Avian influenza overview September-December 2023

Genetic diversity of A(H5N1) avian influenza viruses isolated from birds and seals in Russia in 2023

Thousands of outbreaks of the highly pathogenic avian influenza A(H5N1) virus in birds and an increasing number of mammal infections are registered annually. In 2023, multiple avian influenza outbreaks were registered among wild birds, poultry and seals in Russia. The genetic characterization of seventy-seven avian viruses and three viruses from seals showed that they belonged to the 2.3.4.4b clade and represented four distinct reassortant genotypes. The majority of viruses represented genotype BB, which was widespread in Europe in 2023. Viruses from seals and four viruses from birds, isolated from outbreaks in the Far East region, belonged to the G1 (A3) genotype and had the amino acid substitution N319K in the NP protein, previously associated with an increased virulence for mammals. In addition, one virus of the G10 genotype and two viruses, representing a previously undescribed genotype (designated as Ru-23-G4) were identified. The viruses analyzed showed normal inhibition by neuraminidase inhibitors. Seven viruses had genetic markers of amantadine resistance. All the influenza A(H5N1) viruses studied showed a binding preference for α2-3-linked sialic acids, suggesting a low risk of transmission among humans. Nevertheless, monitoring of reassortment and mammalian adaptation mutations is essential for the timely identification of viruses with increased pandemic potential.

Virological Passive Surveillance of Avian Influenza and Arboviruses in Wild Birds: A Two-Year Study (2023-2024) in Lombardy, Italy

Avian influenza (AI), caused by Alphainfluenzavirus (family Orthomyxoviridae), poses significant threats to poultry, biodiversity, and public health. AI outbreaks in poultry lead to severe economic losses, while highly pathogenic strains (HPAIVs) severely impact wild bird populations, with implications for biodiversity and potential zoonotic risks. Similarly, arboviruses such as West Nile virus (WNV) and Usutu virus (USUV) are emerging zoonoses. WNV can cause severe neurological diseases in birds, humans, and other animals, while USUV significantly affects blackbird populations and has zoonotic potential, though human cases remain rare. This study investigated avian viruses in 1654 wild birds from 75 species that died at the Wildlife Rescue Center in Vanzago, Lombardy, during 2023-2024. Necropsies were conducted, and virological analyses were performed to detect avian influenza viruses, WNV, and USUV. Among the tested birds, 15 were positive for H5N1 HPAIV clade 2.3.4.4b, all in 2023, including 13 Chroicocephalus ridibundus, one Coturnix coturnix, and one Columba palumbus. Additionally, 16 tested positive for WNV (15 for lineage 2 and one for lineage 1), one for USUV, and 11 co-infections WNV/USUV were recorded in 2023-2024. These findings underscore the importance of avian viral passive surveillance in identifying epidemiological trends and preventing transmission to other species, including mammals and humans.

Environmental Suitability of Kazakhstan to Highly Pathogenic Avian Influenza Using Data on Eurasian Outbreaks, 2020-2024

Highly pathogenic avian influenza (HPAI) is a highly contagious disease of domestic, synanthropic, and wild birds that has demonstrated a sharp rise globally since 2020. This study intends to examine environmental and demographic factors most significantly associated with HPAI (H5N1 and H5N8) outbreaks in Kazakhstan, 2020-2024, and to identify areas of potential underreporting of the disease. Two ecological niche models were developed, namely an "occurrence model" (considering climatic and environmental factors influencing the likelihood of HPAI occurrence) and a "reporting model" (that assesses the probability of disease reporting based on human and poultry population demography). Both models were trained using outbreak locations in countries neighboring Kazakhstan (Afghanistan, China, Hong Kong, Iran, Iraq, Pakistan and Russia), and then tested using the HPAI outbreak locations in Kazakhstan. Results suggested a good fit for both models to Kazakhstani outbreaks (test AUC = 0.894 vs. training AUC = 0.915 for "occurrence model", and test AUC = 0.869 vs. training AUC = 0.872 for "reporting model"). A cluster of high occurrence-to-reporting ratio was detected in the south-western region of Kazakhstan, close to the Caspian Sea, suggesting a need for enhancing surveillance efforts in this zone as well as in some other areas of Pavlodar, Northern Kazakhstan, Western Kazakhstan, Qyzylorda, and Eastern Kazakhstan. Results presented here will help inform the design and implementation of control strategies for HPAI in Kazakhstan with the ultimate goal of promoting disease prevention and control in the country.

