Friday, December 12, 2025

#Vaccine-induced #antigenic #drift of a #human-origin #H3N2 #Influenza A virus in swine alters glycan binding and sialic acid avidity

 


Abstract

Interspecies transmission of human influenza A viruses (FLUAV) to swine occurs frequently, yet the molecular factors driving adaptation remain poorly understood. Here we investigated how vaccine-induced immunity shapes the evolution of a human-origin H3N2 virus in pigs using an in vivo sustained transmission model. Pigs (seeders) were vaccinated with a commercial inactivated swine vaccine and then infected with an antigenically distinct FLUAV containing human-origin HA/NA. Contact pigs were introduced two days later. After 3 days, seeder pigs were removed, and new contacts introduced. This was repeated for a total of 4 contacts. Sequencing of nasal swab samples showed the emergence of mutations clustered near the HA receptor binding site, enabling immune escape and abolishing binding to N-glycolylneuraminic acid. Mutant viruses recognized α2,6-sialosides with 3 N-acetyllactosamine repeats, which are rare in swine lungs, while the parental virus bound structures with a minimum of 2 repeats. Adaptative HA mutations enhanced avidity for α2,6-linked sialic acid, likely compensating for the low abundance of extended glycans. Notably, residues outside the canonical HA binding pocket contribute to glycan binding, suggesting a trade-off between receptor breadth and avidity. These findings show that non-neutralizing immunity promotes viral adaptation by fine-tuning receptor engagement and immune evasion.


Competing Interest Statement

The authors have declared no competing interest.

Source: 


Link: https://www.biorxiv.org/content/10.64898/2025.12.10.693614v1

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High pathogenicity avian #influenza virus #H5N1 (clade 2.3.4.4b) drives mass #mortality in Eurasian #crane (Grus grus) populations in #Germany, 2025

 


Abstract

In autumn 2025, an unprecedented mass mortality event was observed among the western migrating subpopulation of Eurasian cranes (Grus grus) in Germany. Systemic infection with highly pathogenic avian influenza virus H5N1, clade 2.3.4.4b, genotype DI.2.1, was identified as the cause of acute death. The gregarious behavior of cranes at feeding and resting sites likely has contributed to the rapid and massive dissemination of viruses within the crane population.


Competing Interest Statement

The authors have declared no competing interest.


Funder Information Declared

European Union, 101084171

Source: 


Link: https://www.biorxiv.org/content/10.64898/2025.12.08.692485v1

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Wednesday, December 10, 2025

Seasonal #influenza - #Global #situation (#WHO, Dec. 10 '25, excerpts)

 


10 December 2025


Situation at a glance

Seasonal influenza (‘the flu’) is an acute respiratory infection caused by influenza viruses that circulate globally and year-round. 

It can cause illness ranging from mild to severe, sometimes resulting in hospitalization or death. 

Seasonal influenza activity has increased globally in recent months, with an increased proportion of seasonal influenza A(H3N2) viruses being detected. 

This rise coincides with the onset of winter in the northern hemisphere and an increase in acute respiratory infections caused by influenza and other respiratory viruses typically observed at this time of year. 

Although global activity remains within expected seasonal ranges, early increases and higher activity than typical at this time of year have been observed in some regions. 

Seasonal influenza viruses, including A(H3N2) viruses, continually evolve over time. 

Since August 2025, there has been a rapid increase of A(H3N2) J.2.4.1 alias K subclade viruses detected from several countries based on available genetic sequence data. 

These subclade K viruses have several changes from related A(H3N2) viruses. 

Current epidemiological data do not indicate an increase in disease severity, although this subclade marks a notable evolution in influenza A(H3N2) viruses. 

Early estimates suggest that the influenza vaccine continues to provide protection against hospital attendance in both children and adults, even though its effectiveness against clinical disease during the current season remains uncertain. 

Vaccines remain essential, especially for people at high risk of influenza complications and their care givers. 

Even if there are some genetic differences between the circulating influenza viruses and the strains included in the vaccines, the seasonal influenza vaccine may still provide protection against drifted viruses and the other virus strains included in the vaccine. 

Vaccination is still expected to protect against severe illness and remains one of the most effective public health measures. 

WHO continues to monitor global influenza activity and influenza viruses, supports countries in surveillance capacity and updates guidance as needed.


Description of the situation

Globally, influenza activity has increased since October 2025 with influenza A viruses predominant among the viruses detected globally.

In many northern hemisphere countries, acute respiratory infection levels increase at this time of year. 

These increases are typically caused by seasonal epidemics of respiratory pathogens such as influenza, respiratory syncytial virus (RSV) and other common respiratory viruses. 

The exact timing of the onset, the duration, magnitude and the severity of each epidemic might vary by location, influenced by multiple factors such as type of circulating viruses (including influenza and other respiratory pathogens), relative population immunity and environmental conditions.

In the northern hemisphere, some countries have reported early starts to the influenza season

In other countries, influenza activity is starting to increase, but has not yet reached the epidemic threshold.

In the southern hemisphere, some countries have had unusually long seasons compared to previous years, with virus activity remaining higher than usual in recent months.

Global influenza surveillance and monitoring is conducted through the Global Influenza Surveillance and Response System (GISRS), a WHO-coordinated network of over 160 institutions in 131 Member States. 

GISRS is tasked with conducting year-round surveillance and monitoring of influenza viruses and serving as the global alert mechanism for the emergence of novel influenza viruses and other respiratory pathogens with pandemic potential.

In the northern hemisphere temperate and sub-tropical countries, areas and territories, influenza activity was generally low from June to August 2025. 

