to these events did not acquire the ability to efficiently transmit between people, therefore sustained human-to-human transmission is thus currently considered unlikely.  


3. What is the likelihood of international spread of avian influenza A(H5) viruses by travellers?  

- Should infected individuals from affected areas travel internationally, their infection may be detected in another country during travel or after arrival. 

- If this were to occur, further communitylevel spread is considered unlikely as current evidence suggests these viruses have not acquired the ability to transmit easily among humans.  


A(H9N2), China  

- Since the last risk assessment of 5 November 2025, China notified WHO of four cases of infection with influenza A(H9N2) on 6 November 2025 and three cases on 12 December 2025. 

- All but two cases were in children

- Cases were detected in Guangdong (one), Guangxi (three), Henan (one) and Hubei (two) provinces. 

- The cases had onsets of symptoms in September, October and November 2025. 

- Four cases had reported exposure to backyard poultry, two had exposure to live poultry markets and the source of exposure for one case was under investigation at the time of reporting. 

- All cases had mild illness and recovered, except one in an elderly person with underlying conditions who was hospitalized at the time of reporting with severe pneumonia. 

- No further cases were detected among contacts of these cases. 

- A(H9) viruses were detected in environmental samples collected during the investigations around some of the cases. 


-- Risk Assessment for avian influenza A(H9N2):   

- 1. What is the global public health risk of additional human cases of infection with avian influenza A(H9N2) viruses?   

- Most human cases follow exposure to the A(H9N2) virus through contact with infected poultry or contaminated environments. 

- Most human infections of A(H9N2) to date have resulted in mild clinical illness

- Since the virus is endemic in poultry in multiple countries in Africa and Asia, further human cases associated with exposure to infected poultry are expected but remain unusual. 

- The impact to public health if additional sporadic cases are detected is minimal

- The overall global public health risk of additional sporadic human cases is low.  


2. What is the likelihood of sustained human-to-human transmission of avian influenza A(H9N2) viruses related to this event?   

- At the present time, no sustained human-to-human transmission has been identified associated with the recently reported human infections with A(H9N2) viruses. 

- Current evidence suggests that A(H9N2) viruses from these cases did not acquire the ability of sustained transmission among humans, therefore sustained human-to-human transmission is thus currently considered unlikely.   


3. What is the likelihood of international spread of avian influenza A(H9N2) virus by travellers?   

- Should infected individuals from affected areas travel internationally, their infection may be detected in another country during travel or after arrival. 

- If this were to occur, further community level spread is considered unlikely as current evidence suggests the A(H9N2) virus subtype has not acquired the ability to transmit easily among humans.   


Swine influenza viruses in humans 

Influenza A(H1N1)v, China 

- Since the last risk assessment of 5 November 2025, the detection of a Eurasian avian-like swine influenza A(H1N1)v virus in a human was reported from China on 12 December 2025. 

- A 60-year-old male from Yunnan province had onset of mild illness on 2 November 2025, was hospitalized on 6 November and discharged on 10 November. 

- He had reported exposure to backyard pigs


Influenza A(H1N2)v, USA 

- A human case of infection with an influenza A(H1N2)v virus was detected in the state of Vermont in an adult who had an onset of symptoms in early October. 

- The individual was briefly hospitalized and has recovered. 

- The investigation conducted by state public health officials was unable to determine the likely source of exposure or if close contacts developed symptoms. 

- According to the report, no human-to-human transmission was identified associated with this case.{12}  


-- Risk Assessment:  

1. What is the public health risk of additional human cases of infection with swine influenza viruses?  

- Swine influenza viruses circulate in swine populations in many regions of the world. 

- Depending on geographic location, the genetic characteristics of these viruses differ. 

- Most human cases are exposed to swine influenza viruses through contact with infected animals or contaminated environments. 

- Human infection tends to result in mild clinical illness in most cases. 

- Since these viruses continue to be detected in swine populations, further human cases are expected. 

- The impact to public health if additional sporadic cases are detected is minimal

- The overall risk of additional sporadic human cases is low.  


2. What is the likelihood of sustained human-to-human transmission of swine influenza viruses?   

- No sustained human-to-human transmission was identified associated with the events described above. 

- Current evidence suggests that contemporary swine influenza viruses have not acquired the ability of sustained transmission among humans, therefore sustained human-to-human transmission is thus currently considered unlikely. 


3. What is the likelihood of international spread of swine influenza viruses by travelers?   

- Should infected individuals from affected areas travel internationally, their infection may be detected in another country during travel or after arrival. 

- If this were to occur, further community level spread is considered unlikely as current evidence suggests that these viruses have not acquired the ability to transmit easily among humans. 


