Tonsil Transcriptome Response to Infection with One of Two PRRS Virus Isolates

Porcine reproductive and respiratory syndrome (PRRS) is the most costly swine disease. Tonsil is a primary tissue for PRRS virus (PRRSV) persistence. To investigate the effect of tonsil viral level and PRRSV isolate on gene expression in the tonsil, RNA-seq was performed on tonsil samples with high and low tonsil virus levels (TV) 42 days post infection (dpi) with a highly pathogenic PRRS isolate, NVSL-97-7985 (NVSL), or a contemporary one, KS-2006-72109 (KS06). For our analyses, 15 NVSL-high TV, 13 NVSL-low TV, 12 KS06-high TV, and 10 KS06-low TV were chosen from two PRRSV infection trials of ~200 commercial nursery pigs from the same genetic source. In total, 11,909 expressed genes were identified in the tonsil, of which 105 were differentially expressed genes (DEGs) (q<0.1) between the high and low TV, 258 between the two isolate infections, and 7 for the interaction between isolate and TV. Using PANTHER, 18 DEGs between the two isolate infections were involved in the integrin signaling pathway (p=7.5E-11) that controls cell survival and cell cycle progression. Overrepresented (p<0.05) gene ontology-biological process terms among DEGs between the two isolate infections included cell-matrix adhesion, cell-cell adhesion, ectoderm development, cellular component morphogenesis, immune system process, and signal transduction. The term immune system process was also overrepresented (p=6.0E-03) among DEGs between the high and low TV. These results contribute to understanding the mechanisms involved in tonsil pathology induced by PRRSV infection in pigs. Support: Genome Canada, USDA-ARS, USDA-NIFA grant 2013-68004-20362 and National Pork Board grants #12-061 and #14-223.