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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:
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. Thu . "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}
}

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Works referenced in this record:

Transient correlation between viremia levels and IL-10 expression in pigs subclinically infected with porcine circovirus type 2 (PCV2)
journal, April 2008


African swine fever: morphopathology of a viral haemorrhagic disease
journal, September 1996

  • Rodriguez, F.; Fernandez, A.; Perez, J.
  • Veterinary Record, Vol. 139, Issue 11
  • DOI: 10.1136/vr.139.11.249

Interferon Lambda Upregulates IDO1 Expression in Respiratory Epithelial Cells After Influenza Virus Infection
journal, July 2015

  • Fox, Julie M.; Crabtree, Jackelyn M.; Sage, Leo K.
  • Journal of Interferon & Cytokine Research, Vol. 35, Issue 7
  • DOI: 10.1089/jir.2014.0052

Expression of porcine CD163 on monocytes/macrophages correlates with permissiveness to African swine fever infection
journal, December 2003

  • S�nchez-Torres, C.; G�mez-Puertas, P.; G�mez-del-Moral, M.
  • Archives of Virology, Vol. 148, Issue 12
  • DOI: 10.1007/s00705-003-0188-4

Immune Surveillance of Unhealthy Cells by Natural Killer Cells
journal, January 2013

  • Iannello, A.; Raulet, D. H.
  • Cold Spring Harbor Symposia on Quantitative Biology, Vol. 78, Issue 0
  • DOI: 10.1101/sqb.2013.78.020255

Genes homologous to ubiquitin-conjugating proteins and eukaryotic transcription factor SII in African swine fever virus
journal, January 1992


A gene expression atlas of the domestic pig
journal, November 2012


Cytosolic phospholipase A 2 : physiological function and role in disease
journal, April 2015


Increase in chemokines CXCL10 and CCL2 in blood from pigs infected with high compared to low virulence African swine fever virus isolates
journal, January 2013

  • Fishbourne, Emma; Hutet, Evelyne; Abrams, Charles
  • Veterinary Research, Vol. 44, Issue 1
  • DOI: 10.1186/1297-9716-44-87

Specific expression of GPR56 by human cytotoxic lymphocytes
journal, July 2011

  • Peng, Yen-Ming; van de Garde, Martijn D. B.; Cheng, Kai-Fong
  • Journal of Leukocyte Biology, Vol. 90, Issue 4
  • DOI: 10.1189/jlb.0211092

CDRK and DRK1 K+ channels have contrasting localizations in sensory systems
journal, August 1993


Ultrastructure of the Liver in Pigs with Experimental African Swine Fever
journal, September 1987


Identification of novel antigens with induced immune response in monoclonal gammopathy of undetermined significance
journal, October 2009


PTH receptor-1 signalling—mechanistic insights and therapeutic prospects
journal, August 2015

  • Cheloha, Ross W.; Gellman, Samuel H.; Vilardaga, Jean-Pierre
  • Nature Reviews Endocrinology, Vol. 11, Issue 12
  • DOI: 10.1038/nrendo.2015.139

Epidemiology of African swine fever virus
journal, April 2013


The transcription factor BATF modulates cytokine-mediated responses in T cells
journal, August 2016


RGS1 Is Expressed in Monocytes and Acts as a GTPase-activating Protein for G-protein-coupled Chemoattractant Receptors
journal, September 1999

  • Denecke, Bernd; Meyerdierks, Anke; Böttger, Erik C.
  • Journal of Biological Chemistry, Vol. 274, Issue 38
  • DOI: 10.1074/jbc.274.38.26860

Identification of CD163 as an antiinflammatory receptor for HMGB1-haptoglobin complexes
journal, May 2016


Perspectives for Monocyte/Macrophage-Based Diagnostics of Chronic Inflammation
journal, January 2016

