Genomic surveillance reveals a novel Shamonda orthobunyavirus causing acute illness in dairy cattle, highlighting potential cross-border viral emergence.
Key Points
To identify the causative pathogen responsible for an outbreak of acute fever, diarrhea, and severe milk yield reduction in French dairy cattle.
Collected and pooled plasma samples from affected dairy cattle presenting with acute clinical signs in eastern France.
Conducted unbiased Oxford Nanopore metagenomic sequencing on pooled plasma to identify viral sequences and reconstruct complete genomes.
Performed phylogenetic analyses on the viral L, M, and S genomic segments to assess evolutionary relationships.
Identified a Simbu serogroup Orthobunyavirus, provisionally designated as European Shamonda Virus, and assembled complete viral genomes.
Phylogenetic clustering demonstrated that segments L and M grouped closely with Nigerian Shamonda virus strains, whereas segment S showed a distinct divergence indicative of genetic reassortment or high mutation rates.
Detected similar viral emergence patterns across neighboring countries, demonstrating multi-country regional spread.