Activity gradually increased in September and continued to increase through November 2025. Influenza A viruses, especially A(H3N2) viruses, predominated during this period (...).

In the southern hemisphere temperate and sub-tropical countries, areas and territories, influenza activity generally decreased from June 2025 and remained low through August. 

However, a slight increase has been observed since September. 

Influenza A(H1N1)pdm09 viruses predominated in June and July; however, A(H3N2) viruses have predominated since September (...).

In tropical areas, there has been sustained influenza activity from June through November. 

Influenza A(H1N1)pdm09 viruses predominated through July. Since then, the proportion of influenza A(H3N2) viruses among reported detections has increased and has become predominant since the end of September (...).

(...)


Genetic characteristics of recent seasonal influenza viruses

Influenza A(H1N1)pdm09 and influenza B/Victoria lineage viruses continue to circulate in all regions albeit at low levels.


Influenza A(H3N2) viruses

Based on genetic sequence data available in GISAID, a mixture of A(H3N2) haemagglutinin (HA) clades and subclades are currently circulating globally; however, there has been a recent and rapid rise in a particular  subclade of A(H3N2), J.2.4.1 (alias subclade K Nextclade/Nextstrain nomenclature). 

A(H3N2) subclade K viruses have genetically drifted from related J.2.4 viruses and have several amino acid changes in their HA in comparison. 

Detections of subclade K viruses are increasing in many parts of the world, with the exception, to date, of South America. 

Subclade K viruses were particularly evident from August 2025 in Australia and New Zealand and have now been detected in more than 34 countries over the last 6 months.

(...)


Overview of seasonal influenza by WHO Region

African region

Influenza detections in the WHO African Region overall increased in October with influenza A(H3N2) predominant. 

The timing and predominant virus varied by zone. 

In the western part of the region, influenza detections increased in September and October with A(H3N2) predominant since October. 

All seasonal subtypes have been detected continuously in the middle and eastern parts of the region. 

Influenza activity peaked in May 2025 in South Africa with almost exclusively A(H3N2) detections; in recent weeks influenza activity has increased slightly but remained low.


Eastern Mediterranean Region

While influenza activity in the WHO Eastern Mediterranean Region overall increased in October with A(H3N2) viruses predominant, there were variations by zone. 

In countries in the northern part of the region, influenza detections increased in October with influenza A(H1N1)pdm09 predominant and lesser proportions of influenza A(H3N2) and B virus detections reported. 

In the Arabian Peninsula, influenza detections also increased in October but with influenza A(H3N2) viruses predominant.


European Region

As of 21 November 2025, reported rates of influenza-like illness (ILI) and/or acute respiratory infection (ARI) in primary care were at baseline levels for most countries and areas of the WHO European Region. 

However, detections were increasing and regionally pooled test percent positivity in primary care sentinel surveillance rose above 10% in weeks 45 and 46 (ending on 15 November), marking the start of the 2025/26 influenza season for the European Region. 

This was approximately four weeks earlier than the median, but not out of the ordinary, with epidemiological trends similar to those observed in the 2022/23 influenza season.

Influenza activity was variable between countries, with those in the west of the Region generally seeing earlier increases of influenza indicators compared to others. 

Influenza admissions, detections, and percent positivity in hospital surveillance were also increasing from inter-seasonal levels, with a higher proportion aged 65 years or older. 

A majority of influenza detections from sentinel and non-sentinel primary care and hospital surveillance systems were A(H3N2) viruses.


Region of the Americas

During the 2025 southern hemisphere season in the Americas, influenza transmission exceeded the seasonal threshold in mid-March, remaining mostly at low to moderate levels. 

Circulation was driven by influenza A(H1N1)pdm09, reaching a peak positivity of 19%. 

Activity then declined to low levels until the end of August, when an increase in circulation was observed, associated with influenza A(H3N2) in Brazil and Chile

As of beginning of November, Chile remains at moderate levels of influenza A(H3N2) transmission, without evidence of increased severity or rises in outpatient consultations. 

As of 4 November 2025, subclade K had not been detected in South America.

In the northern hemisphere countries of the Americas, during week 45 of 2025, seasonal influenza circulation remained low, with influenza A(H1N1)pdm09 predominating in the Caribbean and Central America

In North America, influenza activity—although still low—was increasing, mainly driven by influenza A virus detections. 

While most detections in Mexico were influenza A(H1N1)pdm09, a predominance of influenza A(H3N2) has been observed in the United States and Canada, with growing detections of the A(H3N2) subclade K.


South-East Asia Region

Influenza detections in the South-East Asia Region started increasing from June,  peaked in August and since then  have generally remained low with some exceptions. 

During the 2025 till November, the proportion of Influenza A among all influenza viruses tested positive was 66% Influenza A(H3N2) was the predominant sub-type (43%) in transmission followed by A(H1N1)pdm09 (~20%). 

In Thailand, influenza detections of predominantly A(H3N2) increased in October and November. 

Influenza A(H3N2) detections also increased since July in Bangladesh and October in Sri Lanka

While the region has seen an increase in Influenza A(H3N2), 22 sequences of   subclade K have   been reported in GISAID from Nepal (1), India (4) and Thailand (17) as of 30 November.


Western Pacific Region

Since the beginning of October 2025, influenza seasonal activity has increased in the Western Pacific Region

In some countries, including Japan and the Republic of Korea, the onset of the typical seasonal influenza activity period started earlier than in previous years. 

As of 9 November 2025, influenza positivity ranged from 8% to 56% in the northern hemisphere countries. 