  • Kzhyshkowska, Julia; Gudima, Alexandru; Moganti, Kondaiah
  • Transfusion Medicine and Hemotherapy, Vol. 43, Issue 2
  • DOI: 10.1159/000444943

Pathology of porcine peripheral white blood cells during infection with African swine fever virus
journal, January 2012

  • Karalyan, Zaven; Zakaryan, Hovakim; Arzumanyan, Hranush
  • BMC Veterinary Research, Vol. 8, Issue 1
  • DOI: 10.1186/1746-6148-8-18

Serological and immunohistochemical study of African swine fever in wild boar in Spain
journal, August 1998

  • Perez, J.; Fernandez, A.; Sierra, M. A.
  • Veterinary Record, Vol. 143, Issue 5
  • DOI: 10.1136/vr.143.5.136

Analysis of the Complete Nucleotide Sequence of African Swine Fever Virus
journal, April 1995

  • Yáñez, Rafael J.; Rodrı́guez, Javier M.; Nogal, Maria L.
  • Virology, Vol. 208, Issue 1
  • DOI: 10.1006/viro.1995.1149

Lysosome-Related Effector Vesicles in T Lymphocytes and NK Cells
journal, August 2015

  • Lettau, M.; Kabelitz, D.; Janssen, O.
  • Scandinavian Journal of Immunology, Vol. 82, Issue 3
  • DOI: 10.1111/sji.12337

Differential analysis of gene regulation at transcript resolution with RNA-seq
journal, December 2012

  • Trapnell, Cole; Hendrickson, David G.; Sauvageau, Martin
  • Nature Biotechnology, Vol. 31, Issue 1
  • DOI: 10.1038/nbt.2450

The non-haemadsorbing African swine fever virus isolate ASFV/NH/P68 provides a model for defining the protective anti-virus immune response
journal, March 2001

  • Coelho, Ricardo; Parkhouse, R. M. E.; Cruz, Benedita
  • Journal of General Virology, Vol. 82, Issue 3
  • DOI: 10.1099/0022-1317-82-3-513

Modulation of chemokine and chemokine receptor expression following infection of porcine macrophages with African swine fever virus
journal, March 2013


Human and Mouse Granzyme A Induce a Proinflammatory Cytokine Response
journal, November 2008


Standardization of pathological investigations in the framework of experimental ASFV infections
journal, April 2013


Semaphorin 6D regulates the late phase of CD4+ T cell primary immune responses
journal, August 2008

  • O'Connor, B. P.; Eun, S. -Y.; Ye, Z.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 35
  • DOI: 10.1073/pnas.0803386105

African Swine Fever Virus Isolate, Georgia, 2007
journal, December 2008

  • Rowlands, Rebecca J.; Michaud, Vincent; Heath, Livio
  • Emerging Infectious Diseases, Vol. 14, Issue 12
  • DOI: 10.3201/eid1412.080591

Dynamics of African swine fever virus shedding and excretion in domestic pigs infected by intramuscular inoculation and contact transmission
journal, September 2014

  • Guinat, Claire; Reis, Ana Luisa; Netherton, Christopher L.
  • Veterinary Research, Vol. 45, Issue 1
  • DOI: 10.1186/s13567-014-0093-8

Structural Heterogeneity and Multifunctionality of Lactoferrin
journal, November 2014


Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
journal, December 2008

  • Huang, Da Wei; Sherman, Brad T.; Lempicki, Richard A.
  • Nature Protocols, Vol. 4, Issue 1
  • DOI: 10.1038/nprot.2008.211

African swine fever virus transcription
journal, April 2013


55
journal, September 2013


OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software
journal, November 2014

  • Kriventseva, Evgenia V.; Tegenfeldt, Fredrik; Petty, Tom J.
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1220

African swine fever virus excretion patterns in persistently infected animals: A quantitative approach
journal, December 2012

