The hub genes identified for each tissue type.

Bovine alphaherpesvirus one (BoHV-1) is a primary cause of bovine respiratory disease (BRD), and a leading cause of morbidity and mortality in cattle. The transcriptomic responses of key respiratory and immune associated tissues of dairy calves following experimental challenge with BoHV-1 are unknown. Thus, the study objective was to examine the gene expression profiles of multiple tissue types from dairy calves following an infectious challenge with BoHV-1. Holstein-Friesian bull calves (mean age ± SD 149.2 days ± 23.8; mean weight ± SD 174.6 kg ± 21.3 kg were challenged with either BoHV-1 inoculate (6.3 × 107/mL × 1.35mL) (n = 12) or sterile phosphate buffered saline (n = 6). Animals were euthanised on day 6 post-challenge and tissue samples collected, including bronchial (BLN) and mediastinal lymph nodes (MLN), pharyngeal tonsil (PGT) and healthy (HL) and lesioned right cranial lung (LL). Total RNA was extracted and libraries sequenced on an Illumina NovaSeq 6000. Differential expression analysis was conducted using edgeR and pathways analysed using DAVID. A weighted gene co-expression network analysis (WGCNA) was conducted separately for each tissue type to identify networks significantly associated with BoHV-1 infection. Differentially expressed genes (DEGs) were identified in all tissues (P 2). Thirty-three DEGs were common to all tissues and enriched pathways included Influenza A and Herpes simplex 1 infection (P