Overall risk management recommendations

-- Surveillance and investigations

Due to the constantly evolving nature of influenza viruses, WHO continues to stress the importance of global strategic surveillance in animals and humans to detect virologic, epidemiologic and clinical changes associated with circulating influenza viruses that may affect human (or animal) health. Continued vigilance is needed within affected and neighbouring areas to detect infections in animals and humans. Close collaboration with the animal health and environment sectors is essential to understand the extent of the risk of human exposure and to prevent and control the spread of animal influenza. WHO has published guidance on surveillance for human infections with avian influenza A(H5) viruses

As the extent of influenza virus circulation in animals is not clear, epidemiologic and virologic surveillance and the follow-up of suspected human cases should continue systematically. Guidance on investigation of non-seasonal influenza and other emerging acute respiratory diseases has been published on the WHO website. 

Countries should increase avian influenza surveillance in: 

- domestic and wild birds,

- enhance surveillance for early detection in cattle populations in countries where HPAI is known to be circulating, 

- include HPAI as a differential diagnosis in non-avian species, including cattle and other livestock populations, with high risk of exposure to HPAI viruses; 

- monitor and investigate cases in non-avian species, including livestock, report cases of HPAI in all animal species, including unusual hosts, to WOAH and other international organizations, 

- share genetic sequences of avian influenza viruses in publicly available databases, 

- implement preventive and early response measures to break the HPAI transmission cycle among animals through movement restrictions of infected livestock holdings and strict biosecurity measures in all holdings, 

- employ good production and hygiene practices when handing animal products, and protect persons in contact with suspected/infected animals.{13} 

- More guidance can be found from WOAH and FAO

- When there has been human exposure to a known outbreak of an influenza A virus in domestic poultry, wild birds or other animals – or when there has been an identified human case of infection with such a virus – enhanced surveillance in potentially exposed human populations becomes necessary. 

- Enhanced surveillance should consider the health care seeking behaviour of the population, and could include a range of active and passive health care and/or communitybased approaches, including: 

> enhanced surveillance in local influenza-like illness (ILI)/SARI systems, 

> active screening in hospitals and of groups that may be at higher occupational risk of exposure, and 

> inclusion of other sources such as traditional healers, private practitioners and private diagnostic laboratories. 

Vigilance for the emergence of novel influenza viruses with pandemic potential should be maintained at all times including during a non-influenza emergency. In the context of the cocirculation of SARS-CoV-2 and influenza viruses, WHO has updated and published practical guidance for integrated surveillance


-- Notifying WHO 

All human infections caused by a new subtype of influenza virus are notifiable under the International Health Regulations (IHR, 2005).{14} State Parties to the IHR (2005) are required to immediately notify WHO of any laboratory-confirmed{15} case of a recent human infection caused by an influenza A virus with the potential to cause a pandemic{16}. Evidence of illness is not required for this report. Evidence of illness is not required for this report. 

WHO published the case definition for human infections with avian influenza A(H5) virus requiring notification under IHR (2005): https://www.who.int/teams/global-influenzaprogramme/avian-influenza/case-definitions


-- Virus sharing and risk assessment 

It is critical that these influenza viruses from animals or from humans are fully characterized in appropriate animal or human health influenza reference laboratories. Under WHO’s Pandemic Influenza Preparedness (PIP) Framework, Member States are expected to share influenza viruses with pandemic potential on a timely basis{17} with a WHO Collaborating Centre for influenza of GISRS. The viruses are used by the public health laboratories to assess the risk of pandemic influenza and to develop candidate vaccine viruses.  

The Tool for Influenza Pandemic Risk Assessment (TIPRA) provides an in-depth assessment of risk associated with some zoonotic influenza viruses – notably the likelihood of the virus gaining human-to-human transmissibility, and the impact should the virus gain such transmissibility. TIPRA maps relative risk amongst viruses assessed using multiple elements. The results of TIPRA complement those of the risk assessment provided here, and those of prior TIPRA analyses will be published at http://www.who.int/teams/global-influenza-programme/avian-influenza/toolfor-influenza-pandemic-risk-assessment-(tipra).  


-- Risk reduction 

Given the observed extent and frequency of avian influenza in poultry, wild birds and some wild and domestic mammals, the public should avoid contact with animals that are sick or dead from unknown causes, including wild animals, and should report dead birds and mammals or request their removal by contacting local wildlife or veterinary authorities.  

Eggs, poultry meat and other poultry food products should be properly cooked and properly handled during food preparation. Due to the potential health risks to consumers, raw milk should be avoided. WHO advises consuming pasteurized milk. If pasteurized milk isn’t available, heating raw milk until it boils makes it safer for consumption. 

WHO has published practical interim guidance to reduce the risk of infection in people exposed to avian influenza viruses. 


-- Trade and travellers 

WHO advises that travellers to countries with known outbreaks of animal influenza should avoid farms, contact with animals in live animal markets, entering areas where animals may be slaughtered, or contact with any surfaces that appear to be contaminated with animal excreta. Travelers should also wash their hands often with soap and water. All individuals should follow good food safety and hygiene practices.  

WHO does not advise special traveller screening at points of entry or restrictions with regards to the current situation of influenza viruses at the human-animal interface. For recommendations on safe trade in animals and related products from countries affected by these influenza viruses, refer to WOAH guidance.  