In southern hemisphere countries, influenza activity shows mixed trends; positivity has declined in Australia, remains high in New Zealand and is rapidly increasing in Fiji. 

The elevated influenza activity in New Zealand and Fiji is unusual for this time of the year.

The predominant circulating influenza subtype is influenza A(H3N2), marking a shift from A(H1N1)pdm09, which predominated during the 2024-2025 northern hemisphere winter season. 

The increases in influenza have predominantly been driven by the expansion of A(H3N2) subclade K, which represents 89% of sequences submitted to GISAID from the Western Pacific Region (as of 21 November 2025). 


Epidemiology

Seasonal influenza (the flu) is an acute respiratory infection caused by influenza viruses that circulate globally and year-round. In temperate regions, seasonal influenza typically peaks during the winter months, whereas in tropical areas, influenza viruses can circulate year-round with seasonality and intensity that varies across countries.  

There are four types of influenza viruses, types A, B, C and D. Influenza A and B viruses circulate and cause seasonal epidemics of disease:

Influenza A viruses are further classified into subtypes according to the combinations of the proteins on the surface of the virus. Currently circulating in humans are subtype A(H1N1) and A(H3N2) influenza viruses. Influenza B viruses are not classified into subtypes but can be broken down into lineages. Influenza type B viruses belong to either B/Yamagata or B/Victoria lineage.

Influenza spreads easily between people when they cough or sneeze. Influenza disease can cause illness ranging from mild to severe, sometimes resulting in hospitalization or death. While most individuals recover within a week without need for medical care, influenza can lead to serious complication including death, especially among high-risk groups such as young children, the elderly, pregnant women and those with underlying conditions. Health and care workers are at high risk of acquiring influenza virus infection due to increased exposure to the patients, and of further spreading particularly to vulnerable individuals.


Public health response

WHO is enhancing national, regional, and global capacities for influenza preparedness and response, including:

-- continuous global monitoring of influenza viruses and disease activity;

-- issuing seasonal influenza vaccine composition recommendations for both hemispheres;

-- providing technical guidance to Member States on vaccine selection and campaign timing;

-- supporting countries in developing prevention and control strategies;

-- enhancing diagnostic capabilities and laboratory networks;

-- monitoring vaccine effectiveness and susceptibility to approved antivirals;

-- supporting disease surveillance and outbreak response activities;

-- promoting increased vaccine coverage among high-risk groups;

-- facilitating research and development of new therapeutics and countermeasures; and

-- enhancing risk communication for the onset of the influenza season.


WHO risk assessment

Seasonal influenza activity has increased globally in recent months, and influenza A(H3N2) viruses are predominant

This rise coincides with the onset of winter in the northern hemisphere. 

Epidemics and outbreaks of seasonal influenza and other circulating respiratory viruses can place significant pressure on healthcare systems.  

Although global activity remains within expected seasonal ranges, early increases and higher activity than typical at this time of year have been observed in some regions. 

Seasonal influenza could place significant pressure on healthcare systems even in non-temperate countries. 

Genetically drifted influenza A(H3N2) viruses, known as subclade K viruses, have been detected in many countries. 

While data on how well the vaccine works against clinical disease this season are still limited, vaccination is still expected to protect against severe illness and remains one of the most effective public health measures. 


WHO advice

Surveillance

Due to the constantly evolving nature of influenza viruses, WHO continues to stress the importance of year-round global surveillance to detect and monitor virological, epidemiological and clinical changes associated with emerging or circulating influenza viruses that may affect human health and timely virus sharing for risk assessment.  Countries are encouraged to remain vigilant to the threat of influenza viruses and review any unusual epidemiological patterns.

WHO advises Member States to maintain surveillance for respiratory pathogens through an integrated approach, considering country context, priorities, resources and capacities. WHO has published guidance on integrated respiratory virus surveillance. WHO has also updated guidance on assessing influenza epidemic and pandemic severity, including the impact on healthcare facilities.


Clinical management and prophylaxis

Clinical care for seasonal influenza focuses on identifying illness severity, assessing risk of progression, and linking to definitive care. Most cases are mild and self-limiting, but severe disease, marked by respiratory distress, sepsis, acute respiratory distress syndrome or multi-organ failure, requires urgent supportive care and often hospitalization. Clinical management of influenza involves high-quality supportive care—oxygen therapy, monitoring, hydration and respiratory support—and is foundational to improving outcomes, especially in severe cases.

Diagnostic testing should support rapid decision-making: nucleic acid amplification test (NAAT) is conditionally recommended for confirmation of suspected disease in severely unwell patients, while either NAAT or digital immunoassay may be used for non-severe cases, depending on context and resource availability. Testing should be performed early with the aim of identifying people in need of treatment and linking them to care, including antivirals where indicated.

Patients at high risk of progressing to severe disease are likely to benefit from antiviral to reduce their chance of admission to hospital. High-risk groups include adults ≥65 years, those with immunocompromising conditions, chronic cardiovascular, neurological or respiratory disease; malignancy, pregnancy and diabetes further elevate risk. Individuals ≥85 years or those with multiple risk factors are considered extremely high risk and might be considered for antiviral prophylaxis if exposed to influenza.


Infection prevention and control measures in health-care settings

Seasonal influenza is known to cause health care-associated infection outbreaks, in particular in long-term care facilities. WHO advises the use of syndromic screening at all entry points to health-care settings and as part of daily inpatient assessment to ensure that patients with suspected or confirmed infections that are transmissible in health-care settings, including influenza, are identified as soon as possible and that appropriate transmission-based precautions are implemented. WHO advises the use of droplet precautions when caring for patients with suspected or confirmed influenza. This includes appropriate patient placement (isolation) of suspected or confirmed cases, and the use of a medical mask by all health and care workers and visitors when caring for patients with suspected or confirmed influenza.

