​Monthly summary of sampled birds

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The Nextstrain builds are available on the SENTINEL Wild Birds Group - https://nextstrain.org/groups/SentinelWildBirds

Yearly report 2024-2025

​1. OVERVIEW
SENTINEL Wild Birds aims to enhance the understanding of highly pathogenic avian influenza (HPAI) virus dynamics in wild bird populations by conducting active surveillance at key locations in and near Europe. These locations are divided into the following surveillance nodes: Node 1 Gulf of Finland (Finland, Estonia), Node 2 Southern Baltic Sea (Sweden, Latvia, Lithuania, Poland), Node 4 Eastern Black Sea (Georgia), Node 6 Lake Constance (Germany, Austria, Switzerland), Node 7 Veneto Region (Italy), Node 8 Camargue (France), and Node 9 Gulf of Cadiz (Spain). This yearly summary provides an update on sampled wild birds as part of an early warning system to support wildlife management and disease prevention efforts. The data in this report are based on samples collected from August 19, 2024, to June 11, 2025.

2. RESULT

2.1 DATA COLLECTION
Since sampling of wild birds started in August 2024, a total of 14,037 samples have been collected from 7,485 individuals, some of which were captured on more than one trapping day. The individuals were mostly comprised of wild birds (>97.5%, with 2% domestic mallards and 0.4% mussels) representing 67 taxa across seven nodes in and near Europe (Table 1). Of the 14,037 collected samples, 6,033 (43%) were tracheal/oropharyngeal swabs, 4,443 (32%) cloacal swabs, 2,562 (18%) faecal samples, 672 (5%) feather samples, 130 (1%) combined swabs (choana + cloacal), 62 (<1%) pooled organs, 52 (<1%) nest swabs, 40 (<1%) blood samples, 30 (<1%) mussel samples, and 12 (<1%) choana samples (Table 2). Of all samples, 1,040 (7.4%) from 18 different taxa were positive for avian influenza virus, of which 24 were positive for HPAI virus (Table 1; Figure 1).

The overall bird-level prevalence of avian influenza virus in all submitted samples was 11.8% (Figure 2). The highest overall prevalence of avian influenza virus was found in Southern Baltic Sea (Node 2) with 21.7%. The highest weekly bird-level prevalence peak occurred during week 38, 2024, (70.7%) and was caused by high prevalence in Eastern Black Sea (Node 4) with a prevalence of 79.2% (Figure 2). Among the most frequently sampled birds, mallard had a prevalence of 21.1% (727 of 3,453 individuals), and Eurasian teal 10.1% (113 out of 1,120 individuals).

2.2 GENOMICS SUMMARY
In the first year of the project (August 2024 until June 2025), the project resulted in a total of 212 avian influenza sequences. These sequences were generated across six different sampling nodes: Southern Baltic Sea (Node 2; N=195), Eastern Black Sea (Node 4; N=3), Lake Constance Region (Node 6; N=1), Veneto Region (Node 7; N=4), Camargue Region (Node 8; N=6) and Gulf of Cadiz (Node 9; N=3). Of these 212 sequences, there were 36 H5 avian influenza sequences, which included six H5 HPAI clade 2.3.4.4b sequences, 29 H5 Eurasian non-Goose Guangdong (EA-nonGsGd) low pathogenicity avian influenza (LPAI) sequences, and one sequence for which the H5 clade could not be determined due to the absence of the haemagglutinin (HA) gene sequence (Figure 4).

