Degree Type


Date of Award


Degree Name

Doctor of Philosophy


Animal Science



First Advisor

Susan J. Lamont


Newcastle disease virus (NDV) has devastating impacts on poultry throughout the world. The inbred Fayoumi and Leghorn chicken lines, previously characterized as relatively resistant and susceptible, respectively, to various pathogens were utilized to characterize host response to the NDV vaccine and identify potential genes and pathways associated with NDV resistance. Three-week-old chicks were inoculated with La Sota NDV (challenged) or PBS (nonchallenged) via the oculonasal route. At 2, 6, and 10 days post infection (dpi), approximately one-third of the birds within each line and challenge group were euthanized for tissue collection. At 2 and 6 dpi, lachrymal fluid was collected from all birds for viral quantification using qPCR. At 0 and 10 dpi, serum was collected from all birds to quantify NDV antibody levels using ELISA. The transcriptome response in tracheal epithelial cells, lungs, and Harderian glands from four birds per treatment group (line, dpi, and challenge group; 48 birds total) was analyzed using RNA-seq. These three tissues chosen for their location near the site of infection. A separate study analyzed mean survival time after challenge with velogenic NDV. These studies found the Fayoumi and Leghorn chickens were relatively resistant and susceptible, respectively to lentogenic and velogenic NDV, based on lachrymal fluid viral load, antibody levels, and within-tissue viral transcript counts detected by RNA-seq after the lentogenic challenge, and survival analysis after a velogenic challenge.

The trachea, lung, and Harderian gland RNA-seq data were analyzed individually and jointly to gain a more comprehensive understanding of the impact of lentogenic NDV challenge using differential expression and co-expression analyses. The tissues with detectable viral transcripts, trachea and Harderian gland, activated T cell related pathways after challenge. The challenge had the largest impact on the trachea transcriptome, based on principal component analysis and numbers of differentially expressed genes. In the lung and Harderian gland, especially, the two lines had distinct responses to the virus. The combined tissue analysis revealed clusters of co-expressed genes that were correlated with important factors like line, challenge status, and dpi. Overall, EIF2 signaling, mTOR signaling, collagen related genes, and TNFSF13B / TNFRSF13B were identified as potential candidate genes and pathways related to NDV resistance. Further studies are required to determine and confirm how these genes and pathways impact NDV resistance.


Copyright Owner

Melissa Deist



File Format


File Size

200 pages