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ARS Home » Midwest Area » Ames, Iowa » National Animal Disease Center » Virus and Prion Research » Research » Publications at this Location » Publication #361519

Research Project: Intervention Strategies to Control Endemic and New and Emerging Viral Diseases of Swine

Location: Virus and Prion Research

Title: e-PIG-enetics: Porcine miRNA and tRNA expression during highly pathogenic PRRSV infections

item FLEMING, DAMARIUS - Oak Ridge Institute For Science And Education (ORISE)
item Miller, Laura

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 6/4/2019
Publication Date: 7/7/2019
Citation: Fleming, D.S., Miller, L.C. 2019. e-PIG-enetics: Porcine miRNA and tRNA expression during highly pathogenic PRRSV infections.[abstract]. ISAG 37th International Society for Animal Genetics Conference. p. 211.

Interpretive Summary:

Technical Abstract: Objective Porcine respiratory and reproductive syndrome virus (PRRSV) is a single stranded RNA Arteriviridae virus that causes clinical disease such as respiratory infection, poor growth, reproductive failure, and a loss of homeostasis within porcine hosts leading to poor immune response. Losses to the commercial industry due to PRRSV infections are far-reaching: affecting production on a global scale and liquidating billions of dollars annually from combined direct and indirect costs. Over time regions affected by PRRSV have begun to see an increase in heterologous type 2 PRRSV strains of higher virulence that can considerably alter host immune responses and the ability to maintain homeostasis. Because the loss of host homeostasis can denote underlying changes in gene and regulatory element expression profiles, this study objective aimed to examine the small non-coding response of miRNA and tRNA expression and the roles they play in distorting host immunologic and metabolic function homeostasis during PRRSV infections. Methods The analysis was based on whole blood taken from control and infected pigs at 1, 3, and 8 dpi. Small non-coding RNA expression of both miRNA and tRNA was conducted using HiSat2 for alignment of short sequences to the suscr10.2 genome. A custom GTF file of non-coding RNA was used to determine counts using FeatureCounts and Deseq2 to investigate differential expression. Infected pigs were challenged with the type 2 Chinese HP-PRRSV strain (JXwn06). Results The analysis returned a total of 148 statistically significant (FDR 0.15) miRNAs (n=88) and tRNAs (n=60) that were evaluated for possible pro and anti-viral effects. The tRNA differential expression increased in both magnitude and count as dpi increased, with no statistically significant expression at 1 dpi. The most abundant tRNA amino acid at 3 dpi was alanine, while glycine was the most abundant at 8 dpi. For the miRNAs, focus was put on upregulation that can inhibit gene expression. These results yielded candidates with potential anti and pro-viral actions such as Ssc-miR-125b, which is predicted to limit PRRSV viral levels, and Ssc-miR-145-5p shown to cause alternative macrophage priming.