Martin Beer

Influenza A virus (IAV) pandemics can arise when animal-derived and human-adapted IAVs exchange genome segments; however, whether contemporary clade 2.3.4.4b H5N1 viruses can generate viable reassortants with human IAVs is unclear. Here, we tested the reassortment potential of two clade 2.3.4.4b H5N1 viruses with human-adapted H1N1 and H3N2 IAVs using a biosafe reassortment system. Across multiple coinfection conditions, we genotyped 2,698 plaque-purified viral clones and recovered 20 reassortants (0.74%). Polymerase assays identified human IAV subunits, particularly H1N1 PA or H3N2 PB2, that increased H5N1 polymerase activity. Thus, contemporary clade 2.3.4.4b H5N1 viruses can reassort with human IAVs, but factors beyond polymerase compatibility may limit their recovery.

Shamonda virus (SHAV), which has recently emerged in Central Europe and has caused disease in numerous cattle herds, was detected in brain tissue from two horses that showed clinical signs, including neurological disorder, and underwent pathological examination. The horses reportedly exhibited seizure-like episodes (Horse A) as well as fever and ataxia (Horse B). In both horses, severe lymphohistiocytic meningoencephalitis with hemorrhages was observed in various parts of the central nervous system (CNS), while outside the CNS no abnormalities were found. The virus genome could be detected by RT-qPCR in all examined parts of the CNS of both horses. In a postmortem cerebrospinal fluid sample of one horse, the virus could only be detected with a very low genome load; however, postmortem contamination cannot be completely ruled out. Consistent with the histological findings, no SHAV genome was detected in either the blood or organs outside the CNS. Postmortem, CNS material—especially brainstem tissue—is suitable for detection of histological lesions and virus genomes via RT-qPCR, while intravital diagnostics of a SHAV infection in horses exhibiting neurological signs is at the moment only possible to a very limited extent. The epidemiological role of horses in the SHAV outbreak is currently unclear.

Foot-and-mouth disease (FMD) virus is one of the most feared and most consequential pathogens of livestock worldwide. It can be spread rapidly by the transboundary movement of animals, animal products, and by-products. In January 2025, Germany detected its first FMD outbreak since 1988 in extensively reared water buffalo on a small farm in the state of Brandenburg, directly outside Berlin, the federal capital. Immediate control measures including a standstill for movements of susceptible animals and pre-emptive culling were implemented by the veterinary authorities. Whole-genome sequencing identified the virus as serotype O, topotype ME-SA, lineage SA-2018 and revealed extensive recombination, but cross-neutralization assays suggested good heterologous protection by an O/PanAsia-2 vaccine strain. Epidemiological back-calculation placed the time of virus introduction in late December 2024. Although the entry route remains unresolved, human-associated introduction is most likely. Network analysis revealed minimal farm connectivity, and simulations predicted low potential for onward transmission, which is consistent with the outbreak being ultimately restricted to a single herd. This event underscores the constant and unpredictable risk of introduction of the virus. Early detection through increased awareness and comprehensive differential diagnostics as well as the international collaboration of veterinary services, laboratories, and experts are essential in the face of the global presence of FMD.

Shamonda virus (SHAV), which has recently emerged in Central Europe, was detected in brain tissue from two horses that showed clinical signs including neurological disorder and underwent pathological examination. The horses reportedly exhibited seizure-like episodes (Horse A) as well as fever and ataxia (Horse B). In both horses, severe lymphohistiocytic meningoencephalitis with hemorrhages were observed in various parts of the central nervous system (CNS), while outside the CNS no abnormalities were found. The virus genome could be detected by RT-qPCR in all examined parts of the CNS of both horses. In a postmortem cerebrospinal fluid sample of one horse, the virus could only be detected with a very low genome load; however, postmortem contamination cannot be completely ruled out. Consistent with the histological findings, no SHAV genome was detected in either the blood or organs outside the CNS. Postmortem, CNS material - especially brainstem tissue – is suitable for detection of histological lesions and virus genome via PT-qPCR, while intra vitam diagnostics of a SHAV infection in horses exhibiting neurological signs is at the moment only possible to a very limited extent.