  • de Carvalho Ferreira, H. C.; Weesendorp, E.; Elbers, A. R. W.
  • Veterinary Microbiology, Vol. 160, Issue 3-4
  • DOI: 10.1016/j.vetmic.2012.06.025

CSN5/JAB1 Interacts with the Centromeric Components CENP-T and CENP-W and Regulates Their Proteasome-mediated Degradation
journal, August 2013

  • Chun, Younghwa; Lee, Miae; Park, Byoungwoo
  • Journal of Biological Chemistry, Vol. 288, Issue 38
  • DOI: 10.1074/jbc.M113.469221

Expression, cellular localization and antibody responses of the African swine fever virus genes B602L and K205R
journal, November 2008

  • Gutiérrez-Castañeda, B.; Reis, A. L.; Corteyn, A.
  • Archives of Virology, Vol. 153, Issue 12
  • DOI: 10.1007/s00705-008-0246-z

Circulating MiRNA-122 Levels Are Associated with Hepatic Necroinflammation and Portal Hypertension in HIV/HCV Coinfection
journal, February 2015


Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
journal, May 2016

  • Kuleshov, Maxim V.; Jones, Matthew R.; Rouillard, Andrew D.
  • Nucleic Acids Research, Vol. 44, Issue W1
  • DOI: 10.1093/nar/gkw377

Assembly of African Swine Fever Virus: Quantitative Ultrastructural Analysisin Vitroandin Vivo
journal, October 1996


Prognostic relevance of glycosylation-associated genes in breast cancer
journal, April 2014

  • Milde-Langosch, Karin; Karn, Thomas; Schmidt, Marcus
  • Breast Cancer Research and Treatment, Vol. 145, Issue 2
  • DOI: 10.1007/s10549-014-2949-z

Adenovirus E1A Recruits the Human Paf1 Complex To Enhance Transcriptional Elongation
journal, March 2014

  • Fonseca, G. J.; Cohen, M. J.; Mymryk, J. S.
  • Journal of Virology, Vol. 88, Issue 10
  • DOI: 10.1128/JVI.03518-13

Xk-Related Protein 8 and CED-8 Promote Phosphatidylserine Exposure in Apoptotic Cells
journal, July 2013


Up-Regulation of the ATP-Binding Cassette Transporter A1 Inhibits Hepatitis C Virus Infection
journal, March 2014


The growth of a virulent strain of African swine fever virus in domestic pigs
journal, March 1968


Genetically edited pigs lacking CD163 show no resistance following infection with the African swine fever virus isolate, Georgia 2007/1
journal, January 2017


Review of African swine fever : transmission, spread and control : review article
journal, May 2009

  • Penrith, M-L.; Vosloo, W.
  • Journal of the South African Veterinary Association, Vol. 80, Issue 2
  • DOI: 10.4102/jsava.v80i2.172

Virus-Heat Shock Protein Interaction and a Novel Axis for Innate Antiviral Immunity
journal, September 2012


CD68 on rat macrophages binds tightly to S100A8 and S100A9 and helps to regulate the cells’ immune functions
journal, June 2016


Characterization of the African Swine Fever Virus Structural Protein p14.5: A DNA Binding Protein
journal, March 1997

  • Martinez-Pomares, Luisa; Simon-Mateo, Carmen; Lopez-Otin, Carlos
  • Virology, Vol. 229, Issue 1
  • DOI: 10.1006/viro.1996.8434

African swine fever: a disease characterized by apoptosis.
journal, June 1998


NK-lysin, structure and function of a novel effector molecule of porcine T and NK cells
journal, November 1996


Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool
journal, January 2013


Different routes and doses influence protection in pigs immunised with the naturally attenuated African swine fever virus isolate OURT88/3
journal, February 2017


RIG-I-like receptor regulation in virus infection and immunity
journal, June 2015


Titration of African Swine Fever (ASF) Virus
journal, September 1976


Smad3 mediates TGF-β1 induction of VEGF production in lung fibroblasts
journal, February 2005