Links:  

-- WHO Human-Animal Interface web page https://www.who.int/teams/global-influenza-programme/avian-influenza 

-- WHO Influenza (Avian and other zoonotic) fact sheet https://www.who.int/news-room/fact-sheets/detail/influenza-(avian-and-other-zoonotic) 

-- WHO Protocol to investigate non-seasonal influenza and other emerging acute respiratory diseases https://www.who.int/publications/i/item/WHO-WHE-IHM-GIP-2018.2 

-- WHO Public health resource pack for countries experiencing outbreaks of influenza in animals:  https://www.who.int/publications/i/item/9789240076884 

-- Cumulative Number of Confirmed Human Cases of Avian Influenza A(H5N1) Reported to WHO  https://www.who.int/teams/global-influenza-programme/avian-influenza/avian-a-h5n1-virus 

-- Avian Influenza A(H7N9) Information https://www.who.int/teams/global-influenza-programme/avian-influenza/avian-influenza-a-(h7n9)virus 

-- World Organisation of Animal Health (WOAH) web page: Avian Influenza  https://www.woah.org/en/home/ 

-- Food and Agriculture Organization of the United Nations (FAO) webpage: Avian Influenza https://www.fao.org/animal-health/avian-flu-qa/en/ 

-- OFFLU http://www.offlu.org/ 

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{1} This summary and assessment covers information confirmed during this period and may include information received outside of this period. 

{2} For epidemiological and virological features of human infections with animal influenza viruses not reported in this assessment, see the reports on human cases of influenza at the human-animal interface published in the Weekly Epidemiological Record here.  

{3} World Organisation for Animal Health (WOAH). Avian influenza. Global situation. Available at: https://www.woah.org/en/disease/avian-influenza/#ui-id-2

{4} Food and Agriculture Organization of the United Nations (FAO). Global Avian Influenza Viruses with Zoonotic Potential situation update. Available at: https://www.fao.org/animal-health/situation-updates/global-aiv-withzoonotic-potential

{5} World Health Organization (2012). Rapid risk assessment of acute public health events. World Health Organization. Available at: https://iris.who.int/handle/10665/70810

{6} World Health Organization. Case definitions for the 4 diseases requiring notification to WHO in all circumstances under the International Health Regulations (2005). Case definitions for the four diseases requiring notification in all circumstances under the International Health Regulations (2005).   

{7} World Health Organization (5 December 2025). Disease Outbreak News; Avian Influenza A(H5N5)- United States of America. Available at: https://www.who.int/emergencies/disease-outbreak-news/item/2025DON590

{8} US CDC FluView. Weekly US Influenza Surveillance Report: Key Updates for Week 46, ending November 15, 2025. Available at https://www.cdc.gov/fluview/surveillance/2025-week-46.html

{9} Erdelyan CNG, Kandeil A, Signore AV, et al. Multiple transatlantic incursions of highly pathogenic avian influenza clade 2.3.4.4b A(H5N5) virus into North America and spillover to mammals. Cell Rep. 2024 Jul 23;43(7):114479. doi:10.1016/j.celrep.2024.114479. Epub 2024 Jul 13. PMID:39003741; PMCID:PMC11305400. 

{10}  World Organisation for Animal Health (WOAH). Avian influenza. Global situation. Available at: https://www.woah.org/en/disease/avian-influenza/#ui-id-2

{11} Food and Agriculture Organization of the United Nations. Global Avian Influenza Viruses with Zoonotic Potential situation update. Available at: https://www.fao.org/animal-health/situation-updates/global-aiv-withzoonotic-potential/bird-species-affected-by-h5nx-hpai/en

{12} US CDC FluView. Weekly US Influenza Surveillance Report: Key Updates for Week 46, ending November 15, 2025. Available at https://www.cdc.gov/fluview/surveillance/2025-week-46.html

{13} World Organisation for Animal Health. Statement on High Pathogenicity Avian Influenza in Cattle, 6 December 2024. Available at: https://www.woah.org/en/high-pathogenicity-avian-influenza-hpai-in-cattle/

{14} World Health Organization. Case definitions for the four diseases requiring notification in all circumstances under the International Health Regulations (2005). 

{15} World Health Organization. Manual for the laboratory diagnosis and virological surveillance of influenza (2011). Available at: https://apps.who.int/iris/handle/10665/44518

{16} World Health Organization. Pandemic influenza preparedness framework for the sharing of influenza viruses and access to vaccines and other benefits, 2nd edition. Available at: https://iris.who.int/handle/10665/341850

{17} World Health Organization. Operational guidance on sharing influenza viruses with human pandemic potential (IVPP) under the Pandemic Influenza Preparedness (PIP) Framework (2017). Available at: https://apps.who.int/iris/handle/10665/259402

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Source: 


Link: https://www.who.int/publications/m/item/influenza-at-the-human-animal-interface-summary-and-assessment--19-december-2025

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