Probing host immune response to porcine reproductive and respiratory syndrome virus (PRRSV) infection using 3′RNAseq and NanoString arrays

Porcine reproductive and respiratory syndrome (PRRS) is economically the most important disease of pigs worldwide and, when combined with porcine circovirus(PCV2) coinfection, increases severity of disease. Our goal is to assess the role of host genetics in determining efficacy of PRRS vaccine responses and on resistance/susceptibility to coinfectionchallenge. We performed 3′ RNA-seqand NanoString analyses to explore the blood transcriptome and identify mechanisms and biomarkers involved. We used a nursery pig model in which 50% of 200 pigs received a PRRS vaccination (Vx); after 28 days all were challenged with PRRSV and PCV2. Each pig was genotyped (80K SNP chip) and deeply phenotyped, including repeated blood sampling for viremialevel (VL), and immune proteins, and weight gain (WG). Blood RNA was analyzed to identify differentially expressed (DE) genes associated with anti-viral response phenotypes. Previous work identified a PRRS resistance marker on swine chromosome 4(SSC4) so, for these studies, samples from 7 sib sets (AA or AB for SSC4 marker; with/without Vx; 28 pigs total) were used for RNA preparation from Tempustube-preserved blood samples collected following vaccination (4, 7, 11, 14, 21 days) and challenge (0, 4, 7, 11, 14, 21, 28 days). Samples were subjected to 3′ RNA-seqand swine immune-focused, 220 gene NanoString codeset analyses. Data will be presented on DE gene expression, and particularly on immune related genes, that may contribute to controlling PRRS vaccination and PRRSV and PCV2 challenge responses. Further studies are aimed at identifying genes and biomarkers that regulate anti-viral response phenotypes. Funding: USDA ARS, USDA NIFA grant # 2013-68004-20362.