Whole Transcription Sequencing Analyses of Beef Calves Persistently Infected by Bovine Viral Diarrhea Virus

Bovine Viral Diarrhea Virus (BVDV), one of the contributing pathogens to bovine respiratory disease, is economically one of the most costly pathogens in the cattle industry. Spreading of the virus occurs most frequently from persistent infection (PI) of immunotolerant calves resulting from acute dam exposure during 42-125 days of gestation. A PI calf will shed the virus its entire life, exposing herdmates and penmates to infection. If a genetic marker for resistance to infection could be identified, or if more is understood about the host response to infection, novel control strategies for BVDV could be designed. To examine the host response to PI, blood from 26 naturally infected PI animals with strains 1a (n=10), 1b (n=8), and 2 (n=8) were collected from commercial feedlot calves to compare gene expression among groups using RNA-Sequencing. Data from a high exposure group (n=10) consisting of animals that were not PI themselves but were penned with PIs, and a control group (n=9) of animals that were uninfected and presumed to be unexposed were also included in the analyses. An average of 58 million, stranded, 75bp paired-end reads per individual were sequenced on the Illumina Next-Seq. After quality control the reads were mapped to UMD3.1 and are being examined to identify differential expression among groups. Significant differential expression has been found between PI animals and controls and is being investigated to identify associated genomic variants as well as gene pathways involved in infection.