Claudia Bachofen

We report two cases of equine encephalomyelitis associated with the recently emerged European Shamonda virus type 1 (SHAV-EU1). Shamonda virus has not yet been described in horses but has caused an unprecedented outbreak in cattle in Western Europe this summer (2026). Both horses showed neurological deficits and lymphocytic cerebrospinal fluid pleocytosis associated with encephalomyelitis, vasculitis and hemorrhages in brain and spinal cord. Pan-Simbu RT-qPCR confirmed viral RNA in brain tissue, and Metatranscriptomic sequencing identified full-genome SHAV-EU1 sequences, proofing correlation to the outbreak in Swiss cattle.

We report two cases of equine encephalomyelitis associated with European Shamonda virus type 1 (SHAV-EU1) infection. Both horses showed neurological deficits and lymphocytic cerebrospinal fluid pleocytosis associated with encephalomyelitis, vasculitis and hemorrhages in brain and spinal cord. Metatranscriptomic sequencing identified SHAV-EU1, and pan-Simbu RT-qPCR confirmed viral RNA in brain tissue.

In July 2026, an outbreak of a cattle illness characterized by high fever, diarrhea and reduced milk production, often affecting whole herds, was detected across several regions of northern Switzerland. To investigate the cause of the outbreak, a broad range of diagnostic methods was applied, including pathogen-specific RT-qPCRs, ELISA, serum neutralization test, virus isolation and metagenomic next-generation sequencing. A Shamonda virus (SHAV) was detected in samples from affected cattle, followed by successful virus isolation and complete genome sequencing of all three segments. Viral RNA was also detected in tissue samples from aborted calves, including the brain and spleen, supporting the need for further investigation of the virus in the context of reproductive disease. These findings document the first detection and molecular characterization of a SHAV in Switzerland and demonstrate its widespread circulation in cattle during the 2026 outbreak.

In July 2026, an outbreak of a cattle illness characterized by high fever, diarrhoea and reduced milk production, often affecting whole herds, was detected across several regions of northern Switzerland. To investigate the cause of the outbreak a broad range of diagnostic methods was applied, including pathogen specific RT-qPCRs, ELISA, serum neutralization test, virus isolation and metagenomic next generation sequencing. A Shamonda virus (SHAV) was detected in samples from affected cattle, followed by successful virus isolation and complete genome sequencing of all three segments. Viral RNA was also detected in tissue samples from aborted calves, including brain and spleen, supporting the need for further investigation of the virus in the context of reproductive disease. These findings document the first detection and molecular characterization of a SHAV in Switzerland and demonstrate its widespread circulation in cattle during the 2026 outbreak.

Highly pathogenic avian influenza virus (HPAIV) H5N1 has been detected in dairy cattle in the United States, with high viral loads observed in milk from infected animals. This raises public health concerns regarding potential transmission through exposure to raw milk. The sale of raw milk via vending machines represents a well-established distribution model in many European countries, including Switzerland. Although a notice must be posted on these milk vending machines stating that it is raw milk, together with appropriate processing instructions (heating to over 70 °C required, storage below 5 °C, consumption within 3 days), these notices are sometimes missing, and consumers often do not follow these guidelines. Over a four-month period, spanning from June 2025 to September 2025, 124 raw milk samples were collected from vending machines across Switzerland. Samples were screened for influenza A using reverse-transcription quantitative PCR (RT-qPCR). No samples tested positive for influenza A virus. The data from this study demonstrate the feasibility of implementing a sampling and detection system for HPAIV H5N1 in direct-to consumer raw milk samples and highlight the currently very low risk of HPAIV in raw milk samples sold via vending machines in Switzerland.

Influenza A viruses (IAV) are likely candidates for pandemics. This report summarizes the results of the Swiss national program for surveillance of influenza viruses in pigs and transmissions to humans between 2010 and 2022. Challenges and optimization options in the program are discussed. Nasal swabs or lung tissue samples from pigs with influenza-like signs (e.g. fever, cough) were screened by real-time RT-PCR for swine influenza virus (SIV) genomes, including that of the 2009 pandemic strain A(H1N1)pdm09; positive samples were subtyped for H1, N1, H3 and N2 by RT-PCR and Sanger sequencing. In parallel, humans with influenza-like symptoms and recent contact with diseased pigs were asked to self-sample themselves with a nasal swab. Human swabs were tested for IAV, and positive swabs further subtyped to identify potential cross-species transmission between swine and humans. In the pigs, SIV was detected in 375 of 674 farm visits. H1N1 is the only subtype detected in Swiss pigs so far. The (H1N1)pdm09 strain (HA clade 1A) was only detected in seven out of 375 SIV positive farm visits. Phylogenetic analyses from partial hemagglutinin (HA) and neuraminidase (NA) genome sequences indicate that the remaining pigs were infected with the Eurasian avian lineage (HA clade 1C), which is predominant in swine in Europe. The Swiss H1N1 strains form distinct clusters within HA clades 1C.2.1 and 1C.2.2 and seem to evolve comparably slowly. Infection of humans with SIV was identified in five cases. Sequence analysis assigned the five viruses to the Eurasian avian lineage (C), clades 1C.2.1 and 1C.2.2. There was no evidence for sustained human-to-human transmission. Although no critical IAV variants seem to have emerged so far in Switzerland, further surveillance of influenza viruses at the swine-human interface is of major importance.

