title: Analysis of the swine tracheobronchial lymph node transcriptomic response to infection with a Chinese highly pathogenic strain of porcine reproductive and respiratory syndrome virus.
abstract: BACKGROUND
  Porcine reproductive and respiratory syndrome virus (PRRSV) is a major pathogen of swine worldwide. Emergence in 2006 of a novel highly pathogenic PRRSV (HP-PRRSV) isolate in China necessitated a comparative investigation into the host transcriptome response in tracheobronchial lymph nodes (TBLN) 13 days post-infection with HP-PRRSV rJXwn06, PRRSV strain VR-2332 or sham inocula. RNA from each was prepared for next-generation sequencing. Amplified library constructs were directly sequenced and a list of sequence transcripts and counts was generated using an RNAseq analysis pipeline to determine differential gene expression. Transcripts were annotated and relative abundance was calculated based upon the number of times a given transcript was represented in the library.
  
  
  RESULTS
  Major changes in transcript abundance occurred in response to infection with either PRRSV strain, each with over 630 differentially expressed transcripts. The largest increase in transcript level for either virus versus sham-inoculated controls were three serum amyloid A2 acute-phase isoforms. However, the degree of up or down-regulation of transcripts following infection with HP-PRRSV rJXwn06 was greater than transcript changes observed with US PRRSV VR-2332. Also, of 632 significantly altered transcripts within the HP-PRRSV rJXwn06 library 55 were up-regulated and 69 were down-regulated more than 3-fold, whilst in the US PRRSV VR-2332 library only 4 transcripts were up-regulated and 116 were down-regulated more than 3-fold.
  
  
  CONCLUSIONS
  The magnitude of differentially expressed gene profiles detected in HP-PRRSV rJXwn06 infected pigs as compared to VR-2332 infected pigs was consistent with the increased pathogenicity of the HP-PRRSV in vivo.
authors.affiliation: Virus and Prion Research Unit, National Animal Disease Center-USDA-ARS, Ames, Iowa 50010, USA. laura.miller@ars.usda.gov
authors.forename: Laura C
authors.initials: LC
authors.lastname: Miller
authors.forename: Damarius
authors.initials: D
authors.lastname: Fleming
authors.forename: Andrew
authors.initials: A
authors.lastname: Arbogast
authors.forename: Darrell O
authors.initials: DO
authors.lastname: Bayles
authors.forename: Baoqing
authors.initials: B
authors.lastname: Guo
authors.forename: Kelly M
authors.initials: KM
authors.lastname: Lager
authors.forename: Jamie N
authors.initials: JN
authors.lastname: Henningson
authors.forename: Sarah N
authors.initials: SN
authors.lastname: Schlink
authors.forename: Han-Chun
authors.initials: HC
authors.lastname: Yang
authors.forename: Kay S
authors.initials: KS
authors.lastname: Faaberg
authors.forename: Marcus E
authors.initials: ME
authors.lastname: Kehrli
mesh_terms: D000818:Animals; D002681:China / Q000453:epidemiology; D005786:Gene Expression Regulation / Q000276:immunology*; D008198:Lymph Nodes / Q000378:metabolism* / Q000821:virology; D019318:Porcine Reproductive and Respiratory Syndrome / Q000453:epidemiology / Q000821:virology; D019316:Porcine respiratory and reproductive syndrome virus / Q000235:genetics*; D012313:RNA / Q000235:genetics / Q000378:metabolism; D013552:Swine; D059467:Transcriptome
chemical_list: D012313:RNA