H5 HPAI clade 2.3.4.4b Sequences
The six H5 clade 2.3.4.4b sequences, all of which were of the H5N1 subtype (Figure 5A), were collected from Eastern Black Sea (Node 4; N=2) and Veneto Region (Node 7; N=4). Five of these clade 2.3.4.4b sequences were determined to be of the EA-2024-DI genotype, but in particular the DI.2 sub-lineage which was predominant in Europe during 2024-2025 (EFSA 2025). The EA-2024-DI (DI.2) sequences detected in Veneto Region (Node 7) were all collected from Eurasian teal in October 2024. Analysis of the HA gene sequences showed that these viruses were genetically similar to other EA-2024-DI (DI.2) viruses from across Europe, but particularly sequences from elsewhere in Italy and Romania (Figure 5B). The EA-2024-DI (DI.2) virus from Eastern Black Sea (Node 4) was collected from a mallard in February 2025 and also showed similarity to viruses from across Europe, but particularly sequences from Israel and Hungary (Figure 5C). In addition to the EA-2024-DI (DI.2) HPAI sequences, there was an additional H5 clade 2.3.4.4b sequence generated by Eastern Black Sea (Node 4; Figure 5C). This sample was also collected from a mallard in February 2025, and whilst it showed similarity to the EA-2024-DI genotype across the majority of gene segments, the nucleoprotein (NP) segment was distinct from other EA-2024-DI sequences. The NP segment present in this virus showed high similarity to a H5 LPAI sequence from Eastern Black Sea (Node 4), but also Yearly report 2024-2025 SENTINEL Wild Birds Söderquist, P., Byrne, A., Lewis, N., van Toor, M., Waldenström, J. & SENTINEL Wild Birds Consortium The present document has been produced and adopted by the bodies identified above as authors. This task has been carried out exclusively by the author in the context of a contract between the European Food Safety Authority and the author, awarded fol lowing a tender procedure. The present document is published complying with the transparency principle to which the Authority is subject. It may not be considered as an output adopted by the Authority. The European Food Safety Authority reserves its rights, view and position as regards the issues addressed and the conclusions reached in the present document, without prejudice to the rights of the author. 10 a mixture of other H5 LPAI and HPAI clade 2.3.4.4b sequences from Europe and Asia, including other SENTINEL Wild Bird sampling Nodes nodes (Figure 5D). This H5 clade 2.3.4.4b genotype does not appear to have been detected elsewhere, based on the data available, and represents a novel genotype.

H5 LPAI Sequences
The 29 EA-nonGsGd LPAI sequences were collected from Node 2 Southern Baltic Sea (N=26), Eastern Black Sea (Node 4; N=1), Camargue Region (Node 8; N=1) and Gulf of Cadiz (Node 9; N=1). Among these sequences, multiple were of the H5 subtype: H5N1 (N=1), H5N2 (N=9), H5N3 (N=17) and H5Nx (N=2). The H5 LPAI samples from the Southern Baltic Sea (Node 2) were a mixture of H5N2, H5N3 and H5Nx sequences, all collected in Sweden between October and December 2024, whilst the Eastern Black Sea (Node 4) H5 LPAI was a H5N1, collected from a mallard in September 2024. The H5 LPAI samples from Camargue Region (Node 8) and Gulf of Cadiz (Node 9) were both of the H5N2 subtype but collected from a Eurasian teal in January 2025 and a mallard in December 2024, respectively. Analysis of the HA gene from these H5 LPAI sequences showed that they clustered into two main groups (Figure 6A). One of the groups contains the majority of the H5 LPAI sequences from Southern Baltic Sea (Node 2) Yearly report 2024-2025 SENTINEL Wild Birds Söderquist, P., Byrne, A., Lewis, N., van Toor, M., Waldenström, J. & SENTINEL Wild Birds Consortium The present document has been produced and adopted by the bodies identified above as authors. This task has been carried out exclusively by the author in the context of a contract between the European Food Safety Authority and the author, awarded fol lowing a tender procedure. The present document is published complying with the transparency principle to which the Authority is subject. It may not be considered as an output adopted by the Authority. The European Food Safety Authority reserves its rights, view and position as regards the issues addressed and the conclusions reached in the present document, without prejudice to the rights of the author. 11 and also Camargue Region (Node 8; Figure 6B). The HA sequences of this group show similarity to those collected elsewhere in Europe, but also Asia. The second group contains H5 LPAI sequences from Southern Baltic Sea (Node 2), Eastern Black Sea (Node 4) and Gulf of Cadiz (Node 9) and shows similarity to sequences from elsewhere in Europe (Figure 6C). Similarly to the H5 HPAI sequences, the differential similarity of H5 LPAI sequences to those from elsewhere in Europe and Asia suggests the co-circulation of distinct H5 LPAI lineages within Europe. Analysis of the other gene segments (e.g., the NP segment) shows that these H5 LPAI sequences do show some similarity to contemporary H5 HPAI clade 2.3.4.4b sequences.