  • Kobayashi, Tetsu; Liu, Xiangde; Wen, Fu-Qiang
  • Biochemical and Biophysical Research Communications, Vol. 327, Issue 2
  • DOI: 10.1016/j.bbrc.2004.12.032

A gene atlas of the mouse and human protein-encoding transcriptomes
journal, April 2004

  • Su, A. I.; Wiltshire, T.; Batalov, S.
  • Proceedings of the National Academy of Sciences, Vol. 101, Issue 16
  • DOI: 10.1073/pnas.0400782101

A model for the reaction mechanism of the transglutaminase 3 enzyme
journal, August 2003

  • Ahvazi, Bijan; Steinert, Peter M.
  • Experimental & Molecular Medicine, Vol. 35, Issue 4
  • DOI: 10.1038/emm.2003.31

Synaptotagmin-like proteins control the formation of a single apical membrane domain in epithelial cells
journal, July 2012

  • Gálvez-Santisteban, Manuel; Rodriguez-Fraticelli, Alejo E.; Bryant, David M.
  • Nature Cell Biology, Vol. 14, Issue 8
  • DOI: 10.1038/ncb2541

An eIF2α-binding motif in protein phosphatase 1 subunit GADD34 and its viral orthologs is required to promote dephosphorylation of eIF2α
journal, June 2015

  • Rojas, Margarito; Vasconcelos, Gabriel; Dever, Thomas E.
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 27
  • DOI: 10.1073/pnas.1501557112

Influence of Age and Dose of African Swine Fever Virus Infections on Clinical Outcome and Blood Parameters in Pigs
journal, January 2017

  • Post, Jacob; Weesendorp, Eefke; Montoya, Maria
  • Viral Immunology, Vol. 30, Issue 1
  • DOI: 10.1089/vim.2016.0121

Porcine Circovirus Type 2 (PCV2): Pathogenesis and Interaction with the Immune System
journal, January 2013


Recent advances in the epidemiology, diagnosis and control of diseases caused by porcine circovirus type 2
journal, January 2011

  • Grau-Roma, Llorenç; Fraile, Lorenzo; Segalés, Joaquim
  • The Veterinary Journal, Vol. 187, Issue 1
  • DOI: 10.1016/j.tvjl.2010.01.018

A Simple Method of Estimating Fifty per cent Endpoints12
journal, May 1938


Identification of the principal serological immunodeterminants of African swine fever virus by screening a virus cDNA library with antibody
journal, June 2002


Development of a TaqMan® PCR assay with internal amplification control for the detection of African swine fever virus
journal, January 2003


Perforin oligomers form arcs in cellular membranes: a locus for intracellular delivery of granzymes
journal, August 2014

  • Metkar, S. S.; Marchioretto, M.; Antonini, V.
  • Cell Death & Differentiation, Vol. 22, Issue 1
  • DOI: 10.1038/cdd.2014.110

Mapping and sequence of the gene encoding the African swine fever virion protein of Mr 11500
journal, November 1993


Mild guanidinoacetate increase under partial guanidinoacetate methyltransferase deficiency strongly affects brain cell development
journal, July 2015


African swine fever virus protein p30 interaction with heterogeneous nuclear ribonucleoprotein K (hnRNP-K) during infection
journal, September 2008


Ribo-Zero Gold Kit: improved RNA-seq results after removal of cytoplasmic and mitochondrial ribosomal RNA
journal, October 2011

  • Benes, Vladimir; Blake, Jonathon; Doyle, Ken
  • Nature Methods, Vol. 8, Issue 11
  • DOI: 10.1038/nmeth.f.352

Sialic acid binding receptors (siglecs) expressed by macrophages
journal, November 1999

  • Munday, James; Floyd, Helen; Crocker, Paul R.
  • Journal of Leukocyte Biology, Vol. 66, Issue 5
  • DOI: 10.1002/jlb.66.5.705

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