Comprehensive at-arrival transcriptomic analysis of post-weaned beef cattle uncovers type I interferon and antiviral mechanisms associated with bovine respiratory disease mortality

Background Despite decades of extensive research, bovine respiratory disease (BRD) remains the most devastating in beef cattle production. Establishing a clinical diagnosis often relies upon visual detection non-specific signs, leading to low diagnostic accuracy. Thus, post-weaned are metaphylactically administered antimicrobials at facility arrival, which poses concerns regarding antimicrobial stewardship and resistance. Additionally, there is lack high-quality research that addresses gene-by-environment interactions underlie why some develop BRD die while others survive. Therefore, it necessary decipher underlying host genomic factors associated with mortality versus survival help determine risk severity. Using transcriptomic analysis at-arrival whole blood samples from died BRD, as compared those developed signs but lived (n = 3 DEAD, n ALIVE), we identified differentially expressed genes (DEGs) pathways BRD. evaluated unmapped reads, overlooked within experiments. Results 69 DEGs (FDR<0.10) were between ALIVE DEAD cohorts. Several possess immunological proinflammatory function associations TLR4 IL6. Biological processes, pathways, phenotype related type-I interferon production antiviral defense enriched arrival. Unmapped reads aligned primarily various ungulate assemblies, failed align viral assemblies. Conclusion This study further revealed increased mechanisms upregulated predominantly involved innate immune typically defense, although no reads. Our findings provide targets for highest suggesting type I interferons may be indicative arrival contribute eventual mortality.