Appropriate risk assessment for additional personal protective equipment (e.g. eye protection, filtering facepiece respirators, gown, gloves) should be performed by health and care workers when caring for patients with influenza. 

Increased risk of influenza transmission may occur instances where care activities or patient symptoms are likely to generate splashes or sprays of blood, body fluids, secretions and excretions onto mucosa of eyes, nose or mouth; or if in close contact with a patient with respiratory symptoms (e.g. coughing/sneezing) and sprays of secretions may reach the mucosa of eyes, nose or mouth directly, or indirectly via contaminated hands. When performing an aerosol-generating procedure on patients with suspected or confirmed influenza, patient placement in an airborne infection isolation room as well as airborne and contact precautions with eye protection are advised.


Vaccination

Vaccination is the best way to prevent influenza disease. Safe and effective vaccines have been used for more than 60 years. Influenza viruses are constantly changing, so the composition of the seasonal influenza vaccine is regularly updated to contain viruses that are more related to those circulating. WHO, through the Global Influenza Programme and GISRS, in collaboration with partners, continuously monitors influenza viruses and activity globally and recommends seasonal influenza vaccine compositions in February and September for the following northern and southern hemisphere influenza seasons, respectively.

WHO recommends annual vaccination for high-risk groups, including health and care workers. People should ideally get vaccinated just before the influenza season begins for the most effective coverage, although getting vaccinated at any time during the influenza season can still help prevent flu infections. While the effectiveness of the vaccine may vary across seasons and risk groups, it reduces disease severity and lowers the chance of complications and death. Vaccination is especially important for people at high risk of influenza complications and their caregivers.

Genetic changes or drift can occur in the circulating influenza viruses before or during the influenza season, including during the time between vaccine strain selection and the influenza season. Even if there are some genetic differences between the circulating influenza viruses and the strains that are included in the vaccines, the seasonal influenza vaccine may still provide protection against drifted viruses. Current vaccines include three influenza viruses: influenza A(H1N1)pdm09, influenza A(H3N2) and influenza B/Victoria lineage viruses. Therefore, circulation of a drifted virus does not always result in seasonal influenza vaccines being less effective in offering protection against influenza associated illness.

As of now, it remains unclear how the vaccine will protect against clinical disease during this current season. However, early vaccine effectiveness estimates show the current vaccine is 70 to 75% effective at preventing hospital attendance in children aged 2 to 17 years and 30 to 40% effective in adults.[1],[2]


Public health and social measures in the community

The implementation of appropriate and proportionate public health and social measures (PHSM) is an essential component in the overall response to seasonal influenza epidemics. 

Measures such as performing hand hygiene, respiratory hygiene and cough etiquette as well as voluntary self-isolation and mask wearing of individuals who are symptomatic or have tested positive for influenza viruses can reduce transmission of influenza viruses.  

Countries should consider developing a plan to scale up additional PHSM in the event of high or extraordinarily high epidemics.  


Risk communication and community engagement

Member States should consider to update and strengthen their risk communication and community engagement (RCCE) strategy integrating respiratory viruses. Enhanced risk communication and community engagement approach support empowerment of individuals to make informed decisions, countering misinformation, and community-led protection strategies.

Clear, regular, evidence-based, culturally acceptable and context adapted RCCE approaches are essential for building and maintaining trust with the concerned and affected populations to ensure adoption of interventions, practices and behaviours. For RCCE efforts to be successful, it is vital that national policies for RCCE incorporate community engagement and feedback mechanisms that acknowledge and address contextual challenges faced by different population groups, particularly those made most vulnerable. The integration of RCCE approaches to promote vaccination against influenza is also recommended.

WHO does not recommend any restriction on travel to or trade with the countries named in this report, based on the information available on the current event.  

(...)

Source: 


Link: https://www.who.int/emergencies/disease-outbreak-news/item/2025-DON586

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#Human #Infection with Avian #Influenza #H10N3 Virus, #China, 2024

 


Abstract

We describe the clinical symptoms and epidemiologic characteristics of a patient infected with avian influenza A(H10N3) virus in Guangxi Province, China, in December 2024. Whole-genome sequencing showed that the virus was highly homologous to a virus from Yunnan Province. H10 subtype viruses should be monitored for potential zoonotic or reassortant events.

{From Emerging Infectious Diseases Journal, US CDC.}

Sources: 

Link: https://pubmed.ncbi.nlm.nih.gov/41237415/

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Innate #antiviral readiness drives the expansion of protective T #stem cell memory against #influenza

 


Abstract

The development of T-cell-based influenza vaccines relies on eliciting broad CD8+ T-cell immunity, wherein T stem cell-like memory (TSCM) cells serve as the ultimate long-lived reservoir for immune memory, thereby unlocking the potential for durable protection against viral drift and shift. However, the specific immunological cues that drive the robust expansion and functional preservation of this self-renewing, multipotent subset remain unknown. Here, utilizing multi-omic systems immunology in a pediatric cohort immunized with live attenuated influenza vaccine, we identified the determinants governing the expansion of influenza virus-reactive TSCM cells. We show that a pre-existing state of innate antiviral readiness, defined by a plasmacytoid dendritic cell-associated type I interferon signature, is the requisite condition for a robust TSCM expansion. Mechanistically, this baseline innate state enhances antigen priming and enforces a qualitative divergence in T-cell fate, driving responders toward a functionally poised, Th1-dominant phenotype while non-responders default to a dysfunctional, hyper-proliferative state. To determine the clinical relevance of this cellular subset, we analyzed an independent controlled human influenza challenge study. This validation revealed a critical functional division of labor in host defense: whereas pre-existing antibodies primarily mitigated symptom severity, the baseline frequency of influenza virus-reactive TSCM cells was the strongest predictor of rapid viral load clearance. These findings establish that the expansion of durable cellular memory is not stochastic but is predetermined by the innate cytokine environment, providing a predictive biomarker for patient stratification and a validated target for adjuvants designed to expand the TSCM reservoir deliberately.