Construction and Immune Strategy Optimization of a Vaccine Strain for Influenza A (H5N8) Subtype

Multiple subtypes of avian influenza virus (AIV), including H5N1, H5N6, and H5N8 viruses, are currently co-circulating in wild birds and poultry and causing sporadic human infections. Vaccine development is essential for pandemic preparedness. In this study, we constructed a candidate vaccine virus (CVV) using reverse genetics (RG) based on the sequence of the first human-infected H5N8 subtype AIV, A/Astrakhan/3212/2020 (H5N8). We evaluated the immunogenicity of the rH5N8/PR8 vaccine strain in combination with Alum, ISA51, and MF59 adjuvants, and we optimized immunization strategies including dosage, administration route, and immunization interval in BALB/c mice. Our results demonstrated that a 10 μg dose of inactivated rH5N8/PR8 with MF59 adjuvant, administered intramuscularly twice at 7-day intervals, induced the strongest immune response and effectively protected mice against challenge with wild-type H5N8 AIVs. Since pandemic influenza vaccines typically require tailored vaccination doses and routes specific to their characteristics, this study provides valuable insights for the development of similar vaccine strains with pandemic potential.

Emergence, migration and spreading of the high pathogenicity avian influenza virus H5NX of the Gs/Gd lineage into America

The high pathogenicity avian influenza virus H5N1, which first emerged in the winter of 2021, has resulted in multiple outbreaks across the American continent through the summer of 2023 and they continue based on early 2025 records, presenting significant challenges for global health and food security. The viruses causing the outbreaks belong to clade 2.3.4.4b, which are descendants of the lineage A/Goose/Guangdong/1/1996 (Gs/Gd) through genetic reassortments with several low pathogenicity avian influenza viruses present in populations of Anseriformes and Charadriiformes orders. This review addresses these issues by thoroughly analysing available epidemiological databases and specialized literature reviews. This project explores the mechanisms behind the resurgence of the H5N1 virus. It provides a comprehensive overview of the origin, timeline and factors contributing to its prevalence among wild bird populations on the American continent.

Susceptibility of Mammals to Highly Pathogenic Avian Influenza: A Qualitative Risk Assessment From the Belgian Perspective

AIMS

The world experienced a huge number of outbreaks of highly pathogenic avian influenza (HPAI) in birds, which could represent one of the largest registered epidemics of infectious disease in food-producing animals. Therefore, mammals, including humans, are continuously exposed to HPAI viruses leading to sporadic and sometimes unusual mammal infections. The aim of this paper is to assess the risk of crossing the avian/mammalian species barrier by the currently circulating HPAI viruses, focusing on the epidemiological situation of Belgium, a representative country for Western Europe.

METHODS AND RESULTS

Information on transmission pathways and species susceptibility, based on the experimental and epidemiological data, was reviewed and weighted to assess the risk of mammal infection with HPAI A(H5N1) viruses of the circulating clade 2.3.4.4b. This risk is defined as the likelihood of mammal infection by birds crossed by the clinical consequences of this infection for this animal. From the Belgian perspective, it is concluded that this risk remains 'low' to 'moderate' for captive/domestic mammal species. However, this risk was categorised as 'high' for certain species, i.e. mammals that have the opportunity to have frequent direct or indirect close contacts with infected (dead) birds, such as wild felids, wild mustelids, foxes and wild marine carnivore mammals. For some mammal species, the uncertainty associated with the assessment remains high due to an ever-changing situation.

CONCLUSIONS

The longer the virus will continue to circulate in wildlife/the environment the stronger the probability of contact between infected birds and mammals will become. This will increase the related risk of viral adaptation for efficient transmission between mammal, posing concerns for public health. Regular reassessments based on the field and experimental data are therefore necessary to implement and adapt risk-based mitigation measures. This will require continuous monitoring of avian influenza viruses in both birds and mammals as well as sharing of sequence data.

