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

• Published in: Viruses Vol. 12; no. 12; p. 1451
• Main Authors: Buggiotti, Laura, Cheng, Zhangrui, Wathes, D Claire, GplusE Consortium
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 16.12.2020; MDPI
• Subjects: Animals; Antibiotics; BoHV-4; bovine herpes virus-6; Cattle - virology; Dairy cattle; dairy cows; Disease; Female; Gammaherpesvirinae; Gammaherpesvirinae - genetics; Gammaherpesvirinae - isolation & purification; Gene expression; Genomes; Herpes viruses; Immune system; Insulin-like growth factor I; Interferon; Leukocytes - metabolism; Mastitis; Metabolites; Milk production; Pathogens; Phenotype; Phenotypes; Prevalence; Ribonucleic acid; RNA; RNA-Seq; Transcriptome; Ubiquitin; Ubiquitin-protein ligase; Uterus; Denmark; United Kingdom > UK; Belgium; United States > US; Aarhus Denmark; Germany; Gammaherpesvirinae; bovine herpes virus-6; mastitis; RNA-Seq; leukocyte; dairy cows; endometritis; ISGylation; BoHV-4; interferon
• ISSN: 1999-4915; 1999-4915
• DOI: 10.3390/v12121451

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 = 114) or high (201-1175 and = 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 ( and ), 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.