Competing Interest Statement

A.J.P. was previously the Chair of the UK Department of Health and Social Care's Joint Committee on Vaccination and Immunisation and is a member of WHOs Product Development Advisory Committee. The A.G.-S. laboratory has received research support from Avimex, Dynavax, Pharmamar, 7Hills Pharma, ImmunityBio, and Accurius. A.G.-S. has consulting agreements for the following companies involving cash and/or stock: Castlevax, Amovir, Vivaldi Biosciences, Contrafect, 7Hills Pharma, Avimex, Pagoda, Accurius, Esperovax, Applied Biological Laboratories, Pharmamar, CureLab Oncology, CureLab Veterinary, Synairgen, Paratus, Pfizer, Virofend and Prosetta. A.G.-S. has been an invited speaker in meeting events organized by Seqirus, Janssen, Abbott, Astrazeneca and Novavax. 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, US. Other authors declare no competing interests.


Funder Information Declared

European Commission Marie Sklodowska-Curie Fellowship, 796636

NIAID, 75N93021C00014

Flu Lab

Source: 


Link: https://www.biorxiv.org/content/10.64898/2025.12.06.692757v1

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#Kazakhstan - #Influenza A #H5 viruses of high pathogenicity (Inf. with) (non-poultry including wild birds) (2017-) - Immediate notification [FINAL]


{Greylag Goose}

{Mallards}

A Greylag Goose, two Mallards  in Aqmola Region.

Source: 


Link: https://wahis.woah.org/#/in-review/7093

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

 


The outbreak affecting captive birds was in an establishment with 4 laying hens, 1 cock and 1 runner duck located in Harju county, Viimsi parish. The outbreak was confirmed on the 9th of December 2025 based on analysis performed tracheal and brain samples at the National Centre for Laboratory Research and Risk Assessment, and in accordance with the case definition. Measures were only applied in the outbreak establishment. Based on a risk assessment, no restricted zone was established around the affected establishment in accordance with Article 21(3)(g). The establishment concerned kept only 6 captive birds and they had no direct or indirect contact with poultry or other establishments keeping captive birds. In the establishment, all captive birds were already dead. No culling was necessary. Preliminary cleaning and disinfection was applied.

Source: 


Link: https://wahis.woah.org/#/in-review/7092

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Foraging #ecology drives viral community structure in #NZ's aquatic #birds

 


Abstract

Wild migratory birds play a major role in the global spread of viruses, yet the diversity, host range and transmission patterns of viruses harboured by migratory species in Aotearoa/New Zealand remain largely unknown. This knowledge gap is critical given New Zealand's position along major migratory flyways spanning Oceania, Antarctica and east Asia, where understanding viral diversity is key to assessing the risk of viral introductions such as highly pathogenic avian influenza virus and viral dispersal across these regions. To address this, we conducted the first large-scale metatranscriptomic survey of wild birds from New Zealand and its subantarctic islands, collecting 1,348 samples from 31 host species spanning four avian orders. We identified 118 avian viruses from 17 families, including 107 novel species, greatly expanding our knowledge of avian viral diversity. Viral communities differed significantly by host order and foraging behaviour, with scavenger birds harbouring more diverse viromes than non-scavengers. Although no HPAI subtypes were detected, we recovered a low-pathogenic avian influenza A/H1N9 virus from red knots (Calidris canutus) and a divergent tobanivirus from Auckland Island teal (Anas aucklandica), the first putative avian member of the Tobaniviridae. Notably, we detected 12 mammalian-associated viruses, primarily in scavenger birds, including Hedgehog hepatovirus, Rabbit haemorrhagic disease virus 2, and sea lion astroviruses, with mammalian host reads confirming their dietary origin. This study establishes the first virome baseline for New Zealand's migratory birds, highlighting the ecological role of foraging in shaping viral communities and improving regional preparedness for HPAI and other emerging avian pathogens.


Competing Interest Statement

The authors have declared no competing interest.


Funder Information Declared

Te Niwha, New Zealand's Infectious Disease Research Platform, TN/SWC/24/UoOJG

Source: 


Link: https://www.biorxiv.org/content/10.64898/2025.12.09.693119v1

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Tuesday, December 9, 2025

Distinctive viral #genome #signatures are linked to repeated #mammalian #spillovers of #H5N1 in North #America

 


Abstract

Highly pathogenic avian influenza H5N1 rarely infects mammals. In 2024-2025, however, genotypes B3.13 and D1.1 caused two independent spillovers into U.S. dairy cattle. By analysing 26,930 complete H5N1 genomes from global surveillance, we identified 73 major viral groups, most of which show continent-specific distribution in Europe, Asia, Africa, and North America. North American viruses exhibit higher genetic diversity in specific viral segments, including variants potentially associated with mammalian adaptation. Both dairy-cattle-associated B3.13 and D1.1 genotypes originate from the same geographic macro-area, suggesting a possible regional hotspot where avian-mammalian interfaces may facilitate viral adaptation. Our findings place the U.S. outbreaks in a global framework and indicate that North American H5N1 may be predisposed to cross-species transmission.