Improvements in RNA and DNA nanopore sequencing allow for rapid genetic characterization of avian influenza

Avian influenza virus (AIV) currently causes a panzootic with extensive mortality in wild birds, poultry, and wild mammals, thus posing a major threat to global health and underscoring the need for efficient monitoring of its distribution and evolution. We here utilized a well-defined AIV strain to systematically investigate AIV genetic characterization through rapid, portable nanopore sequencing by comparing the latest DNA and RNA nanopore sequencing approaches and various computational pipelines for viral consensus sequence generation and phylogenetic analysis. We show that the latest direct RNA nanopore sequencing updates improve consensus sequence generation, but that the application of the latest DNA nanopore chemistry after reverse transcription and amplification outperforms, such native viral RNA sequencing by achieving higher sequencing accuracy and throughput. We additionally leveraged the direct RNA nanopore sequencing data for the detection of RNA modifications, such as N 6-methyladenosine and pseudouridine, which play a role in viral immune evasion. Finally, we applied these sequencing approaches together with portable AIV diagnosis and quantification tools to environmental samples from a poultry farm, demonstrating the feasibility of nanopore sequencing for on-site non-invasive AIV monitoring in real-world outbreak scenarios.

European Food Safety Authority, European Centre for Disease Prevention and Control, European Union Reference Laboratory for Avian Influenza, Alexakis L, Buczkowski H, Ducatez M, Fusaro A, Gonzales JL, Kuiken T, Ståhl K, Staubach C, Svartström O, Terregino C, Willgert K, Melo M, Kohnle L. Avian influenza overview September-December 2024

Between 21 September and 6 December 2024, 657 highly pathogenic avian influenza (HPAI) A(H5N1) and A(H5N5) virus detections were reported in domestic (341) and wild (316) birds across 27 countries in Europe. Many HPAI outbreaks in domestic birds were clustered in areas with high poultry density and characterised by secondary farm-to-farm spread. Waterfowl, particularly the mute swan, were primarily affected during this reporting period, with HPAI virus detections focused on south-eastern Europe. Notably, A(H5N5) viruses expanded their geographic and host range, resulting in a surge in detections and mortality events described in gulls and crows. No new HPAI virus detections in mammals were reported in Europe during this reporting period, but the number of dairy cattle farms reportedly affected in the United States of America (USA) rose to >800 in 16 States, and HPAI virus was identified in two pigs in a mixed-species farm. Between 21 September and 11 December 2024, 56 new human cases with avian influenza virus infection were reported from North America (45 A(H5N1) cases), Viet Nam (one A(H5)) and China (ten A(H9N2) cases). Most of the A(H5) human cases in North America (95.6%, n = 43/45) had reported exposure to poultry, live poultry markets, or dairy cattle prior to avian influenza virus detection or onset of illness. Human infections with avian influenza viruses remain rare and no evidence of human-to-human transmission has been documented in the reporting period. The risk of infection with currently circulating avian A(H5) influenza viruses of clade 2.3.4.4b in Europe remains low for the general public in the European Union/European Economic Area (EU/EEA). The risk of infection remains low-to-moderate for those occupationally or otherwise exposed to infected animals or contaminated environments.

European Food Safety Authority (EFSA), Abrahantes JC, Aznar I, Catalin I, Kohnle L, Mulligan KF, Mur L, Stoicescu A, van Houtum A, Zancanaro G. Avian influenza annual report 2023