The bespoke Nextstrain builds used for real-time genomic analysis of the H5 sequences generated by the sampling nodes through the SENTINEL Wild Birds are publicly available (https://nextstrain.org/groups/SentinelWildBirds).

Non-H5 Sequences
In addition to the H5 genome sequences, 177 non-H5 avian influenza sequences have been generated during the first year of the SENTINEL Wild Birds project. These sequences span a wide array of HA subtypes from H1 to H12, in combination with all possible neuraminidase (NA) subtypes (N1 to N9), and have been collected across several sampling nodes: Southern Yearly report 2024-2025 SENTINEL Wild Birds Söderquist, P., Byrne, A., Lewis, N., van Toor, M., Waldenström, J. & SENTINEL Wild Birds Consortium The present document has been produced and adopted by the bodies identified above as authors. This task has been carried out exclusively by the author in the context of a contract between the European Food Safety Authority and the author, awarded fol lowing a tender procedure. The present document is published complying with the transparency principle to which the Authority is subject. It may not be considered as an output adopted by the Authority. The European Food Safety Authority reserves its rights, view and position as regards the issues addressed and the conclusions reached in the present document, without prejudice to the rights of the author. 12 Baltic Sea (Node 2), Lake Constance Region (Node 6), Camargue Region (Node 8) and Gulf of Cadiz (Node 9). Future genomic analysis within the SENTINEL Wild Birds project will seek to incorporate these non-H5 sequences in combination with the H5 LPAI and HPAI sequences to better understand the interplay between different avian influenza subtypes and how this contributes to genetic diversity within Europe.

3. CONCLUSION
During the first year of the SENTINEL Wild Birds project (August 2024 until June 2025), extensive surveillance was carried out across seven nodes in and near Europe. A total of 14,037 samples were collected from 7,485 individuals representing 67 taxa. These included primarily tracheal/oropharyngeal and cloacal swabs, but also faecal samples, feathers, blood, and environmental samples.

Avian influenza virus (AIV) was detected in multiple locations and taxa, with a total of 1,040 samples testing positive. Of these, 24 were confirmed as HPAI viruses. HPAI cases were restricted in time and space, primarily detected in Italy in late September to early October 2024 and again in mid-November 2024 (in Eurasian teal) but also in Georgia in September (in mallard).

The overall bird-level prevalence of AIV across the project was variable over time and geography. It peaked during the autumn migration period, with the highest prevalence observed in Georgia in September and Sweden in late October. The species that was sampled most frequently was mallard. We also found some of the highest prevalence values in that species. Another species with notable AIV prevalence was the Eurasian teal, particularly during autumn. Prevalence dropped markedly during spring and early summer 2025, with few detections after March, and none in June. This seasonal trend reflects established patterns of avian influenza circulation in wild birds, with peak prevalence during autumn migration and low circulation during the breeding season.

