Mining the Unmapped Reads in Bovine RNA-Seq Data Reveals the Prevalence of Bovine Herpes Virus-6 in European Dairy Cows and the Associated Changes in Their Phenotype and Leucocyte Transcriptome

Microbial RNA is detectable in host samples by aligning unmapped reads from RNA sequencing against taxon reference sequences, generating a score proportional to the microbial load. An RNA-Seq data analysis showed that 83.5% of leukocyte samples from six dairy herds in different EU countries contained bovine herpes virus-6 (BoHV-6). Phenotypic data on milk production, metabolic function, and disease collected during their first 50 days in milk (DIM) were compared between cows with low (1–200 and n = 114) or high (201–1175 and n = 24) BoHV-6 scores. There were no differences in milk production parameters, but high score cows had numerically fewer incidences of clinical mastitis (4.2% vs. 12.2%) and uterine disease (54.5% vs. 62.7%). Their metabolic status was worse, based on measurements of IGF-1 and various metabolites in blood and milk. A comparison of the global leukocyte transcriptome between high and low BoHV-6 score cows at around 14 DIM yielded 485 differentially expressed genes (DEGs). The top pathway from Gene Ontology (GO) enrichment analysis was the immune system process. Down-regulated genes in the high BoHV-6 cows included those encoding proteins involved in viral detection (DDX6 and DDX58), interferon response, and E3 ubiquitin ligase activity. This suggested that BoHV-6 may largely evade viral detection and that it does not cause clinical disease in dairy cows.