All European Union (EU) Member States (MSs), along with Iceland, Norway, Switzerland and the United Kingdom (Northern Ireland), conduct surveillance for avian influenza (AI) in poultry and wild birds. EFSA, upon mandate of the European Commission, compiles and analyses this data in an annual report. This summary highlights findings from the 2023 surveillance activities. In 2023, 31 reporting countries (RCs) visited 21,183 poultry establishments (PEs). Of these, 18,557 underwent serological investigations, 2460 underwent virological investigations and 166 underwent both. Among the 18,723 PEs sampled for serological testing, 29 PEs (0.15%) were seropositive for influenza A(H5/H7) viruses, more in detail: 27 PEs tested positive for A(H5), 1 tested positive for A(H7) and 1 tested positive for both strains. These were found in eight RCs (Bulgaria, Poland, Germany, Spain, Sweden, Norway, Iceland and Finland). Of the 2626 PEs sampled for virological testing, 180 PEs (6.85%) were positive for influenza A(H5/H7) viruses. More precisely, 178 tested positive for A(H5), of which 161 positive for HPAI (H5N1) and 2 tested positive for A(H7). Positive PEs were reported by 12 RCs covering 14 different poultry categories. A total of 51,411 wild birds were sampled, with 6717 (13.07%) testing positive for HPAIVs by PCR from 25 RCs. Subtype A(H5N1) was the main influenza A virus identified (6531; 97%), similar to 2022. Twenty RCs reported 1940 wild birds testing positive for LPAI or AIV of unknown pathogenicity. For these, 1372 (67.5%) were nor A(H5) or A(H7), while 568 (29.3%) tested positive for A(H5). These findings reflect the ongoing efforts in early detection and monitoring of avian influenza to mitigate the risk of outbreaks in poultry populations throughout Europe.

Natural infection of common cranes (Grus grus) with highly pathogenic avian influenza H5N1 in Serbia

Introduction

The late autumn epizootic of the highly pathogenic avian influenza virus (HPAIV) subtype H5N1 in Serbia in 2023 caused massive mortality in the migratory population of common cranes (Grus Grus). This is the first time HPAIV has been identified in the common crane in Serbia, leading to mass mortality of this bird species.

Methods

To understand the pathological impact of HPAIV in cranes, we evaluated the pathological changes in the tissues of common cranes. Additionally, we report genomic characterization of HPAI/H5N1. In total, 14 juvenile common crane carcasses were examined.

Results

Infected birds primarily exhibited neurologic signs, including ataxia and incoordination. Grossly, necrotizing pancreatitis was the most common finding, while microscopic lesions included necrosis, inflammation and hemorrhages in the lungs, spleen, brain, liver and kidneys. Based on RT-PCR, all birds were infected with the HPAI H5N1 virus, as viral RNA was detected in all 14 selected tissues. Genetic analysis revealed that our H5N1 isolate could be grouped with highly pathogenic avian influenza clade 2.3.4.4b, subgroup DA, and is very closely related to the H5N1 strains isolated from the common crane and turkey from Croatia, the common crane from Italy and the Ural owl from Slovakia.

Discussion

Our findings showed that common cranes are highly susceptible to natural infection with the HPAI H5N1 virus of clade 2.3.4.4b and may serve as bio-sentinels for the presence of the HPAI virus in wildlife.

Emergence of highly pathogenic avian influenza viruses H5N1 and H5N5 in white-tailed eagles, 2021-2023

Highly pathogenic avian influenza (HPAI) poses a substantial threat to several raptors. Between 2021 and 2023, HPAI viruses (HPAIVs) of the Goose/Guangdong lineage H5 clade 2.3.4.4b became widespread in wild birds in Norway, and H5N1 and H5N5 viruses were detected in 31 white-tailed eagles (Haliaeetus albicilla, WTEs). Post-mortem examinations of four WTEs revealed no macroscopic pathological findings. Microscopic examinations showed the presence of myocardial and splenic necroses and a few lesions in the brain. In situ hybridization revealed the presence of the virus in several organs, suggesting a multisystemic infection. The detection of HPAIV H5N5 in a WTE in February 2022 marked the first recorded occurrence of this subtype in Norway. Since then, the virus has persisted, sporadically being detected in WTEs and other wild bird species. Phylogenetic analyses reveal that at least two distinct incursions of HPAIV H5N1 Eurasian (EA) genotype C affected WTEs, likely introduced by migratory birds from Eurasia and seabirds entering from Western and Central Europe. Some WTE isolates from 2021 to 2022 clustered with those from Canada and Ireland, aligning with the transatlantic spread of H5N1. Others were related to the 2021 mass mortality of great skuas in the UK or outbreaks in seabird populations, including gannets, gulls and terns, during 2022 in the North Sea region. This suggests that the WTEs were likely preying on the affected birds. Our study highlights that WTEs can act as sentinels for some HPAIV strains, but the absence of several known circulating genotypes in WTEs suggests varying pathogenic effects on this species.