Within the first year of the SENTINEL Wild Bird project, 212 avian influenza genome sequences have been generated across six sampling nodes within the project. The majority of these sequences (N=177) have been non-H5 avian influenza viruses, but six H5 HPAI and 29 H5 LPAI sequences have also been produced. Within the H5 HPAI sequences, all were clade 2.3.4.4b, and most sequences were of the EA-2024-DI (DI.2) genotype, which has been the predominant genotype detected in wild birds and poultry in Europe over the last year. In addition to the EA-2024-DI detections, a novel H5 clade 2.3.4.4b genotype was detected in this project. This novel genotype was identified in Eastern Black Sea (Node 4), which sits at the confluence of multiple avian migratory flyways, including the Mediterranean and Central Asian flyways. This detection highlights how the SENTINEL Wild Birds project is already contributing to early detection and characterisation of H5 HPAI diversity in wild birds. Analysis of the H5 LPAI sequences demonstrates linkages between sampling nodes and similarity to H5 HPAI sequences. The real-time genomic analysis of the H5 avian influenza sequences generated within the project is made available through a bespoke public Nextstrain group, and future work will seek to incorporate non-H5 sequences into these analyses to better understand the similarity between H5 and non-H5 avian influenza sequences and to characterize linkages between sampling nodes and identify the responsible hosts.

Overall, the first year of the SENTINEL Wild Birds project has provided valuable insights into the temporal and spatial dynamics of avian influenza virus in wild bird populations across the European region. The successful implementation of coordinated fieldwork, diagnostics, and genomic analysis across multiple countries and nodes demonstrates the strength of this collaborative surveillance effort. In the second year of the project, efforts will focus on further optimising sampling strategies and analysis of data. These improvements will strengthen the project’s role as an early warning system for avian influenza in Europe.

REFERENCES
EFSA (European Food Safety Authority), ECDC (European Centre for Disease Prevention and Control), EURL (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, and Kohnle L. (2025). Scientific report: Avian influenza overview December 2024–March 2025. EFSA Journal 2025; 23(4):9352, 73 pp.

ACKNOWLEDGMENT
This report is based on data collected and analysed by fieldworkers, laboratory personnel, and node coordinators from the following organizations and institutions:

Node 1: LABRIS, Riigi Laboriuuringute ja Riskihindamise Keskus (Estonia); Ruokavirasto, Finnish Food Authority (Finland); University of Turku (Finland)

Node 2: Swedish National Veterinary Institute (SVA) (Sweden); Linnaeus University (Sweden); Institute of Food Safety, Animal Health and Environment “BIOR” (Latvia); National Food and Veterinary Risk Assessment Institute (Lithuania); State Food and Veterinary Service (Lithuania); National Veterinary Research Institute (Poland)

Node 4: Centre of Wildlife Disease Ecology (CWDE), Ilia State University; State Laboratory of Agriculture of Georgia

Node 6: Austrian Agency for Health and Food Safety (AGES) (Austria); Verein für die Betreuung des Naturschutzgebietes Rheindelta (Naturschutzverein Rheindelta) (Austria); Friedrich-Loeffler-Institute (FLI) (Germany); Max-Planck-Institut für Verhaltensbiologie (MPI) (Germany); National Reference Centre for Poultry and Rabbit Diseases (NRGK) (Switzerland); Swiss Institute for Virology and Immunology (IVI) (Switzerland)

Node 7: Istituto Zooprofilattico Sperimentale delle Venezie; Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA)

Node 8: École Nationale Vétérinaire de Toulouse (ENVT); INRAE (Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement); La Tour du Valat; Conservatoire d’Espaces Naturels d’Occitanie (CEN Occitanie); Laboratoire Départemental du Gard; Office Français de la Biodiversité (OFB); Ministère de l’Agriculture et de la Souveraineté Alimentaire; Muséum national d’Histoire naturelle (MNHN); Agence nationale de sécurité sanitaire de l’alimentation, de l’environnement et du travail (ANSES)

Node 9: Martina Ferraguti, Josué Martínez-de la Puente, and Jordi Figuerola at Estación Biológica de Doñana (EBD-CSIC); Ursula Höfle at Grupo de Sanidad y Biotecnología (SaBio), Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC); Elisa Pérez-Ramírez and Jovita Fernández-Pinero at Centro de Investigación en Sanidad Animal (CISA-INIA-CSIC) (Spain)