(1) Background: Horses infected by a tick-borne encephalitis virus (TBEV) can develop clinically apparent infections. In humans, vaccination is the most effective preventive measure, while a vaccine is not available for horses. The objective of this study was to describe the immune response in horses after a TBEV vaccination with a human vaccine. (2) Materials and Methods: Seven healthy horses were randomised to a treatment or a control group in a stratified fashion based on TBEV–IgG concentrations on day −4. The treatment group (n = 4) was intramuscularly vaccinated using an inactivated human TBEV vaccine on days 0 and 28; the control group (n = 3) did not receive an injection. A clinical examination and blood sampling were performed on day –4, 0, 2, 4, 6, 8, 10, 14, 28, 30, 32, 34, 36, 38, 43, 56, 84, and 373. A linear mixed model analysis was used to compare IgG and IgM concentrations, neutralising antibody (nAb) titres, leucocyte count, serum amyloid A (SAA), and fibrinogen and globulin concentrations between the groups and time points. (3) Results: The clinical examination was normal in all horses at all time points. There were no significant changes in SAA, globulin, and fibrinogen concentrations and leucocyte count between the groups or time points (all p > 0.05). There was no significant increase in IgG, IgM, or nAb titres in the control group over time (all p > 0.05). In the vaccination group, there was a significant increase in IgG concentration and nAb titres after the second vaccination (p < 0.0001). There was no significant increase in IgM antibodies after the TBEV vaccination (all p > 0.05). One horse in the vaccination group had an IgM concentration above the laboratory reference on day 10. (4) Conclusions: The human TBEV vaccine did not have side effects when used in healthy horses in this study. A significant rise in TBEV-specific IgG antibodies and nAbs after the second vaccination was observed. However, IgG and nAb titres have been shown to decrease within 1 year after vaccination. The results of this study indicate that a vaccination with a human vaccine only induces a mild rise in IgM antibodies and only in previously naive horses. With no significant changes to inflammatory parameters in the vaccinated horses, it remains unclear whether vaccination with the human vaccine leads to protective immunity.

Rotavirus (RV) infections are the most important viral cause of diarrhea in piglets in Switzerland and are thought to cause substantial economic losses to the pig industry. However, no data are available on the occurrence and dynamics of the main porcine RV species, namely RVA, RVB, and RVC, and the diversity of the circulating strains. We therefore tested fecal samples from a cross-sectional (n = 95) and a longitudinal (n = 48) study for RVA, RVB, and RVC by real-time RT-PCR and compared the results of the cross-sectional study to postmortem findings. In addition, eight samples were fully genotyped by using next-generation sequencing. In the cross-sectional study, triple RV infections significantly correlated with diarrhea and wasting and were most frequent in the weaned age group. In the longitudinal study, the shedding of RV peaked one week after weaning and decreased thereafter. Here, mainly double infections were seen, and only a few animals showed diarrhea. The full-genome sequencing revealed a genotype pattern similar to other European countries and, importantly, co-infection by up to four RVA strains. Our results imply that the weaning of piglets may trigger not only RV shedding but facilitate co-infection of multiple RV species and strains in the same host.

Serum prevalence of Torque teno sus viruses (TTSuV1 and k2; family Anelloviridae) is known to be high in the porcine population worldwide but pathogenesis and associated pathomorphological lesions remain to be elucidated. In this study, quantitative real-time PCR for detection of TTSuV1 was performed in 101 porcine samples of brain tissue, with animals showing inflammatory lesions or no histological changes. Additionally, a pathomorphological and immunohistochemical characterization of possible lesions was carried out. Selected cases were screened by TTSuV1 in situ hybridization. Furthermore, TTSuV1 quantitative real-time PCR in splenic and pulmonary tissue and in situ hybridization (ISH) in spleen, lungs, mesenteric lymph node, heart, kidney, and liver were performed in 22 animals. TTSuV1 was detected by PCR not only in spleen and lung but also in brain tissue (71.3%); however, in general, spleen and lung tissue displayed lower Ct values than the brain. Positive TTSuV1 results were frequently associated with the morphological diagnosis of non-suppurative encephalitis. Single TTSuV1-positive lymphocytes were detected by ISH in the brain but also in lungs, spleen, mesenteric lymph node and in two cases of non-suppurative myocarditis. A pathogenetic role of a TTSuV1 infection as a co-factor for non-suppurative encephalitides cannot be ruled out.