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Title: Gene expression analysis of whole blood RNA from pigs infected with low and high pathogenic African swine fever viruses

Abstract

African swine fever virus (ASFV) is a macrophage-tropic virus responsible for ASF, a transboundary disease that threatens swine production world-wide. Since there are no vaccines available to control ASF after an outbreak, obtaining an understanding of the virus-host interaction is important for developing new intervention strategies. In this study, a whole transcriptomic RNA-Seq method was used to characterize differentially expressed genes in pigs infected with a low pathogenic ASFV isolate, OUR T88/3 (OURT), or the highly pathogenic Georgia 2007/1 (GRG). After infection, pigs infected with OURT showed no or few clinical signs; whereas, GRG produced clinical signs consistent with acute ASF. RNA-Seq detected the expression of ASFV genes from the whole blood of the GRG, but not the OURT pigs, consistent with the pathotypes of these strains and the replication of GRG in circulating monocytes. Even though GRG and OURT possess different pathogenic properties, there was significant overlap in the most upregulated host genes. A small number of differentially expressed microRNAs were also detected in GRG and OURT pigs. These data confirm previous studies describing the response of macrophages and lymphocytes to ASFV infection, as well as reveal unique gene pathways upregulated in response to infection with GRG.

Authors:
 [1];  [2];  [3];  [4];  [1];  [4];  [4];  [4];  [4];  [4];  [2];  [4]
  1. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Physical & Life Sciences Directorate
  2. Kansas State Univ., Manhattan, KS (United States). Department of Diagnostic Medicine and Pathobiology
  3. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Computation Directorate
  4. CSIRO Australian Animal Health Laboratory, Geelong, Victoria (Australia)
Publication Date:
Research Org.:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1395491
Grant/Contract Number:
AC52-07NA27344
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 7; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; Gene expression; Infectious-diesease diagnostics; Virology

Citation Formats

Jaing, Crystal, Rowland, Raymond R. R., Allen, Jonathan E., Certoma, Andrea, Thissen, James B., Bingham, John, Rowe, Brenton, White, John R., Wynne, James W., Johnson, Dayna, Gaudreault, Natasha N., and Williams, David T.. Gene expression analysis of whole blood RNA from pigs infected with low and high pathogenic African swine fever viruses. United States: N. p., 2017. Web. doi:10.1038/s41598-017-10186-4.
Jaing, Crystal, Rowland, Raymond R. R., Allen, Jonathan E., Certoma, Andrea, Thissen, James B., Bingham, John, Rowe, Brenton, White, John R., Wynne, James W., Johnson, Dayna, Gaudreault, Natasha N., & Williams, David T.. Gene expression analysis of whole blood RNA from pigs infected with low and high pathogenic African swine fever viruses. United States. doi:10.1038/s41598-017-10186-4.
Jaing, Crystal, Rowland, Raymond R. R., Allen, Jonathan E., Certoma, Andrea, Thissen, James B., Bingham, John, Rowe, Brenton, White, John R., Wynne, James W., Johnson, Dayna, Gaudreault, Natasha N., and Williams, David T.. 2017. "Gene expression analysis of whole blood RNA from pigs infected with low and high pathogenic African swine fever viruses". United States. doi:10.1038/s41598-017-10186-4. https://www.osti.gov/servlets/purl/1395491.
@article{osti_1395491,
title = {Gene expression analysis of whole blood RNA from pigs infected with low and high pathogenic African swine fever viruses},
author = {Jaing, Crystal and Rowland, Raymond R. R. and Allen, Jonathan E. and Certoma, Andrea and Thissen, James B. and Bingham, John and Rowe, Brenton and White, John R. and Wynne, James W. and Johnson, Dayna and Gaudreault, Natasha N. and Williams, David T.},
abstractNote = {African swine fever virus (ASFV) is a macrophage-tropic virus responsible for ASF, a transboundary disease that threatens swine production world-wide. Since there are no vaccines available to control ASF after an outbreak, obtaining an understanding of the virus-host interaction is important for developing new intervention strategies. In this study, a whole transcriptomic RNA-Seq method was used to characterize differentially expressed genes in pigs infected with a low pathogenic ASFV isolate, OUR T88/3 (OURT), or the highly pathogenic Georgia 2007/1 (GRG). After infection, pigs infected with OURT showed no or few clinical signs; whereas, GRG produced clinical signs consistent with acute ASF. RNA-Seq detected the expression of ASFV genes from the whole blood of the GRG, but not the OURT pigs, consistent with the pathotypes of these strains and the replication of GRG in circulating monocytes. Even though GRG and OURT possess different pathogenic properties, there was significant overlap in the most upregulated host genes. A small number of differentially expressed microRNAs were also detected in GRG and OURT pigs. These data confirm previous studies describing the response of macrophages and lymphocytes to ASFV infection, as well as reveal unique gene pathways upregulated in response to infection with GRG.},
doi = {10.1038/s41598-017-10186-4},
journal = {Scientific Reports},
number = 1,
volume = 7,
place = {United States},
year = 2017,
month = 8
}

Journal Article:
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  • Viral molecular epidemiology has traditionally analyzed variation in single genes. Whole genome phylogenetic analysis of 123 concatenated genes from 11 ASFV genomes, including E75, a newly sequenced virulent isolate from Spain, identified two clusters. One contained South African isolates from ticks and warthog, suggesting derivation from a sylvatic transmission cycle. The second contained isolates from West Africa and the Iberian Peninsula. Two isolates, from Kenya and Malawi, were outliers. Of the nine genomes within the clusters, seven were within p72 genotype 1. The 11 genomes sequenced comprised only 5 of the 22 p72 genotypes. Comparison of synonymous and non-synonymous mutationsmore » at the genome level identified 20 genes subject to selection pressure for diversification. A novel gene of the E75 virus evolved by the fusion of two genes within the 360 multicopy family. Comparative genomics reveals high diversity within a limited sample of the ASFV viral gene pool.« less
  • Titration experiments in swine macrophages have shown that African swine fever virus infectivity was not enhanced in the presence of antiviral antibodies. The early viral protein synthesis and the viral DNA replication in swine macrophages infected with virus-antibody complexes were inhibited in the presence of high doses of uv-inactivated virus, which saturated specific virus receptors, but not when Fc receptors were saturated with antibodies. These results indicate that African swine fever virus does not infect swine macrophages through Fc receptors and that the normal entry pathway through virus receptors is not bypassed by the virus-antibody complexes.
  • Many stages of African swine fever virus infection have not yet been studied in detail. To track the behavior of African swine fever virus (ASFV) in the infected cells in real time, we produced an infectious recombinant ASFV (B54GFP-2) that expresses and incorporates into the virus particle a chimera of the p54 envelope protein fused to the enhanced green fluorescent protein (EGFP). The incorporation of the fusion protein into the virus particle was confirmed immunologically and it was determined that p54-EGFP was fully functional by confirmation that the recombinant virus made normal-sized plaques and presented similar growth curves to themore » wild-type virus. The tagged virus was visualized as individual fluorescent particles during the first stages of infection and allowed to visualize the infection progression in living cells through the viral life cycle by confocal microscopy. In this work, diverse potential applications of B54GFP-2 to study different aspects of ASFV infection are shown. By using this recombinant virus it was possible to determine the trajectory and speed of intracellular virus movement. Additionally, we have been able to visualize for first time the ASFV factory formation dynamics and the cytophatic effect of the virus in live infected cells. Finally, we have analyzed virus progression along the infection cycle and infected cell death as time-lapse animations.« less