The virus identified in livestock in Europe during the summer of 2026 belongs to the genus Orthobunyavirus. Although it is closely related to Shamonda, it represents a genetically distinct virus. Its identification relied on the power of metagenomics.
Metagenomics has marked a turning point in research. By sequencing all the nucleic acids present in a clinical sample, it can identify, in a single analysis, virtually every microorganism the sample contains: bacteria, viruses, fungi and parasites alike. This represents a paradigm shift away from the traditional a priori approach. Conventional diagnostic testing is hypothesis-driven: it targets only agents already known to be associated with a given clinical syndrome. Metagenomics, by contrast, is hypothesis-free, making it possible to detect rare, unexpected or entirely novel pathogens. Combined with high-throughput sequencing, it can also be applied to large numbers of samples in parallel.
This approach was applied in summer 2026 on samples collected from cattle in France and northern Europe. Affected cows initially showed fever and diarrhea; the disease then progressed to reduced milk production and stillbirths. As the pathogen causing the epizootic was undefined, metagenomics allowed research teams to identify it.
The joint research unit IHAP (Host–pathogen interactions) of France’s National Research Institute for Agriculture, Food and Environment (INRAE) and the National Veterinary School of Toulouse (ENVT) identified a virus never before detected in Europe, most likely transmitted by biting midges (Culicoides). Their findings were confirmed by work conducted simultaneously by teams at the Friedrich-Loeffler-Institut (FLI) in Germany. (Both INRAE and FLI are members of PREZODE.)
Simbu serogroup of orthobunyaviruses
“The virus we identified belongs to the Simbu serogroup of orthobunyaviruses, which cause diseases in livestock. It is most closely related to Shamonda viruses, with which it shares two of three genome segments. Two clades have been identified – named EU1 and EU2 variants of Shamonda. They differ slightly from the strain first isolated from cattle in Nigeria in 1965, and later in Japan. Neither had a high impact at the time, so there was little investigation, research, or literature on it,” explains Professor Jean-Luc Guérin, Director of the IHAP Unit.
The EU1 and EU2 variants affect mostly cattle, rarely horses. Spontaneous abortions have been reported; Congenital malformation may appear when the calving season begins. Veterinarians and farmers monitor the situation to avoid the disease spreading.
The virus has also similarities to the Schmallenberg virus, which emerged in European herds in 2011, infecting cows and sheep.
Investigation on a human case
In October, a medical team at a Lyon hospital (in France), treating a patient with a severe encephalitis form of cancer, performed metagenomic analysis on cerebrospinal sample to identify any infectious pathogens. They detected a genotype identical to the EU1 variant. Although cross-species transmission cannot be ruled out, experts and practitioners consider the zoonotic risk to be extremely low: the case is isolated and atypical, and no conclusions can be extrapolated from it. Public health authorities, researchers, as well as international organizations are investigating. “This viral emergence in livestock at the European scale, as well as the human case, shows that early detection of emerging risks can rely on an association of clinical surveillance on animals as on humans, science and advanced technology,” concludes Prof. Guérin.