Competing Interest Statement

The authors have declared no competing interest.


Funder Information Declared

NextGenerationEU, PRIN PNRR 2022 (Italian Ministry of University and Research), P2022CNN2J

Source: 


Link: https://www.biorxiv.org/content/10.64898/2025.12.09.693147v1

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Evolutionary trajectories and #zoonotic #potential of a #PB2 #mutation triad (I147T, K339T, and A588T) in avian #influenza viruses

 


Abstract

Efficient replication of influenza A viruses (IAVs) requires balanced activities of hemagglutinin (HA), neuraminidase (NA), and the RNA polymerase complex, whose functions are strongly influenced by PB2 mutations. We previously revealed three distinct evolutionary pathways for PB2 mutations, with two pathways leading to the emergence of viral strains responsible for human seasonal infections and the 2009 pandemic, and a third pathway giving rise to H5Nx highly pathogenic avian influenza viruses (HPAIVs) defined by a triad of mutations (I147T, K339T, and A588T) that occasionally spill over to humans. Here, we investigated the zoonotic risk posed by this triad and elucidated its evolutionary relationship with HA, NA, and vaccination. Recombinant PR8 and clade 2.3.2.1c H5N1 viruses carrying the triad replicated efficiently in embryonated chicken eggs and had moderate replication efficiency in mammalian cells; moreover, mice infected with these viral strains exhibited milder weight loss and lower lung titers than those infected with the E627K-carrying strain. Sequence analysis of H5Nx viruses revealed early emergence and long-term persistence of the triad across diverse genotypes, which was closely linked to HA glycosylation and NA-stalk truncation. However, the prevalence of these viral strains declined significantly after successive H5 poultry-vaccination campaigns. These data indicate that the triad provides a replication advantage compatible with both poultry and mammalian hosts but confers only moderate mammalian pathogenicity and that sustained vaccination can restrain the spread of viral strains with these mutations. Continuous molecular surveillance of PB2 alongside HA and NA remains essential for preventing H5Nx zoonotic threats. 

Please check and confirm that the authors and their respective affiliations have been correctly identified and amend if necessary. I have checked and modifed the email addresses of the corresponding authors. I confirm the information of other authors are correct.

Source: 


Link: https://link.springer.com/article/10.1186/s13567-025-01680-z

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#Korea (Rep. of) - #Influenza A #H5N6 viruses of high pathogenicity (Inf. with) (non-poultry including wild birds) (2017-) - Immediate notification

 


A Common Teal in Jeollanam-do Region.

Source: 


Link: https://wahis.woah.org/#/in-review/7034

____

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

 


{England, Kent}

Laying flock with around 31K birds. Samples taken were positive for HPAI H5N1. Birds presented clinical signs prior to testing.

{England, Suffolk}

Backyard flock. Samples taken were positive for HPAI H5N1. Birds presented clinical signs of AI prior to testing.

Source: 


Link: https://wahis.woah.org/#/in-review/7081

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#Safety and immunogenicity of a live-attenuated #chikungunya virus #vaccine in #adolescents: final results from a ... phase 3 trial in endemic areas of #Brazil

 


Summary

Background

Chikungunya outbreaks have recurred in Brazil since 2014. Building on earlier 28-day post-vaccination data, we now report 12-month safety and immunogenicity results of the VLA1553 vaccine in Brazilian adolescents.

Methods

In this double-blind, randomised, placebo-controlled, phase 3 trial, generally healthy adolescents aged 12–17 years were recruited at ten sites across Brazil. Individuals were excluded for immune-mediated or chronic arthritis or arthralgia, who are are immunologically compromised, or any recent live vaccines. Random allocation via simple block randomisation in a 2:1 ratio was stratified by baseline IgG and IgM serostatus by ELISA to receive a single intramuscular dose of VLA1553 or placebo. Assessed in the per-protocol population 28 days after vaccination, the primary endpoint was the proportion of baseline seronegative participants with chikungunya virus neutralising antibody levels assessed by a serum dilution achieving a 50% plaque reduction in a micro plaque reduction neutralisation test with a titre of 150 or more, an accepted surrogate of protection. Safety was assessed in all vaccinated participants and covered by several secondary trial endpoints; immunogenicity formed a prespecified subset for analysis. The trial is registered with ClinicalTrials.gov (NCT04650399) and is complete.

Findings

Between Feb 14, 2022, and Feb 16, 2024, 754 participants were vaccinated (502 [67%] with VLA1553 and 252 [33%] with placebo), with a per-protocol population of 351 participants for immunogenicity analyses (303 in the VLA1553 group and 48 in the placebo group). 406 (54%) of all participants were female and 348 (46%) participants were male; the median age was 15·0 years, and the majority of participants were White (245 [33%]), followed by 214 (28%) other and 192 (26%) multiracial. In baseline seronegative participants, VLA1553 induced seroprotective chikungunya virus neutralising antibody levels in 248 of 251 participants (98·8% [95% CI 96·5–99·8]) 28 days after vaccination, which was sustained in 232 of 236 participants (98·3% [95·7–99·5]) at 12 months post-vaccination. VLA1553 was generally well tolerated, with the vast majority (2082 [97%] of 2155) of adverse events of mild or moderate intensity. When compared with placebo, participants exposed to VLA1553 had a significantly higher frequency of related adverse events (352 [70%] of 502 vs 122 [48%] of 252; p<0·0001), mostly headache, injection site pain, myalgia, fever, and fatigue. One serious adverse event of high-grade fever was classified possibly related to VLA1553. Among 81 adverse events of special interest (ie, symptoms suggesting chikungunya-like disease), 16 were classified as related to trial vaccination (15 in the VLA1553 group and one in the placebo group), mostly early onset events usually starting during the first week after vaccination. Late onset adverse events of special interest showed no medically relevant differences between treatment groups. Nine adolescents had short-lived, usually mild recurring episodes of arthralgia (seven with VLA1553 and two with placebo) with a median duration of 1 day (cumulative range 1–7 days). One further participant with a history of chikungunya virus infection experienced recurring arthralgia followed by long-term polyarthralgia in several joints starting 148 days post-vaccination, classified unrelated to VLA1553. None of the recurring events of arthralgia was medically attended.

