Impact of Porcine Arterivirus, Influenza B, and Their Coinfection on Antiviral Response in the Porcine Lung

Abstract

Interferon (IFN) cytokines induce an autonomous antiviral state in cells of the infected site to restrict virus spreading and critically regulate overall antiviral response. The antiviral state leads to host protection through expression of hundreds of IFN-stimulated genes that restrict viral infection through multiple mechanisms, for example, directly in viral genome degradation and indirectly through cellular metabolic inhibition. Young pigs were split into four treatment groups: control, porcine reproductive and respiratory syndrome virus (PRRSV, also known as porcine arterivirus) infected, influenza B virus (IBV) infected, and IBV/PRRSV coinfection. Lung tissue was collected at 3, 5, and 7 days post infection (dpi) for control, PRRSV and IBV/PRRSV coinfection, and at 3 and 5 dpi for IBV. Transcriptomic analysis, using usegalaxy.org tools, was performed against the S.scrofa 11.1 reference genome. Differentially expressed gene (DEG) analysis was carried out using DeSeq2 based on the model treatment + dpi + treatment:dpi + E. Downstream analysis examined the interaction of DEG at each dpi for over-enriched gene ontology (G.O.) terms and pathways. Comparisons of the infected groups vs. the controls yielded a total of (n = 1412) DEGs for the PRRSV group and (n = 1578) for the IBV/PRRSV group across all timepoints. The IBV group had (n = 64) total DEGs across 3 and 5 dpi. Expression data were considered statistically significant based on false discovery rate (FDR) ⫹ 0.1. Venn diagram comparisons of the DEGs across dpi showed that groups shared only 16 DEGs at 3 dpi, no DEGs were shared at 5 dpi, and for 7 dpi, only the PRRSV and IBV/PRRSV groups were compared and shared a total of 43 DEGs. Across the comparisons, differential expression was observed in antiviral genes such as IRF1, MX1, and OAS2. The IBV and IBV/PRRSV groups showed higher expression of antiviral genes at earlier dpi than the PRRSV group. Additionally, downregulated genes from the comparisons clustered around Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways effecting lung development and cellular integrity. Early expression of host IFN and antiviral genes may lead to viral RNA degradation, and assembly and transcription inhibition in the IBV infections. In comparison, expression of antiviral genes in the PRRSV group decreased across time. The decrease may explain why PRRSV infections persist, while IBV clears. Moreover, all infected groups showed prolonged upregulation in neutrophil degranulation pathway activity, possibly exacerbating symptomatic lung lesion pathology seen in these respiratory infections.

Time Series Transcriptomic Analysis of Bronchoalveolar Lavage Cells from Piglets Infected with Virulent or Low-Virulent Porcine Reproductive and Respiratory Syndrome Virus 1

“…Interestingly, Lena-infected pigs showed 5 DEGs, which were upregulated from 1 to 13 dpi, with three of them ( CSF1 , CCL4 , and EDN1 ) showing striking inflammatory properties, such as monocyte and macrophage proliferation and differentiation ( CSF1 ) ( 60 ), vasoconstriction and pro-inflammatory response associated with acute lung injury (ALI) ( EDN1 ) ( 61 ), or neutrophil migration ( CCL4 ) ( 62 ). Although, PAMs are the key players during PRRSV infection, the GO analysis suggests that chemotaxis of neutrophils and their likely degranulation are continued over the time points ( 25 , 46 ), leading to alveolar–capillary barrier damage, increased vascular permeability, and hence, a higher extent of lung damage, as has been observed in this study.…”

“…In our case, a screen of ISGs, enriched in IFN-I signaling pathway, was upregulated in BAL cells from both virulent Lena-infected ( BST2 , IFI6 , IFITM1 , ISG15 , ISG20 , MX1 , OASL , RSAD2 , STAT1 ) and low-virulent 3249-infected piglets ( EIF2AK4 , GBP1 , MX1 ) from 3 and 6 dpi onwards, respectively. Interferon regulatory factors (IRF) have been also found to be overexpressed in PAMs infected in vitro with Lena and Lelystad virus strains ( 29 ), as well as during the early stage of PRRSV-2 infection ( 24 , 46 , 47 ). Many of these upregulated genes could point to a continuous antiviral state ( 45 , 48 ), since ISG20 , MX1 , and RSAD2 have the capacity to inhibit viral replication ( 49 – 51 ), nevertheless, PRRSV has been reported to inhibit IRF3 as well as several of these ISGs such as STAT1 , ISG15 , and IFITM1 ( 52 , 53 ), by viral non-structural proteins (nsp1α, nsp1β, nsp2, nsp4, and nsp11) ( 53 – 56 ).…”

Simultaneous Infection With Porcine Reproductive and Respiratory Syndrome and Influenza Viruses Abrogates Clinical Protection Induced by Live Attenuated Porcine Reproductive and Respiratory Syndrome Vaccination

“…We sought to dissect the mechanisms underlying these opposing effects of co-infection in immunized and non-immunized animals at day 5 post-infection. The reduced PRRSV load in unimmunized co-infected animals has been suggested to be due to the early type I IFN response triggered by H3N2 ( 19 , 53 ). In this study, analysis of gene expression in the lungs, did not reveal significant differences in the expression of IFN-α, which may be due to the timing of sampling (5 days post-infection).…”

Transcriptomic Analysis of Liver Indicates Novel Vaccine to Porcine Reproductive and Respiratory Virus Promotes Homeostasis in T-Cell and Inflammatory Immune Responses Compared to a Commercial Vaccine in Pigs

“…The virus exists as two separate types, PRRSV-1 and PRRSV-2, originally named for the geographic regions in which they originated ( 3 ). The challenge with combating PRRSV is a combination of the effect of an extraordinary rate of mutation, the ability to infect macrophages, and subversion of host immune response through a series of actions leading to both immunomodulation and immune evasion ( 4 , 5 ). PRRSV's ability to suppress interferon signaling compromises the antiviral response.…”