African swine fever virus (ASFV) causes a severe hemorrhagic disease in Eurasian suids, whereas African suids are considered susceptible, but resistant to disease. To investigate the basis of this differential clinical fate, domestic pigs, Eurasian wild boar, red river hogs and common warthogs were inoculated with the virulent ASFV strain Armenia08. Host responses to ASFV infection were characterized using classical virological and immunological methods, supplemented by pathology and multi-omics analyses integrating single-cell RNA sequencing, transcriptomics and proteomics. Domestic pigs and wild boar developed acute-lethal disease with high viraemia, while red river hogs and warthogs remained clinically unaffected despite detectable viral replication. Disease severity correlated with the abundance of ASFV-positive monocytes and pronounced inflammatory signatures in Eurasian suids. By contrast, African suids exhibited limited monocyte infection, preserved MHC class II-mediated antigen presentation, and myeloid cell composition. These findings identify coordinated immune regulation and restricted monocyte vulnerability to viral immune evasion mechanisms as key features underlying ASFV tolerance in African suids.

The highly pathogenic avian influenza viruses of subtype H5N1 represent a major threat to animal and public health. The current panzootic with H5 clade 2.3.4.4b has caused numerous, widespread outbreaks in various domestic and wild avian species with high mortalities, massive losses, and a high frequency of spillover events to unexpected novel mammalian hosts, such as dairy cows. The global H5N1 situation raises serious concerns about zoonotic risks due to effective mammal-to-mammal transmission. Therefore, it is critical to increase surveillance intensity of a broadened species range, particularly at the human-animal interface. For this purpose, reliable and cost-effective serological tools that are easy to perform and suitable for high-throughput screening are critically needed. The newly developed double-antigen enzyme-linked immunosorbent assay format employing a luminescence-based detection technology has demonstrated compliance with such prerequisites. The assay allowed sensitive and specific detection of antibodies directed against H5 hemagglutinin of clade 2.3.4.4b in a wide range of birds and mammals, including humans. Furthermore, it allowed differentiating H5 anti-head-specific from cross-reacting anti-stalk antibodies, which represents a valuable feature with regard to the monitoring of future vaccination programs with H5-specific vaccines. Thus, the assay is a significant contribution to existing serological diagnostic tests for a clade-optimized and species-independent detection of influenza A virus antibodies. IMPORTANCE: The ongoing highly pathogenic avian influenza virus H5N1 panzootic has caused numerous outbreaks in domestic and wild animals, with frequent spillover events to unexpected host species, which underscores the importance of intensified surveillance. However, sensitive and specific multi-species serological assays represent a major gap. For this purpose, we developed a novel double-antigen enzyme-linked immunosorbent assay that employs an innovative luminescence-based readout strategy. The test allowed a highly sensitive and specific detection of H5-specific antibodies in a wide range of avian and mammalian species, including humans. It therefore represents a valuable contribution to improving species-independent serological diagnostic tools for the detection of influenza A virus antibodies.

Following the emergence of Shamonda virus (SHAV) in Europe in 2026, we identified a second, genetically distinct SHAV clade in cattle in Germany. Consistent differences across all three genome segments together with divergent regional distribution patterns indicate independent introductions. We have designated the two clades as SHAV Europe 1 (SHAV-EU1) and SHAV Europe 2 (SHAV-EU2). The unexpected co-circulation of these two clades has important implications for diagnostics, surveillance, host range assessment, risk evaluation, and control measures.