Interpretation

VLA1553 was generally safe and induced seroprotective titres up to 12 months in nearly all adolescents, with favourable safety data in those who were seropositive. The data support the use of VLA1553 for the prevention of disease caused by the chikungunya virus among adolescents and in endemic regions.

Funding

Coalition for Epidemic Preparedness Innovations and EU Horizon 2020.

Translation

For the Portuguese translation of the abstract see Supplementary Materials section.

Source: 


Link: https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(25)00631-0/abstract?rss=yes

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Pre-existing cross-reactive #immunity to highly pathogenic avian #influenza 2.3.4.4b #H5N1 virus in the #USA

 


Abstract

The unprecedented 2.3.4.4b. A(H5N1) outbreak in dairy cattle, poultry, and spillover to humans in the United States (US) poses a major public health threat. Population immunity is a critical component of influenza pandemic risk assessment. We assessed the pre-existing cross-reactive immunity to 2.3.4.4b A(H5N1) viruses and analyzed 1794 sera from 723 people (0.5–88 yrs) in multiple US geographic regions during 2021–2024. Pre-existing neutralizing and hemagglutinin (HA)-head-binding antibodies to A(H5N1) were low, but there were substantial cross-reactive binding antibodies to N1 neuraminidase (NA) of 2.3.4.4b A(H5N1). Antibodies to group 1 HA stalk were also prevalent and increased with age. A(H1N1)pdm09 infection and influenza vaccination did not induce neutralizing antibodies to A(H5N1) viruses but induced significant rise of functional NA inhibition (NAI) antibodies to N1 of 2.3.4.4b A(H5N1), and group 1 HA stalk antibodies. Moreover, pre-pandemic stockpiled 2.3.4.4c vaccine can elicit cross-reactive neutralizing antibodies to 2.3.4.4b A(H5N1) viruses. Understanding population susceptibility is essential for pandemic preparedness.

Source: 


Link: https://www.nature.com/articles/s41467-025-66431-2

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#Ecology of low pathogenicity avian #influenza virus #H7 in wild #birds in south-eastern #Australia prior to emergence of high pathogenicity avian influenza H7 in #poultry

 


Abstract

Adding to the global burden of high pathogenicity avian influenza (HPAI) H5N1, an unprecedented five HPAI H7 outbreaks occurred globally in 2024. Of these, three occurred in southeast Australia, with the independent emergence of HPAI H7N9, H7N8, and H7N3, resulting in the destruction of 2 million poultry. Historical data demonstrates that H7 outbreaks in Australia do not occur randomly, rather, there is a strong association between the timing of the previous H7 outbreaks and rainfall patterns in southeastern Australia. We aimed to address a hypothesis wherein prior to H7 outbreaks in poultry, there was a detectable change in H7 prevalence and/or virus diversity in wild bird populations. We addressed this using virological and serological surveillance data generated from multiple programs. Despite the collection of thousands of samples, there was only weak evidence to support our hypothesis, which provides strong incentive to evaluate current surveillance approaches for the purposes of risk prediction. However, in alignment with a previous analysis, there is strong support for a relationship between H7 outbreak probability and rainfall patterns across southeast Australia. Overall, improved understanding of the ecology and evolution of H5 and H7 viruses in wild bird reservoirs is pivotal to global disease preparedness and response.


Competing Interest Statement

The authors have declared no competing interest.


Funder Information Declared

Australian Department of Agriculture Fisheries and Forestry

Australian Department for Health and Aged Care

Source: 


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Monday, December 8, 2025

#Mpox - Multi-country external #situation #report no. 60 published 8 December 2025 (#WHO, summary)

 


{Summary}

Highlights   

All clades of the monkeypox virus (MPXV) continue to circulate. 

- When mpox outbreaks are not rapidly contained and human-to-human transmission is not interrupted, there is a risk of sustained community transmission.  

In October 2025, 44 countries, across all WHO regions, reported a total of 2501 new confirmed mpox cases, including 12 deaths (case fatality ratio [CFR] 0.5%). 

- About 75% of these cases were reported in the African Region

- All regions, apart from the South-East Asia Region observed a decline in confirmed cases in October, compared to September 2025.     

Twenty-one countries in Africa have reported active transmission of mpox in the last six weeks (12 October – 23 November 2025), with 1734 confirmed cases, including 10 deaths (CFR 0.6%) reported during this period. 

- Countries reporting the highest number of cases in this period are the Democratic Republic of the Congo, Liberia, Ghana, Kenya and Uganda; with all of them showing a downward trend in cases in recent weeks. 

One country, Mali, has reported mpox for the first time. 

- The case reported a recent history of travel to Guinea

- Genomic sequencing analysis is ongoing to determine the MPXV clade.  

Greece has reported detection of clade Ib MPXV for the first time.   