Novel Epidemiologic Features of High Pathogenicity Avian Influenza Virus A H5N1 2.3.3.4b Panzootic: A Review

Avian influenza is one of the most devastating avian diseases. The current high pathogenicity avian influenza (HPAI) A virus H5N1 clade 2.3.4.4b epizootic began in the 2020-2021 season, and has caused a panzootic, considered one of the worst ever reported. The present panzootic has novel epidemiological features that represent a challenge for its prevention and control. This review examines key epidemiological changes of the disease such as seasonality, geographic spread, and host range. The seasonality of the virus has changed, and contrary to previous avian influenza epizootics, this subclade was able to persist during boreal summer. Its geographic range has expanded, with reports in all continents except Australia. During this epizootic, HPAIV H5N1 has broadened its host range, infecting hundreds of bird species, and causing the death of thousands of wild birds and over 300 million poultry. The number and diversity of mammal species infected by H5N1 2.3.4.4b is unprecedented. Although considered low, this strain's potential to spillover to humans should not be underestimated, especially considering the current extremely high viral circulation in animals and increasing adaptation to mammals. Overall, HPAI A(H5N1) clade 2.3.4.4b represents an ongoing and growing threat to poultry, wildlife, and human health.

Novel Genotypes of Highly Pathogenic Avian Influenza H5N1 Clade 2.3.4.4b Viruses, Germany, November 2023

Several subtypes and many different genotypes of highly pathogenic avian influenza viruses of subtype H5 clade 2.3.4.4b have repeatedly caused outbreaks in Germany. Four new highly pathogenic avian influenza genotypes emerged in November 2023 after reassortment with low pathogenicity precursors, replacing genotype BB, which had dominated in Europe since 2022.

Proposal for a Global Classification and Nomenclature System for A/H9 Influenza Viruses

Influenza A/H9 viruses circulate worldwide in wild and domestic avian species, continuing to evolve and posing a zoonotic risk. A substantial increase in human infections with A/H9N2 subtype avian influenza viruses (AIVs) and the emergence of novel reassortants carrying A/H9N2-origin internal genes has occurred in recent years. Different names have been used to describe the circulating and emerging A/H9 lineages. To address this issue, an international group of experts from animal and public health laboratories, endorsed by the WOAH/FAO Network of Expertise on Animal Influenza, has created a practical lineage classification and nomenclature system based on the analysis of 10,638 hemagglutinin sequences from A/H9 AIVs sampled worldwide. This system incorporates phylogenetic relationships and epidemiologic characteristics designed to trace emerging and circulating lineages and clades. To aid in lineage and clade assignment, an online tool has been created. This proposed classification enables rapid comprehension of the global spread and evolution of A/H9 AIVs.

US Public Health Preparedness and Response to Highly Pathogenic Avian Influenza A(H5N1) Viruses

US public health preparedness and response to highly pathogenic avian influenza A(H5N1) viruses are assessed in this survey study conducted by the CDC.

Outbreaks of H5N1 High Pathogenicity Avian Influenza in South Africa in 2023 Were Caused by Two Distinct Sub-Genotypes of Clade 2.3.4.4b Viruses

In 2023, South Africa continued to experience sporadic cases of clade 2.3.4.4b H5N1 high-pathogenicity avian influenza (HPAI) in coastal seabirds and poultry. Active environmental surveillance determined that H5Nx, H7Nx, H9Nx, H11Nx, H6N2, and H12N2, amongst other unidentified subtypes, circulated in wild birds and ostriches in 2023, but that H5Nx was predominant. Genome sequencing and phylogenetic analysis of confirmed H5N1 HPAI cases determined that only two of the fifteen sub-genotypes that circulated in South Africa in 2021-2022 still persisted in 2023. Sub-genotype SA13 remained restricted to coastal seabirds, with accelerated mutations observed in the neuraminidase protein. SA15 caused the chicken outbreaks, but outbreaks in the Paardeberg and George areas, in the Western Cape province, and the Camperdown region of the KwaZulu-Natal province were unrelated to each other, implicating wild birds as the source. All SA15 viruses contained a truncation in the PB1-F2 gene, but in the Western Cape SA15 chicken viruses, PA-X was putatively expressed as a novel isoform with eight additional amino acids. South African clade 2.3.4.4b H5N1 viruses had comparatively fewer markers of virulence and pathogenicity compared to European strains, a possible reason why no spillover to mammals has occurred here yet.