Background: Despite its importance for Culicoides -borne disease risk assessment, the winter activity of species of this biting midge genus remains poorly characterized. Moreover, information on virus circulation in winter-active Culicoides vectors, both under endemic conditions and during outbreaks, is almost non-existent. Methods: UV-light traps to collect Culicoides biting midges were operated once a week for 24 h in cattle, sheep, goat and horse stables at 12 to 55 locations during four consecutive winter periods (November 1 to March 31, 2021 to 2025) throughout Germany. Collected females of the genus Culicoides were morphologically assigned to Obsoletus Group or Pulicaris Complex. Temperature data were recorded to relate biting midge activity to temperatures. Screening for bluetongue virus (BTV), Schmallenberg virus and epizootic hemorrhagic disease virus was done by real-time RT-PCR on 1,581 pools (46,358 females) of both groups collected before (winter 2022/2023) and during the BTV serotype 3 (BTV-3) outbreak (winters 2023/2024 and 2024/2025). Results: Culicoides collections displayed notable variation between sites and months. November and March accounted for 95% of captures, while mid-winter months (December to February) yielded only 5%, with January and February each contributing 1% of total captures. The March 2024 and 2025 activity peaks coincided with mild temperatures and the inclusion of new monitoring sites, suggesting that one or both factors contributed. Although blood-fed females were very rare during mid-winter, their abundance often exceeded the EU threshold for parous Culicoides to define a vector-free period of < 5 individuals per trap and night. However, only a single Culicoides pool from November 2024 tested positive for BTV-3-RNA. All other pools were negative for all three viruses. Conclusions: Potential Culicoides vectors are active and feed on blood in livestock housings during wintertime. The presence of blood-fed females, exceeding the EU threshold, challenges the concept of a ‘vector-free period’. However, despite extensive monitoring over four years including outbreak conditions, only one virus-positive Culicoides pool was detected during winter. Combined with the very low number of biting midges and the temperatures not allowing virus replication in arthropods, virus circulation during wintertime appears to be hardly existent even under endemic or outbreak conditions. Considering both Culicoides activity and virus circulation, the findings suggest that the risk of BTV infection in ruminants via biting midges during the central European winter (December to March) is negligible. BTV overwintering in central Europe likely depends on either rare infection events in ruminants and vectors during winter that sustain viremia until spring, or on persistence mechanisms that are currently unknown.

Global SARS-CoV-2 surveillance based on consensus genome sequences has enabled unprecedented tracking of viral spread and evolution but provides limited resolution of intra-sample diversity and limited sensitivity for the reliable detection of recombinant genomes. Here, we analyzed 3,360 SARS-CoV-2 genomes generated through regional surveillance in northeastern Germany (Mecklenburg–Western Pomerania) between 2022 and 2025. Reconstruction of local spatio-temporal variant dynamics revealed substantial lineage diversity, regional deviations from global circulation patterns, and periods of intense co-circulation favoring co-infection and recombination. To systematically identify recombinant genomes, we implemented a two-stage framework combining high-sensitivity consensus-based screening (REcombination BARcode detector REBAR) with targeted raw-read validation. Among 61 candidate recombinants, 21 were supported by read-level evidence, including 17 previously unrecognized genomes. Recombinant breakpoints clustered in functionally relevant genomic regions, particularly around ORF1b and the spike gene, indicating non-random patterns of genome exchange. Despite frequent co-infections, only a small subset of recombinants showed evidence of onward transmission, suggesting that successful establishment represents a major constraint on recombinant SARS-CoV-2 evolution. Our findings demonstrate that recombination-aware genomic surveillance complements routine consensus genome surveillance by resolving intra-sample diversity and recombinant diversity while remaining scalable for population-level implementation.

Since mid-June 2026, an acute, non-fatal syndrome with high herd morbidity, reduced milk yield, diarrhea, fever and lethargy affected dairy cattle in southern Germany and Switzerland. Major viral pathogens were excluded. Pan-Simbuvirus PCR first detected an orthobunyavirus, subsequently confirmed by metagenomic sequencing, which enabled recovery of a complete “Shamonda-like” genome. One sentence summary line: More than a decade after the emergence of Schmallenberg virus in 2011, a novel “Shamonda-like” orthobunyavirus of the Simbu serogroup has now emerged in Central Europe.