New imported cases of mpox due to clade Ib MPXV detected among travellers have been reported in Belgium, Germany, Greece, and the United Kingdom of Great Britain and Northern Ireland. 

Since the last report, at least 15 cases of mpox due to clade Ib MPXV have been detected among individuals who self-identify as men who have sex with men.   

Outside Africa, local transmission of clade Ib MPXV has been occurring in Italy, the Netherlands, Portugal and Spain, the United States of America and Malaysia

(...)

Source: 


Link: https://www.who.int/publications/m/item/multi-country-outbreak-of-mpox--external-situation-report--60---8-december-2025

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#Nomenclature for #tracking of genetic #variation of seasonal #influenza viruses

 


Abstract

Background

Genomic surveillance of human seasonal influenza viruses is an essential component of the Global Influenza Surveillance and Response system (GISRS) and informs the recommendations for the seasonal influenza vaccine composition. Phylogenetic analysis of viral genome sequences is used to identify groups of viruses sharing potential antigenic change and computational models are used to predict which viral variants are likely to circulate at high levels in upcoming seasons. To facilitate discussion and reporting of genetic diversity, as well as to communicate antigen recommendations, up-to-date and sufficiently granular definitions of genetic clades are important. 

Methods

A nomenclature system for segments 4 (haemagglutinin) and 6 (neuraminidase) of human A(H3N2), A(H1N1)pdm09, and influenza B

Results

We devised a clade suggestion algorithm that proposes new subclades based on criteria including (i) the number of sequences in the group, (ii) the divergence from the directly ancestral clade, and (iii) the number and quality of amino acid substitutions on the branch leading to the common ancestor of the subclade. Algorithmic clade proposals were reviewed and assigned a systematic hierarchical label consisting of a leading letter, followed by numbers (e.g., G.1.3). Names are kept short by aliasing, that is collapsing prefixes into unique letters. Subclade definitions are shared openly to promote adoption and tool development. Nextclade is supporting this new nomenclature and it is being used routinely by the GISRS network. 

Conclusions

With increasing genomic surveillance, the need for up-to-date classification schemes is growing and we hope that the current dynamic proposal will adapt to growing data volumes and aid in simplifying the interpretation of these data.


Competing Interest Statement

RAN has received consulting fees from Moderna TX and BioNTech. DEW is currently employed by GSK.


Funding Statement

This work was supported by core funding from the Francis Crick Institute from Cancer Research UK, the UK Medical Research Council, and the Wellcome Trust.

Source: 


Link: https://www.medrxiv.org/content/10.64898/2025.12.06.25341755v1

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#UK: New #mpox #strain identified in #England (#UKHSA, Dec. 8 '25)

 


Latest update

The UK Health Security Agency (UKHSA) has identified a new recombinant mpox virus in England in an individual who had recently travelled to Asia.  

-- Genomic sequencing showed that the mpox genome contained elements of clade Ib and IIb mpox

-- This is not unexpected as both clades are circulating, but highlights the continued potential for mpox virus to evolve and the importance of continued genomic surveillance.    

-- UKHSA continues to assess the significance of the strain.  

Dr Katy Sinka, Head of Sexually Transmitted Infections at UKHSA, said:   

''Our genomic testing has enabled us to detect this new mpox strain. It’s normal for viruses to evolve, and further analysis will help us understand more about how mpox is changing.  

''Although mpox infection is mild for many, it can be severe. Getting vaccinated is a proven effective way to protect yourself against severe disease, so please make sure to get the jab if you are eligible.  

''It is important to remain alert to the risks from this unpleasant illness. Anyone who thinks they may have mpox should contact NHS 111 for advice on what to do.

-- The UK has a routine mpox vaccination programme in place for eligible groups, including those who have multiple sexual partners, participate in group sex, or visit sex-on-premises venues. Studies show the vaccine is around 75% to 80% effective in protecting against mpox.  

UKHSA has shared its findings with relevant international partners, including the World Health Organization (WHO), to support global monitoring efforts.

Source: 


 Link: https://www.gov.uk/government/news/ukhsa-detects-first-case-of-clade-ib-mpox

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Sunday, December 7, 2025

Comparison of efficacy, #safety, immune response of dNS1 #LAIV and cold-adapted LAIV in a mouse #model

 


Abstract

Influenza remains a significant global public health concern. Live-attenuated influenza vaccines (LAIVs) are recognized as effective interventions for influenza prevention. Currently, two types of LAIVs are licensed for human use: one developed through cold-adapted viral gene mutation and the other through the deletion of the viral NS1 gene. However, the similarities and differences in these two LAIVs’ efficacy, safety, and immune responses have not been thoroughly studied. This study constructed a gene-deficient live-attenuated vaccine strain, CA4-dNS1, and a gene locus-mutated attenuated vaccine strain, CA4-cold, to compare their in vivo and in vitro replication capacity, broad-spectrum protective efficacy, safety, and immunogenicity. The results showed that both LAIVs provide comparable broad-spectrum protection against lethal H1N1 and H5N1 influenza challenges in mice and induce similar humoral and mucosal immune responses. Notably, the CA4-cold vaccine strain induces superior influenza memory T-cell responses, while the CA4-dNS1 vaccine strain demonstrates greater safety. These findings underscore the importance of gene modification in LAIVs in striking a balance between their safety and efficacy. The NS1 gene-deficient CA4-dNS1 strain may offer a more advantageous approach for developing next-generation LAIVs and other intranasal influenza virus vectored vaccines due to enhanced safety.

Source: 


Link: https://www.nature.com/articles/s41541-025-01320-9

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