European Food Safety Authority (EFSA), European Centre for Disease Prevention and Control (ECDC), Adlhoch C, Alm E, Enkirch T, Lamb F, Melidou A, Willgert K, Marangon S, Monne I, Stegeman JA, Delacourt R, Baldinelli F, Broglia A. Drivers for a pandemic due to avian influenza and options for One Health mitigation measures

Avian influenza viruses (AIV) remain prevalent among wild bird populations in the European Union and European Economic Area (EU/EEA), leading to significant illness in and death of birds. Transmission between bird and mammal species has been observed, particularly in fur animal farms, where outbreaks have been reported. While transmission from infected birds to humans is rare, there have been instances of exposure to these viruses since 2020 without any symptomatic infections reported in the EU/EEA. However, these viruses continue to evolve globally, and with the migration of wild birds, new strains carrying potential mutations for mammalian adaptation could be selected. If avian A(H5N1) influenza viruses acquire the ability to spread efficiently among humans, large-scale transmission could occur due to the lack of immune defences against H5 viruses in humans. The emergence of AIV capable of infecting mammals, including humans, can be facilitated by various drivers. Some intrinsic drivers are related to virus characteristics or host susceptibility. Other drivers are extrinsic and may increase exposure of mammals and humans to AIV thereby stimulating mutation and adaptation to mammals. Extrinsic drivers include the ecology of host species, such as including wildlife, human activities like farming practices and the use of natural resources, climatic and environmental factors. One Health measures to mitigate the risk of AIV adapting to mammals and humans focus on limiting exposure and preventing spread. Key options for actions include enhancing surveillance targeting humans and animals, ensuring access to rapid diagnostics, promoting collaboration between animal and human sectors, and implementing preventive measures such as vaccination. Effective communication to different involved target audiences should be emphasised, as well as strengthening veterinary infrastructure, enforcing biosecurity measures at farms, and reducing wildlife contact with domestic animals. Careful planning of poultry and fur animal farming, especially in areas with high waterfowl density, is highlighted for effective risk reduction.

European Food Safety Authority, European Centre for Disease Prevention and Control, European Union Reference Laboratory for Avian Influenza, Fusaro A, Gonzales JL, Kuiken T, Mirinavičiūtė G, Niqueux É, Ståhl K, Staubach C, Svartström O, Terregino C, Willgert K, Baldinelli F, Delacourt R, Georganas A, Kohnle L. Avian influenza overview December 2023-March 2024

Between 2 December 2023 and 15 March 2024, highly pathogenic avian influenza (HPAI) A(H5) outbreaks were reported in domestic (227) and wild (414) birds across 26 countries in Europe. Compared to previous years, although still widespread, the overall number of HPAI virus detections in birds was significantly lower, among other reasons, possibly due to some level of flock immunity in previously affected wild bird species, resulting in reduced contamination of the environment, and a different composition of circulating A(H5N1) genotypes. Most HPAI outbreaks reported in poultry were primary outbreaks following the introduction of the virus by wild birds. Outside Europe, the majority of outbreaks in poultry were still clustered in North America, while the spread of A(H5) to more naïve wild bird populations on mainland Antarctica is of particular concern. For mammals, A(H5N5) was reported for the first time in Europe, while goat kids in the United States of America represented the first natural A(H5N1) infection in ruminants. Since the last report and as of 12 March 2024, five human avian influenza A(H5N1) infections, including one death, three of which were clade 2.3.2.1c viruses, have been reported by Cambodia. China has reported two human infections, including one fatal case, with avian influenza A(H5N6), four human infections with avian influenza A(H9N2) and one fatal case with co-infection of seasonal influenza A(H3N2) and avian influenza A(H10N5). The latter case was the first documented human infection with avian influenza A(H10N5). Human infections with avian influenza remain rare and no sustained human-to-human infection has been observed. The risk of infection with currently circulating avian H5 influenza viruses of clade 2.3.4.4b in Europe remains low for the general population in the EU/EEA. The risk of infection remains low to moderate for those occupationally or otherwise exposed to infected animals.