Researchers detected a novel Shamonda virus in French dairy cattle
Reports began in June from cattle herds in the French departments of Doubs and Ain, followed in July by similar episodes in Savoie and Haute-Savoie. The clinical signs included short-lived fever, diarrhoea, depression or anorexia, and substantial but reversible falls in milk output. Comparable episodes were later confirmed in Germany, Switzerland and the Netherlands.
An investigation of nine initially affected herds found that bulk milk production had declined by between 15% and 75%. The share of cows with diarrhoea varied from 8% to 100% across the herds, which contained between 25 and 275 animals. Individual diarrhoeal episodes usually lasted one to six days. Tests targeting Schmallenberg virus, which was considered during the early investigation, were negative.
Researchers collected plasma and faecal material from 14 symptomatic cows on three farms in Haute-Savoie. The animals had developed fever or depression within the previous 48 hours and were still showing signs when sampled. The material was grouped into three plasma pools and three faecal pools before analysis.
Using sequence-independent amplification and Oxford Nanopore sequencing, the team found orthobunyavirus reads in each plasma pool, numbering about 4,700, 43,500 and 7,500 respectively. Fewer than 1,000 reads were found in each faecal pool. The analysis produced complete coding sequences for the virus’s L and M genome segments and a partial 775-nucleotide S segment. Further testing of five herds in three other French regions produced two additional complete genomes.
The virus was subsequently sought in samples from 33 affected herds collected between July 28th and August 11th, as well as aborted-fetus samples from 18 additional herds collected between July 27th and August 11th. Both a broad Simbu-group test and a test developed specifically for European Shamonda Virus detected viral RNA in every sample examined. In the 18 herds investigated for abortions, farmers had reported fever and depression in cows two to four weeks before the abortions. Viral RNA was found consistently in placentas or fetal organs, including the spleen and brain; brain tissue was positive in six fetuses.
Genetic analysis placed the French and German viruses in a separate Shamonda lineage. Their L and M segments were closest to a Nigerian strain isolated from cattle in 1965, sharing 93.02% and 92.63% nucleotide identity with it. The French and German viruses shared 99.93% identity in both segments. Their S segments were identical to each other but did not group directly with the Nigerian S sequences. The authors said that this pattern could reflect a high mutation rate or reassortment, although the available data did not establish when, where or in which lineage such an event might have occurred.
The researchers classified the virus within the species Orthobunyavirus schmallenbergense on the basis of amino-acid similarity, while describing it as a new Shamonda lineage because of its distinct genetic position. They said the detections in France and Germany were the first reported molecular identifications of a Shamonda orthobunyavirus in Europe. No evidence currently shows that the virus infects humans. The study called for further veterinary and laboratory surveillance, including investigation of Culicoides midges, reproductive outcomes and archived samples.
