Identification, Isolation and Genomic Characterization of an Emerging Shamonda Virus Variant Associated with Bovine Disease in Switzerland

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Abstract
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.

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