Comparison of the transcriptome response within the swine tracheobronchial lymphnode following infection with PRRSV, PCV-2 or IAV-S

Authors: Miller, Laura; FLEMING, DAMARIUS - Orise Fellow; Lager, Kelly

Submitted to: Pathogens
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/4/2020
Publication Date: 2/5/2020
Citation: Miller, L.C., Fleming, D.S., Lager, K.M. 2020. Comparison of the transcriptome response within the swine tracheobronchial lymphnode following infection with PRRSV, PCV-2 or IAV-S. Pathogens. 9(2):99. https://doi.org/10.3390/pathogens9020099.
DOI: https://doi.org/10.3390/pathogens9020099

Interpretive Summary: Porcine reproductive and respiratory syndrome virus (PRRSV) is a major respiratory pathogen of swine that has become extremely costly to the swine industry worldwide, often causing losses in production and animal life due to ease of spread. However, the intracellular changes that occur in pigs following viral respiratory infections are still scantily understood for PRRSV, as well as, other viral respiratory infections. The aim of this study was to acquire a better understanding of PRRS disease by comparing gene expression changes that occur in tracheobronchial lymph nodes (TBLN) of pigs infected with either PRRSV, porcine circovirus type 2 (PCV2), or swine influenza A virus (IAV-S) infections. The study identified and compared gene expression changes in the TBLN of pigs following infection by PRRSV, PCV2, IAV, or sham inoculation. Total RNA was pooled for each group and time-point (1, 3, 6, and 14 DPI) to make 16 libraries, for analysis by Digital Gene Expression Tag Profiling (DGETP). The data underwent standard filtering to generate a list of sequence tag raw counts that were then analyzed using multidimensional and differential expression statistical tests. The results showed that PRRSV, IAV-S and PCV-2 viral infections followed a clinical course in the pigs typical of experimental infection of young pigs with these viruses. Gene expression results echoed this course, as well as, uncovered genes related to shared and unique host immune responses to the 3 viruses. By testing and observing the host response to other respiratory viruses, our study has elucidated similarities and differences that can assist in development of vaccines and therapeutics that shorten or prevent a chronic PRRSV infection.

Technical Abstract: Porcine reproductive and respiratory syndrome virus (PRRSV) is a major pathogen of swine. Here we identified and compared gene expression changes in tracheobronchial lymph nodes (TBLN) following viral infection using Digital Gene Expression Tag Profiling (DGETP). Pigs were infected with 1 x 10E5 cell culture infectious dose 50% per pig of PRRSV (strain SDSU73), porcine circovirus type 2 (PCV2; group 2), or swine influenza A virus (IAV-S; A/SW/OH/511445/2007). Pigs were allotted to one of 4 treatment groups: sham inoculated control, PRRSV-challenge, PCV2-challenge, or IAV-S-challenge. On 0 dpi pigs received an intranasal challenge with 2 ml of either sham or virus inoculum. Control pigs were sham inoculated with tissue culture supernatant. Five pigs from each group were euthanized and necropsied on 1, 3, 6, and 14 dpi. Body temperatures of pigs euthanized on 14 dpi were recorded daily. At necropsy, lungs were scored for gross lesions. TBLN were homogenized and aliquots used for RNA extraction or immunophenotyped by flow cytometry analysis and cytokine expression. Total RNA was pooled for each group and timepoint to make 16 libraries, for analysis by DGETP using the whole-genome expression analysis platform (Illumina Technologies). Data underwent image analysis, base calling, and standard filtering to generate a list of sequence tags and counts. Multidimensional statistical tests and clustering analysis identified significant changes in tag abundance. In all we were able to identify 3,689 genes in total that could be annotated to the S.scrofa 10.2 genome. Based on the statistically significant (Q = 0.1) threshold for those genes, we were able to make the following observations: for PCV-2 only 78 genes were significant with 44% downregulated and 56% upregulated; PRRSV had a total of 308 DEG with 43% down regulated and 57% upregulated; and IAV-S had a total of 215 DEG with 35% of them being downregulated and 65% being upregulated. Transcripts with changes in abundance were mapped to known metabolic, signaling and other pathways/networks. Gaining insight into how PRRSV causes disease may aid development of more efficacious vaccines.